Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcvcf.c @ 69:33d812a61356

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
parents
children
comparison
equal deleted inserted replaced
67:0e9998148a16 69:33d812a61356
1 /* Generated by Cython 3.0.11 */
2
3 /* BEGIN: Cython Metadata
4 {
5 "distutils": {
6 "define_macros": [
7 [
8 "BUILDING_WHEEL",
9 null
10 ]
11 ],
12 "depends": [
13 "/project/htslib/htslib/bgzf.h",
14 "/project/htslib/htslib/cram.h",
15 "/project/htslib/htslib/faidx.h",
16 "/project/htslib/htslib/hfile.h",
17 "/project/htslib/htslib/hts.h",
18 "/project/htslib/htslib/kstring.h",
19 "/project/htslib/htslib/sam.h",
20 "/project/htslib/htslib/tbx.h",
21 "/project/htslib/htslib/vcf.h",
22 "/project/htslib/htslib/vcfutils.h",
23 "/project/pysam/htslib_util.h",
24 "/project/pysam/pysam_stream.h"
25 ],
26 "extra_compile_args": [
27 "-Wno-unused",
28 "-Wno-strict-prototypes",
29 "-Wno-sign-compare",
30 "-Wno-error=declaration-after-statement"
31 ],
32 "extra_link_args": [
33 "-Wl,-rpath,$ORIGIN"
34 ],
35 "include_dirs": [
36 "pysam",
37 "/project/pysam",
38 "/project/htslib",
39 "/project/samtools",
40 "/project/samtools/lz4",
41 "/project/bcftools",
42 "/project"
43 ],
44 "language": "c",
45 "libraries": [
46 "z",
47 "lzma",
48 "bz2",
49 "z",
50 "m",
51 "curl",
52 "crypto",
53 "chtslib.cpython-37m-x86_64-linux-gnu",
54 "cutils.cpython-37m-x86_64-linux-gnu"
55 ],
56 "library_dirs": [
57 "/project/pysam",
58 "/project",
59 "build/lib.linux-x86_64-cpython-37/pysam",
60 "build/lib.linux-x86_64-cpython-37/pysam",
61 "build/lib.linux-x86_64-cpython-37/pysam",
62 "build/lib.linux-x86_64-cpython-37/pysam",
63 "build/lib.linux-x86_64-cpython-37/pysam",
64 "build/lib.linux-x86_64-cpython-37/pysam",
65 "build/lib.linux-x86_64-cpython-37/pysam",
66 "build/lib.linux-x86_64-cpython-37/pysam",
67 "build/lib.linux-x86_64-cpython-37/pysam",
68 "build/lib.linux-x86_64-cpython-37/pysam",
69 "build/lib.linux-x86_64-cpython-37/pysam",
70 "build/lib.linux-x86_64-cpython-37/pysam",
71 "build/lib.linux-x86_64-cpython-37/pysam"
72 ],
73 "name": "pysam.libcvcf",
74 "sources": [
75 "pysam/libcvcf.pyx"
76 ]
77 },
78 "module_name": "pysam.libcvcf"
79 }
80 END: Cython Metadata */
81
82 #ifndef PY_SSIZE_T_CLEAN
83 #define PY_SSIZE_T_CLEAN
84 #endif /* PY_SSIZE_T_CLEAN */
85 #if defined(CYTHON_LIMITED_API) && 0
86 #ifndef Py_LIMITED_API
87 #if CYTHON_LIMITED_API+0 > 0x03030000
88 #define Py_LIMITED_API CYTHON_LIMITED_API
89 #else
90 #define Py_LIMITED_API 0x03030000
91 #endif
92 #endif
93 #endif
94
95 #include "Python.h"
96
97 #if PY_MAJOR_VERSION >= 3
98 #define __Pyx_PyFloat_FromString(obj) PyFloat_FromString(obj)
99 #else
100 #define __Pyx_PyFloat_FromString(obj) PyFloat_FromString(obj, NULL)
101 #endif
102
103
104 #if PY_MAJOR_VERSION <= 2
105 #define PyDict_GetItemWithError _PyDict_GetItemWithError
106 #endif
107
108
109 #if (PY_VERSION_HEX < 0x030700b1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030600)) && !defined(PyContextVar_Get)
110 #define PyContextVar_Get(var, d, v) ((d) ? ((void)(var), Py_INCREF(d), (v)[0] = (d), 0) : ((v)[0] = NULL, 0) )
111 #endif
112
113 #ifndef Py_PYTHON_H
114 #error Python headers needed to compile C extensions, please install development version of Python.
115 #elif PY_VERSION_HEX < 0x02070000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000)
116 #error Cython requires Python 2.7+ or Python 3.3+.
117 #else
118 #if defined(CYTHON_LIMITED_API) && CYTHON_LIMITED_API
119 #define __PYX_EXTRA_ABI_MODULE_NAME "limited"
120 #else
121 #define __PYX_EXTRA_ABI_MODULE_NAME ""
122 #endif
123 #define CYTHON_ABI "3_0_11" __PYX_EXTRA_ABI_MODULE_NAME
124 #define __PYX_ABI_MODULE_NAME "_cython_" CYTHON_ABI
125 #define __PYX_TYPE_MODULE_PREFIX __PYX_ABI_MODULE_NAME "."
126 #define CYTHON_HEX_VERSION 0x03000BF0
127 #define CYTHON_FUTURE_DIVISION 1
128 #include <stddef.h>
129 #ifndef offsetof
130 #define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
131 #endif
132 #if !defined(_WIN32) && !defined(WIN32) && !defined(MS_WINDOWS)
133 #ifndef __stdcall
134 #define __stdcall
135 #endif
136 #ifndef __cdecl
137 #define __cdecl
138 #endif
139 #ifndef __fastcall
140 #define __fastcall
141 #endif
142 #endif
143 #ifndef DL_IMPORT
144 #define DL_IMPORT(t) t
145 #endif
146 #ifndef DL_EXPORT
147 #define DL_EXPORT(t) t
148 #endif
149 #define __PYX_COMMA ,
150 #ifndef HAVE_LONG_LONG
151 #define HAVE_LONG_LONG
152 #endif
153 #ifndef PY_LONG_LONG
154 #define PY_LONG_LONG LONG_LONG
155 #endif
156 #ifndef Py_HUGE_VAL
157 #define Py_HUGE_VAL HUGE_VAL
158 #endif
159 #define __PYX_LIMITED_VERSION_HEX PY_VERSION_HEX
160 #if defined(GRAALVM_PYTHON)
161 /* For very preliminary testing purposes. Most variables are set the same as PyPy.
162 The existence of this section does not imply that anything works or is even tested */
163 #define CYTHON_COMPILING_IN_PYPY 0
164 #define CYTHON_COMPILING_IN_CPYTHON 0
165 #define CYTHON_COMPILING_IN_LIMITED_API 0
166 #define CYTHON_COMPILING_IN_GRAAL 1
167 #define CYTHON_COMPILING_IN_NOGIL 0
168 #undef CYTHON_USE_TYPE_SLOTS
169 #define CYTHON_USE_TYPE_SLOTS 0
170 #undef CYTHON_USE_TYPE_SPECS
171 #define CYTHON_USE_TYPE_SPECS 0
172 #undef CYTHON_USE_PYTYPE_LOOKUP
173 #define CYTHON_USE_PYTYPE_LOOKUP 0
174 #if PY_VERSION_HEX < 0x03050000
175 #undef CYTHON_USE_ASYNC_SLOTS
176 #define CYTHON_USE_ASYNC_SLOTS 0
177 #elif !defined(CYTHON_USE_ASYNC_SLOTS)
178 #define CYTHON_USE_ASYNC_SLOTS 1
179 #endif
180 #undef CYTHON_USE_PYLIST_INTERNALS
181 #define CYTHON_USE_PYLIST_INTERNALS 0
182 #undef CYTHON_USE_UNICODE_INTERNALS
183 #define CYTHON_USE_UNICODE_INTERNALS 0
184 #undef CYTHON_USE_UNICODE_WRITER
185 #define CYTHON_USE_UNICODE_WRITER 0
186 #undef CYTHON_USE_PYLONG_INTERNALS
187 #define CYTHON_USE_PYLONG_INTERNALS 0
188 #undef CYTHON_AVOID_BORROWED_REFS
189 #define CYTHON_AVOID_BORROWED_REFS 1
190 #undef CYTHON_ASSUME_SAFE_MACROS
191 #define CYTHON_ASSUME_SAFE_MACROS 0
192 #undef CYTHON_UNPACK_METHODS
193 #define CYTHON_UNPACK_METHODS 0
194 #undef CYTHON_FAST_THREAD_STATE
195 #define CYTHON_FAST_THREAD_STATE 0
196 #undef CYTHON_FAST_GIL
197 #define CYTHON_FAST_GIL 0
198 #undef CYTHON_METH_FASTCALL
199 #define CYTHON_METH_FASTCALL 0
200 #undef CYTHON_FAST_PYCALL
201 #define CYTHON_FAST_PYCALL 0
202 #ifndef CYTHON_PEP487_INIT_SUBCLASS
203 #define CYTHON_PEP487_INIT_SUBCLASS (PY_MAJOR_VERSION >= 3)
204 #endif
205 #undef CYTHON_PEP489_MULTI_PHASE_INIT
206 #define CYTHON_PEP489_MULTI_PHASE_INIT 1
207 #undef CYTHON_USE_MODULE_STATE
208 #define CYTHON_USE_MODULE_STATE 0
209 #undef CYTHON_USE_TP_FINALIZE
210 #define CYTHON_USE_TP_FINALIZE 0
211 #undef CYTHON_USE_DICT_VERSIONS
212 #define CYTHON_USE_DICT_VERSIONS 0
213 #undef CYTHON_USE_EXC_INFO_STACK
214 #define CYTHON_USE_EXC_INFO_STACK 0
215 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
216 #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
217 #endif
218 #undef CYTHON_USE_FREELISTS
219 #define CYTHON_USE_FREELISTS 0
220 #elif defined(PYPY_VERSION)
221 #define CYTHON_COMPILING_IN_PYPY 1
222 #define CYTHON_COMPILING_IN_CPYTHON 0
223 #define CYTHON_COMPILING_IN_LIMITED_API 0
224 #define CYTHON_COMPILING_IN_GRAAL 0
225 #define CYTHON_COMPILING_IN_NOGIL 0
226 #undef CYTHON_USE_TYPE_SLOTS
227 #define CYTHON_USE_TYPE_SLOTS 0
228 #ifndef CYTHON_USE_TYPE_SPECS
229 #define CYTHON_USE_TYPE_SPECS 0
230 #endif
231 #undef CYTHON_USE_PYTYPE_LOOKUP
232 #define CYTHON_USE_PYTYPE_LOOKUP 0
233 #if PY_VERSION_HEX < 0x03050000
234 #undef CYTHON_USE_ASYNC_SLOTS
235 #define CYTHON_USE_ASYNC_SLOTS 0
236 #elif !defined(CYTHON_USE_ASYNC_SLOTS)
237 #define CYTHON_USE_ASYNC_SLOTS 1
238 #endif
239 #undef CYTHON_USE_PYLIST_INTERNALS
240 #define CYTHON_USE_PYLIST_INTERNALS 0
241 #undef CYTHON_USE_UNICODE_INTERNALS
242 #define CYTHON_USE_UNICODE_INTERNALS 0
243 #undef CYTHON_USE_UNICODE_WRITER
244 #define CYTHON_USE_UNICODE_WRITER 0
245 #undef CYTHON_USE_PYLONG_INTERNALS
246 #define CYTHON_USE_PYLONG_INTERNALS 0
247 #undef CYTHON_AVOID_BORROWED_REFS
248 #define CYTHON_AVOID_BORROWED_REFS 1
249 #undef CYTHON_ASSUME_SAFE_MACROS
250 #define CYTHON_ASSUME_SAFE_MACROS 0
251 #undef CYTHON_UNPACK_METHODS
252 #define CYTHON_UNPACK_METHODS 0
253 #undef CYTHON_FAST_THREAD_STATE
254 #define CYTHON_FAST_THREAD_STATE 0
255 #undef CYTHON_FAST_GIL
256 #define CYTHON_FAST_GIL 0
257 #undef CYTHON_METH_FASTCALL
258 #define CYTHON_METH_FASTCALL 0
259 #undef CYTHON_FAST_PYCALL
260 #define CYTHON_FAST_PYCALL 0
261 #ifndef CYTHON_PEP487_INIT_SUBCLASS
262 #define CYTHON_PEP487_INIT_SUBCLASS (PY_MAJOR_VERSION >= 3)
263 #endif
264 #if PY_VERSION_HEX < 0x03090000
265 #undef CYTHON_PEP489_MULTI_PHASE_INIT
266 #define CYTHON_PEP489_MULTI_PHASE_INIT 0
267 #elif !defined(CYTHON_PEP489_MULTI_PHASE_INIT)
268 #define CYTHON_PEP489_MULTI_PHASE_INIT 1
269 #endif
270 #undef CYTHON_USE_MODULE_STATE
271 #define CYTHON_USE_MODULE_STATE 0
272 #undef CYTHON_USE_TP_FINALIZE
273 #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1 && PYPY_VERSION_NUM >= 0x07030C00)
274 #undef CYTHON_USE_DICT_VERSIONS
275 #define CYTHON_USE_DICT_VERSIONS 0
276 #undef CYTHON_USE_EXC_INFO_STACK
277 #define CYTHON_USE_EXC_INFO_STACK 0
278 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
279 #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
280 #endif
281 #undef CYTHON_USE_FREELISTS
282 #define CYTHON_USE_FREELISTS 0
283 #elif defined(CYTHON_LIMITED_API)
284 #ifdef Py_LIMITED_API
285 #undef __PYX_LIMITED_VERSION_HEX
286 #define __PYX_LIMITED_VERSION_HEX Py_LIMITED_API
287 #endif
288 #define CYTHON_COMPILING_IN_PYPY 0
289 #define CYTHON_COMPILING_IN_CPYTHON 0
290 #define CYTHON_COMPILING_IN_LIMITED_API 1
291 #define CYTHON_COMPILING_IN_GRAAL 0
292 #define CYTHON_COMPILING_IN_NOGIL 0
293 #undef CYTHON_CLINE_IN_TRACEBACK
294 #define CYTHON_CLINE_IN_TRACEBACK 0
295 #undef CYTHON_USE_TYPE_SLOTS
296 #define CYTHON_USE_TYPE_SLOTS 0
297 #undef CYTHON_USE_TYPE_SPECS
298 #define CYTHON_USE_TYPE_SPECS 1
299 #undef CYTHON_USE_PYTYPE_LOOKUP
300 #define CYTHON_USE_PYTYPE_LOOKUP 0
301 #undef CYTHON_USE_ASYNC_SLOTS
302 #define CYTHON_USE_ASYNC_SLOTS 0
303 #undef CYTHON_USE_PYLIST_INTERNALS
304 #define CYTHON_USE_PYLIST_INTERNALS 0
305 #undef CYTHON_USE_UNICODE_INTERNALS
306 #define CYTHON_USE_UNICODE_INTERNALS 0
307 #ifndef CYTHON_USE_UNICODE_WRITER
308 #define CYTHON_USE_UNICODE_WRITER 0
309 #endif
310 #undef CYTHON_USE_PYLONG_INTERNALS
311 #define CYTHON_USE_PYLONG_INTERNALS 0
312 #ifndef CYTHON_AVOID_BORROWED_REFS
313 #define CYTHON_AVOID_BORROWED_REFS 0
314 #endif
315 #undef CYTHON_ASSUME_SAFE_MACROS
316 #define CYTHON_ASSUME_SAFE_MACROS 0
317 #undef CYTHON_UNPACK_METHODS
318 #define CYTHON_UNPACK_METHODS 0
319 #undef CYTHON_FAST_THREAD_STATE
320 #define CYTHON_FAST_THREAD_STATE 0
321 #undef CYTHON_FAST_GIL
322 #define CYTHON_FAST_GIL 0
323 #undef CYTHON_METH_FASTCALL
324 #define CYTHON_METH_FASTCALL 0
325 #undef CYTHON_FAST_PYCALL
326 #define CYTHON_FAST_PYCALL 0
327 #ifndef CYTHON_PEP487_INIT_SUBCLASS
328 #define CYTHON_PEP487_INIT_SUBCLASS 1
329 #endif
330 #undef CYTHON_PEP489_MULTI_PHASE_INIT
331 #define CYTHON_PEP489_MULTI_PHASE_INIT 0
332 #undef CYTHON_USE_MODULE_STATE
333 #define CYTHON_USE_MODULE_STATE 1
334 #ifndef CYTHON_USE_TP_FINALIZE
335 #define CYTHON_USE_TP_FINALIZE 0
336 #endif
337 #undef CYTHON_USE_DICT_VERSIONS
338 #define CYTHON_USE_DICT_VERSIONS 0
339 #undef CYTHON_USE_EXC_INFO_STACK
340 #define CYTHON_USE_EXC_INFO_STACK 0
341 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
342 #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
343 #endif
344 #undef CYTHON_USE_FREELISTS
345 #define CYTHON_USE_FREELISTS 0
346 #elif defined(Py_GIL_DISABLED) || defined(Py_NOGIL)
347 #define CYTHON_COMPILING_IN_PYPY 0
348 #define CYTHON_COMPILING_IN_CPYTHON 0
349 #define CYTHON_COMPILING_IN_LIMITED_API 0
350 #define CYTHON_COMPILING_IN_GRAAL 0
351 #define CYTHON_COMPILING_IN_NOGIL 1
352 #ifndef CYTHON_USE_TYPE_SLOTS
353 #define CYTHON_USE_TYPE_SLOTS 1
354 #endif
355 #ifndef CYTHON_USE_TYPE_SPECS
356 #define CYTHON_USE_TYPE_SPECS 0
357 #endif
358 #undef CYTHON_USE_PYTYPE_LOOKUP
359 #define CYTHON_USE_PYTYPE_LOOKUP 0
360 #ifndef CYTHON_USE_ASYNC_SLOTS
361 #define CYTHON_USE_ASYNC_SLOTS 1
362 #endif
363 #ifndef CYTHON_USE_PYLONG_INTERNALS
364 #define CYTHON_USE_PYLONG_INTERNALS 0
365 #endif
366 #undef CYTHON_USE_PYLIST_INTERNALS
367 #define CYTHON_USE_PYLIST_INTERNALS 0
368 #ifndef CYTHON_USE_UNICODE_INTERNALS
369 #define CYTHON_USE_UNICODE_INTERNALS 1
370 #endif
371 #undef CYTHON_USE_UNICODE_WRITER
372 #define CYTHON_USE_UNICODE_WRITER 0
373 #ifndef CYTHON_AVOID_BORROWED_REFS
374 #define CYTHON_AVOID_BORROWED_REFS 0
375 #endif
376 #ifndef CYTHON_ASSUME_SAFE_MACROS
377 #define CYTHON_ASSUME_SAFE_MACROS 1
378 #endif
379 #ifndef CYTHON_UNPACK_METHODS
380 #define CYTHON_UNPACK_METHODS 1
381 #endif
382 #undef CYTHON_FAST_THREAD_STATE
383 #define CYTHON_FAST_THREAD_STATE 0
384 #undef CYTHON_FAST_GIL
385 #define CYTHON_FAST_GIL 0
386 #ifndef CYTHON_METH_FASTCALL
387 #define CYTHON_METH_FASTCALL 1
388 #endif
389 #undef CYTHON_FAST_PYCALL
390 #define CYTHON_FAST_PYCALL 0
391 #ifndef CYTHON_PEP487_INIT_SUBCLASS
392 #define CYTHON_PEP487_INIT_SUBCLASS 1
393 #endif
394 #ifndef CYTHON_PEP489_MULTI_PHASE_INIT
395 #define CYTHON_PEP489_MULTI_PHASE_INIT 1
396 #endif
397 #ifndef CYTHON_USE_MODULE_STATE
398 #define CYTHON_USE_MODULE_STATE 0
399 #endif
400 #ifndef CYTHON_USE_TP_FINALIZE
401 #define CYTHON_USE_TP_FINALIZE 1
402 #endif
403 #undef CYTHON_USE_DICT_VERSIONS
404 #define CYTHON_USE_DICT_VERSIONS 0
405 #undef CYTHON_USE_EXC_INFO_STACK
406 #define CYTHON_USE_EXC_INFO_STACK 0
407 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
408 #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
409 #endif
410 #ifndef CYTHON_USE_FREELISTS
411 #define CYTHON_USE_FREELISTS 0
412 #endif
413 #else
414 #define CYTHON_COMPILING_IN_PYPY 0
415 #define CYTHON_COMPILING_IN_CPYTHON 1
416 #define CYTHON_COMPILING_IN_LIMITED_API 0
417 #define CYTHON_COMPILING_IN_GRAAL 0
418 #define CYTHON_COMPILING_IN_NOGIL 0
419 #ifndef CYTHON_USE_TYPE_SLOTS
420 #define CYTHON_USE_TYPE_SLOTS 1
421 #endif
422 #ifndef CYTHON_USE_TYPE_SPECS
423 #define CYTHON_USE_TYPE_SPECS 0
424 #endif
425 #ifndef CYTHON_USE_PYTYPE_LOOKUP
426 #define CYTHON_USE_PYTYPE_LOOKUP 1
427 #endif
428 #if PY_MAJOR_VERSION < 3
429 #undef CYTHON_USE_ASYNC_SLOTS
430 #define CYTHON_USE_ASYNC_SLOTS 0
431 #elif !defined(CYTHON_USE_ASYNC_SLOTS)
432 #define CYTHON_USE_ASYNC_SLOTS 1
433 #endif
434 #ifndef CYTHON_USE_PYLONG_INTERNALS
435 #define CYTHON_USE_PYLONG_INTERNALS 1
436 #endif
437 #ifndef CYTHON_USE_PYLIST_INTERNALS
438 #define CYTHON_USE_PYLIST_INTERNALS 1
439 #endif
440 #ifndef CYTHON_USE_UNICODE_INTERNALS
441 #define CYTHON_USE_UNICODE_INTERNALS 1
442 #endif
443 #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2
444 #undef CYTHON_USE_UNICODE_WRITER
445 #define CYTHON_USE_UNICODE_WRITER 0
446 #elif !defined(CYTHON_USE_UNICODE_WRITER)
447 #define CYTHON_USE_UNICODE_WRITER 1
448 #endif
449 #ifndef CYTHON_AVOID_BORROWED_REFS
450 #define CYTHON_AVOID_BORROWED_REFS 0
451 #endif
452 #ifndef CYTHON_ASSUME_SAFE_MACROS
453 #define CYTHON_ASSUME_SAFE_MACROS 1
454 #endif
455 #ifndef CYTHON_UNPACK_METHODS
456 #define CYTHON_UNPACK_METHODS 1
457 #endif
458 #ifndef CYTHON_FAST_THREAD_STATE
459 #define CYTHON_FAST_THREAD_STATE 1
460 #endif
461 #ifndef CYTHON_FAST_GIL
462 #define CYTHON_FAST_GIL (PY_MAJOR_VERSION < 3 || PY_VERSION_HEX >= 0x03060000 && PY_VERSION_HEX < 0x030C00A6)
463 #endif
464 #ifndef CYTHON_METH_FASTCALL
465 #define CYTHON_METH_FASTCALL (PY_VERSION_HEX >= 0x030700A1)
466 #endif
467 #ifndef CYTHON_FAST_PYCALL
468 #define CYTHON_FAST_PYCALL 1
469 #endif
470 #ifndef CYTHON_PEP487_INIT_SUBCLASS
471 #define CYTHON_PEP487_INIT_SUBCLASS 1
472 #endif
473 #if PY_VERSION_HEX < 0x03050000
474 #undef CYTHON_PEP489_MULTI_PHASE_INIT
475 #define CYTHON_PEP489_MULTI_PHASE_INIT 0
476 #elif !defined(CYTHON_PEP489_MULTI_PHASE_INIT)
477 #define CYTHON_PEP489_MULTI_PHASE_INIT 1
478 #endif
479 #ifndef CYTHON_USE_MODULE_STATE
480 #define CYTHON_USE_MODULE_STATE 0
481 #endif
482 #if PY_VERSION_HEX < 0x030400a1
483 #undef CYTHON_USE_TP_FINALIZE
484 #define CYTHON_USE_TP_FINALIZE 0
485 #elif !defined(CYTHON_USE_TP_FINALIZE)
486 #define CYTHON_USE_TP_FINALIZE 1
487 #endif
488 #if PY_VERSION_HEX < 0x030600B1
489 #undef CYTHON_USE_DICT_VERSIONS
490 #define CYTHON_USE_DICT_VERSIONS 0
491 #elif !defined(CYTHON_USE_DICT_VERSIONS)
492 #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX < 0x030C00A5)
493 #endif
494 #if PY_VERSION_HEX < 0x030700A3
495 #undef CYTHON_USE_EXC_INFO_STACK
496 #define CYTHON_USE_EXC_INFO_STACK 0
497 #elif !defined(CYTHON_USE_EXC_INFO_STACK)
498 #define CYTHON_USE_EXC_INFO_STACK 1
499 #endif
500 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
501 #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
502 #endif
503 #ifndef CYTHON_USE_FREELISTS
504 #define CYTHON_USE_FREELISTS 1
505 #endif
506 #endif
507 #if !defined(CYTHON_FAST_PYCCALL)
508 #define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
509 #endif
510 #if !defined(CYTHON_VECTORCALL)
511 #define CYTHON_VECTORCALL (CYTHON_FAST_PYCCALL && PY_VERSION_HEX >= 0x030800B1)
512 #endif
513 #define CYTHON_BACKPORT_VECTORCALL (CYTHON_METH_FASTCALL && PY_VERSION_HEX < 0x030800B1)
514 #if CYTHON_USE_PYLONG_INTERNALS
515 #if PY_MAJOR_VERSION < 3
516 #include "longintrepr.h"
517 #endif
518 #undef SHIFT
519 #undef BASE
520 #undef MASK
521 #ifdef SIZEOF_VOID_P
522 enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) };
523 #endif
524 #endif
525 #ifndef __has_attribute
526 #define __has_attribute(x) 0
527 #endif
528 #ifndef __has_cpp_attribute
529 #define __has_cpp_attribute(x) 0
530 #endif
531 #ifndef CYTHON_RESTRICT
532 #if defined(__GNUC__)
533 #define CYTHON_RESTRICT __restrict__
534 #elif defined(_MSC_VER) && _MSC_VER >= 1400
535 #define CYTHON_RESTRICT __restrict
536 #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
537 #define CYTHON_RESTRICT restrict
538 #else
539 #define CYTHON_RESTRICT
540 #endif
541 #endif
542 #ifndef CYTHON_UNUSED
543 #if defined(__cplusplus)
544 /* for clang __has_cpp_attribute(maybe_unused) is true even before C++17
545 * but leads to warnings with -pedantic, since it is a C++17 feature */
546 #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
547 #if __has_cpp_attribute(maybe_unused)
548 #define CYTHON_UNUSED [[maybe_unused]]
549 #endif
550 #endif
551 #endif
552 #endif
553 #ifndef CYTHON_UNUSED
554 # if defined(__GNUC__)
555 # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
556 # define CYTHON_UNUSED __attribute__ ((__unused__))
557 # else
558 # define CYTHON_UNUSED
559 # endif
560 # elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
561 # define CYTHON_UNUSED __attribute__ ((__unused__))
562 # else
563 # define CYTHON_UNUSED
564 # endif
565 #endif
566 #ifndef CYTHON_UNUSED_VAR
567 # if defined(__cplusplus)
568 template<class T> void CYTHON_UNUSED_VAR( const T& ) { }
569 # else
570 # define CYTHON_UNUSED_VAR(x) (void)(x)
571 # endif
572 #endif
573 #ifndef CYTHON_MAYBE_UNUSED_VAR
574 #define CYTHON_MAYBE_UNUSED_VAR(x) CYTHON_UNUSED_VAR(x)
575 #endif
576 #ifndef CYTHON_NCP_UNUSED
577 # if CYTHON_COMPILING_IN_CPYTHON
578 # define CYTHON_NCP_UNUSED
579 # else
580 # define CYTHON_NCP_UNUSED CYTHON_UNUSED
581 # endif
582 #endif
583 #ifndef CYTHON_USE_CPP_STD_MOVE
584 #if defined(__cplusplus) && (\
585 __cplusplus >= 201103L || (defined(_MSC_VER) && _MSC_VER >= 1600))
586 #define CYTHON_USE_CPP_STD_MOVE 1
587 #else
588 #define CYTHON_USE_CPP_STD_MOVE 0
589 #endif
590 #endif
591 #define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None)
592 #ifdef _MSC_VER
593 #ifndef _MSC_STDINT_H_
594 #if _MSC_VER < 1300
595 typedef unsigned char uint8_t;
596 typedef unsigned short uint16_t;
597 typedef unsigned int uint32_t;
598 #else
599 typedef unsigned __int8 uint8_t;
600 typedef unsigned __int16 uint16_t;
601 typedef unsigned __int32 uint32_t;
602 #endif
603 #endif
604 #if _MSC_VER < 1300
605 #ifdef _WIN64
606 typedef unsigned long long __pyx_uintptr_t;
607 #else
608 typedef unsigned int __pyx_uintptr_t;
609 #endif
610 #else
611 #ifdef _WIN64
612 typedef unsigned __int64 __pyx_uintptr_t;
613 #else
614 typedef unsigned __int32 __pyx_uintptr_t;
615 #endif
616 #endif
617 #else
618 #include <stdint.h>
619 typedef uintptr_t __pyx_uintptr_t;
620 #endif
621 #ifndef CYTHON_FALLTHROUGH
622 #if defined(__cplusplus)
623 /* for clang __has_cpp_attribute(fallthrough) is true even before C++17
624 * but leads to warnings with -pedantic, since it is a C++17 feature */
625 #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
626 #if __has_cpp_attribute(fallthrough)
627 #define CYTHON_FALLTHROUGH [[fallthrough]]
628 #endif
629 #endif
630 #ifndef CYTHON_FALLTHROUGH
631 #if __has_cpp_attribute(clang::fallthrough)
632 #define CYTHON_FALLTHROUGH [[clang::fallthrough]]
633 #elif __has_cpp_attribute(gnu::fallthrough)
634 #define CYTHON_FALLTHROUGH [[gnu::fallthrough]]
635 #endif
636 #endif
637 #endif
638 #ifndef CYTHON_FALLTHROUGH
639 #if __has_attribute(fallthrough)
640 #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
641 #else
642 #define CYTHON_FALLTHROUGH
643 #endif
644 #endif
645 #if defined(__clang__) && defined(__apple_build_version__)
646 #if __apple_build_version__ < 7000000
647 #undef CYTHON_FALLTHROUGH
648 #define CYTHON_FALLTHROUGH
649 #endif
650 #endif
651 #endif
652 #ifdef __cplusplus
653 template <typename T>
654 struct __PYX_IS_UNSIGNED_IMPL {static const bool value = T(0) < T(-1);};
655 #define __PYX_IS_UNSIGNED(type) (__PYX_IS_UNSIGNED_IMPL<type>::value)
656 #else
657 #define __PYX_IS_UNSIGNED(type) (((type)-1) > 0)
658 #endif
659 #if CYTHON_COMPILING_IN_PYPY == 1
660 #define __PYX_NEED_TP_PRINT_SLOT (PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x030A0000)
661 #else
662 #define __PYX_NEED_TP_PRINT_SLOT (PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000)
663 #endif
664 #define __PYX_REINTERPRET_FUNCION(func_pointer, other_pointer) ((func_pointer)(void(*)(void))(other_pointer))
665
666 #ifndef CYTHON_INLINE
667 #if defined(__clang__)
668 #define CYTHON_INLINE __inline__ __attribute__ ((__unused__))
669 #elif defined(__GNUC__)
670 #define CYTHON_INLINE __inline__
671 #elif defined(_MSC_VER)
672 #define CYTHON_INLINE __inline
673 #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
674 #define CYTHON_INLINE inline
675 #else
676 #define CYTHON_INLINE
677 #endif
678 #endif
679
680 #define __PYX_BUILD_PY_SSIZE_T "n"
681 #define CYTHON_FORMAT_SSIZE_T "z"
682 #if PY_MAJOR_VERSION < 3
683 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
684 #define __Pyx_DefaultClassType PyClass_Type
685 #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
686 PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
687 #else
688 #define __Pyx_BUILTIN_MODULE_NAME "builtins"
689 #define __Pyx_DefaultClassType PyType_Type
690 #if CYTHON_COMPILING_IN_LIMITED_API
691 static CYTHON_INLINE PyObject* __Pyx_PyCode_New(int a, int p, int k, int l, int s, int f,
692 PyObject *code, PyObject *c, PyObject* n, PyObject *v,
693 PyObject *fv, PyObject *cell, PyObject* fn,
694 PyObject *name, int fline, PyObject *lnos) {
695 PyObject *exception_table = NULL;
696 PyObject *types_module=NULL, *code_type=NULL, *result=NULL;
697 #if __PYX_LIMITED_VERSION_HEX < 0x030B0000
698 PyObject *version_info;
699 PyObject *py_minor_version = NULL;
700 #endif
701 long minor_version = 0;
702 PyObject *type, *value, *traceback;
703 PyErr_Fetch(&type, &value, &traceback);
704 #if __PYX_LIMITED_VERSION_HEX >= 0x030B0000
705 minor_version = 11;
706 #else
707 if (!(version_info = PySys_GetObject("version_info"))) goto end;
708 if (!(py_minor_version = PySequence_GetItem(version_info, 1))) goto end;
709 minor_version = PyLong_AsLong(py_minor_version);
710 Py_DECREF(py_minor_version);
711 if (minor_version == -1 && PyErr_Occurred()) goto end;
712 #endif
713 if (!(types_module = PyImport_ImportModule("types"))) goto end;
714 if (!(code_type = PyObject_GetAttrString(types_module, "CodeType"))) goto end;
715 if (minor_version <= 7) {
716 (void)p;
717 result = PyObject_CallFunction(code_type, "iiiiiOOOOOOiOO", a, k, l, s, f, code,
718 c, n, v, fn, name, fline, lnos, fv, cell);
719 } else if (minor_version <= 10) {
720 result = PyObject_CallFunction(code_type, "iiiiiiOOOOOOiOO", a,p, k, l, s, f, code,
721 c, n, v, fn, name, fline, lnos, fv, cell);
722 } else {
723 if (!(exception_table = PyBytes_FromStringAndSize(NULL, 0))) goto end;
724 result = PyObject_CallFunction(code_type, "iiiiiiOOOOOOOiOO", a,p, k, l, s, f, code,
725 c, n, v, fn, name, name, fline, lnos, exception_table, fv, cell);
726 }
727 end:
728 Py_XDECREF(code_type);
729 Py_XDECREF(exception_table);
730 Py_XDECREF(types_module);
731 if (type) {
732 PyErr_Restore(type, value, traceback);
733 }
734 return result;
735 }
736 #ifndef CO_OPTIMIZED
737 #define CO_OPTIMIZED 0x0001
738 #endif
739 #ifndef CO_NEWLOCALS
740 #define CO_NEWLOCALS 0x0002
741 #endif
742 #ifndef CO_VARARGS
743 #define CO_VARARGS 0x0004
744 #endif
745 #ifndef CO_VARKEYWORDS
746 #define CO_VARKEYWORDS 0x0008
747 #endif
748 #ifndef CO_ASYNC_GENERATOR
749 #define CO_ASYNC_GENERATOR 0x0200
750 #endif
751 #ifndef CO_GENERATOR
752 #define CO_GENERATOR 0x0020
753 #endif
754 #ifndef CO_COROUTINE
755 #define CO_COROUTINE 0x0080
756 #endif
757 #elif PY_VERSION_HEX >= 0x030B0000
758 static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int p, int k, int l, int s, int f,
759 PyObject *code, PyObject *c, PyObject* n, PyObject *v,
760 PyObject *fv, PyObject *cell, PyObject* fn,
761 PyObject *name, int fline, PyObject *lnos) {
762 PyCodeObject *result;
763 PyObject *empty_bytes = PyBytes_FromStringAndSize("", 0);
764 if (!empty_bytes) return NULL;
765 result =
766 #if PY_VERSION_HEX >= 0x030C0000
767 PyUnstable_Code_NewWithPosOnlyArgs
768 #else
769 PyCode_NewWithPosOnlyArgs
770 #endif
771 (a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, name, fline, lnos, empty_bytes);
772 Py_DECREF(empty_bytes);
773 return result;
774 }
775 #elif PY_VERSION_HEX >= 0x030800B2 && !CYTHON_COMPILING_IN_PYPY
776 #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
777 PyCode_NewWithPosOnlyArgs(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
778 #else
779 #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
780 PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
781 #endif
782 #endif
783 #if PY_VERSION_HEX >= 0x030900A4 || defined(Py_IS_TYPE)
784 #define __Pyx_IS_TYPE(ob, type) Py_IS_TYPE(ob, type)
785 #else
786 #define __Pyx_IS_TYPE(ob, type) (((const PyObject*)ob)->ob_type == (type))
787 #endif
788 #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_Is)
789 #define __Pyx_Py_Is(x, y) Py_Is(x, y)
790 #else
791 #define __Pyx_Py_Is(x, y) ((x) == (y))
792 #endif
793 #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsNone)
794 #define __Pyx_Py_IsNone(ob) Py_IsNone(ob)
795 #else
796 #define __Pyx_Py_IsNone(ob) __Pyx_Py_Is((ob), Py_None)
797 #endif
798 #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsTrue)
799 #define __Pyx_Py_IsTrue(ob) Py_IsTrue(ob)
800 #else
801 #define __Pyx_Py_IsTrue(ob) __Pyx_Py_Is((ob), Py_True)
802 #endif
803 #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsFalse)
804 #define __Pyx_Py_IsFalse(ob) Py_IsFalse(ob)
805 #else
806 #define __Pyx_Py_IsFalse(ob) __Pyx_Py_Is((ob), Py_False)
807 #endif
808 #define __Pyx_NoneAsNull(obj) (__Pyx_Py_IsNone(obj) ? NULL : (obj))
809 #if PY_VERSION_HEX >= 0x030900F0 && !CYTHON_COMPILING_IN_PYPY
810 #define __Pyx_PyObject_GC_IsFinalized(o) PyObject_GC_IsFinalized(o)
811 #else
812 #define __Pyx_PyObject_GC_IsFinalized(o) _PyGC_FINALIZED(o)
813 #endif
814 #ifndef CO_COROUTINE
815 #define CO_COROUTINE 0x80
816 #endif
817 #ifndef CO_ASYNC_GENERATOR
818 #define CO_ASYNC_GENERATOR 0x200
819 #endif
820 #ifndef Py_TPFLAGS_CHECKTYPES
821 #define Py_TPFLAGS_CHECKTYPES 0
822 #endif
823 #ifndef Py_TPFLAGS_HAVE_INDEX
824 #define Py_TPFLAGS_HAVE_INDEX 0
825 #endif
826 #ifndef Py_TPFLAGS_HAVE_NEWBUFFER
827 #define Py_TPFLAGS_HAVE_NEWBUFFER 0
828 #endif
829 #ifndef Py_TPFLAGS_HAVE_FINALIZE
830 #define Py_TPFLAGS_HAVE_FINALIZE 0
831 #endif
832 #ifndef Py_TPFLAGS_SEQUENCE
833 #define Py_TPFLAGS_SEQUENCE 0
834 #endif
835 #ifndef Py_TPFLAGS_MAPPING
836 #define Py_TPFLAGS_MAPPING 0
837 #endif
838 #ifndef METH_STACKLESS
839 #define METH_STACKLESS 0
840 #endif
841 #if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL)
842 #ifndef METH_FASTCALL
843 #define METH_FASTCALL 0x80
844 #endif
845 typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs);
846 typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args,
847 Py_ssize_t nargs, PyObject *kwnames);
848 #else
849 #if PY_VERSION_HEX >= 0x030d00A4
850 # define __Pyx_PyCFunctionFast PyCFunctionFast
851 # define __Pyx_PyCFunctionFastWithKeywords PyCFunctionFastWithKeywords
852 #else
853 # define __Pyx_PyCFunctionFast _PyCFunctionFast
854 # define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords
855 #endif
856 #endif
857 #if CYTHON_METH_FASTCALL
858 #define __Pyx_METH_FASTCALL METH_FASTCALL
859 #define __Pyx_PyCFunction_FastCall __Pyx_PyCFunctionFast
860 #define __Pyx_PyCFunction_FastCallWithKeywords __Pyx_PyCFunctionFastWithKeywords
861 #else
862 #define __Pyx_METH_FASTCALL METH_VARARGS
863 #define __Pyx_PyCFunction_FastCall PyCFunction
864 #define __Pyx_PyCFunction_FastCallWithKeywords PyCFunctionWithKeywords
865 #endif
866 #if CYTHON_VECTORCALL
867 #define __pyx_vectorcallfunc vectorcallfunc
868 #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET PY_VECTORCALL_ARGUMENTS_OFFSET
869 #define __Pyx_PyVectorcall_NARGS(n) PyVectorcall_NARGS((size_t)(n))
870 #elif CYTHON_BACKPORT_VECTORCALL
871 typedef PyObject *(*__pyx_vectorcallfunc)(PyObject *callable, PyObject *const *args,
872 size_t nargsf, PyObject *kwnames);
873 #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET ((size_t)1 << (8 * sizeof(size_t) - 1))
874 #define __Pyx_PyVectorcall_NARGS(n) ((Py_ssize_t)(((size_t)(n)) & ~__Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET))
875 #else
876 #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET 0
877 #define __Pyx_PyVectorcall_NARGS(n) ((Py_ssize_t)(n))
878 #endif
879 #if PY_MAJOR_VERSION >= 0x030900B1
880 #define __Pyx_PyCFunction_CheckExact(func) PyCFunction_CheckExact(func)
881 #else
882 #define __Pyx_PyCFunction_CheckExact(func) PyCFunction_Check(func)
883 #endif
884 #define __Pyx_CyOrPyCFunction_Check(func) PyCFunction_Check(func)
885 #if CYTHON_COMPILING_IN_CPYTHON
886 #define __Pyx_CyOrPyCFunction_GET_FUNCTION(func) (((PyCFunctionObject*)(func))->m_ml->ml_meth)
887 #elif !CYTHON_COMPILING_IN_LIMITED_API
888 #define __Pyx_CyOrPyCFunction_GET_FUNCTION(func) PyCFunction_GET_FUNCTION(func)
889 #endif
890 #if CYTHON_COMPILING_IN_CPYTHON
891 #define __Pyx_CyOrPyCFunction_GET_FLAGS(func) (((PyCFunctionObject*)(func))->m_ml->ml_flags)
892 static CYTHON_INLINE PyObject* __Pyx_CyOrPyCFunction_GET_SELF(PyObject *func) {
893 return (__Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_STATIC) ? NULL : ((PyCFunctionObject*)func)->m_self;
894 }
895 #endif
896 static CYTHON_INLINE int __Pyx__IsSameCFunction(PyObject *func, void *cfunc) {
897 #if CYTHON_COMPILING_IN_LIMITED_API
898 return PyCFunction_Check(func) && PyCFunction_GetFunction(func) == (PyCFunction) cfunc;
899 #else
900 return PyCFunction_Check(func) && PyCFunction_GET_FUNCTION(func) == (PyCFunction) cfunc;
901 #endif
902 }
903 #define __Pyx_IsSameCFunction(func, cfunc) __Pyx__IsSameCFunction(func, cfunc)
904 #if __PYX_LIMITED_VERSION_HEX < 0x030900B1
905 #define __Pyx_PyType_FromModuleAndSpec(m, s, b) ((void)m, PyType_FromSpecWithBases(s, b))
906 typedef PyObject *(*__Pyx_PyCMethod)(PyObject *, PyTypeObject *, PyObject *const *, size_t, PyObject *);
907 #else
908 #define __Pyx_PyType_FromModuleAndSpec(m, s, b) PyType_FromModuleAndSpec(m, s, b)
909 #define __Pyx_PyCMethod PyCMethod
910 #endif
911 #ifndef METH_METHOD
912 #define METH_METHOD 0x200
913 #endif
914 #if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc)
915 #define PyObject_Malloc(s) PyMem_Malloc(s)
916 #define PyObject_Free(p) PyMem_Free(p)
917 #define PyObject_Realloc(p) PyMem_Realloc(p)
918 #endif
919 #if CYTHON_COMPILING_IN_LIMITED_API
920 #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0)
921 #define __Pyx_PyFrame_SetLineNumber(frame, lineno)
922 #else
923 #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0)
924 #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno)
925 #endif
926 #if CYTHON_COMPILING_IN_LIMITED_API
927 #define __Pyx_PyThreadState_Current PyThreadState_Get()
928 #elif !CYTHON_FAST_THREAD_STATE
929 #define __Pyx_PyThreadState_Current PyThreadState_GET()
930 #elif PY_VERSION_HEX >= 0x030d00A1
931 #define __Pyx_PyThreadState_Current PyThreadState_GetUnchecked()
932 #elif PY_VERSION_HEX >= 0x03060000
933 #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet()
934 #elif PY_VERSION_HEX >= 0x03000000
935 #define __Pyx_PyThreadState_Current PyThreadState_GET()
936 #else
937 #define __Pyx_PyThreadState_Current _PyThreadState_Current
938 #endif
939 #if CYTHON_COMPILING_IN_LIMITED_API
940 static CYTHON_INLINE void *__Pyx_PyModule_GetState(PyObject *op)
941 {
942 void *result;
943 result = PyModule_GetState(op);
944 if (!result)
945 Py_FatalError("Couldn't find the module state");
946 return result;
947 }
948 #endif
949 #define __Pyx_PyObject_GetSlot(obj, name, func_ctype) __Pyx_PyType_GetSlot(Py_TYPE(obj), name, func_ctype)
950 #if CYTHON_COMPILING_IN_LIMITED_API
951 #define __Pyx_PyType_GetSlot(type, name, func_ctype) ((func_ctype) PyType_GetSlot((type), Py_##name))
952 #else
953 #define __Pyx_PyType_GetSlot(type, name, func_ctype) ((type)->name)
954 #endif
955 #if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT)
956 #include "pythread.h"
957 #define Py_tss_NEEDS_INIT 0
958 typedef int Py_tss_t;
959 static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) {
960 *key = PyThread_create_key();
961 return 0;
962 }
963 static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) {
964 Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t));
965 *key = Py_tss_NEEDS_INIT;
966 return key;
967 }
968 static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) {
969 PyObject_Free(key);
970 }
971 static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) {
972 return *key != Py_tss_NEEDS_INIT;
973 }
974 static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) {
975 PyThread_delete_key(*key);
976 *key = Py_tss_NEEDS_INIT;
977 }
978 static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) {
979 return PyThread_set_key_value(*key, value);
980 }
981 static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) {
982 return PyThread_get_key_value(*key);
983 }
984 #endif
985 #if PY_MAJOR_VERSION < 3
986 #if CYTHON_COMPILING_IN_PYPY
987 #if PYPY_VERSION_NUM < 0x07030600
988 #if defined(__cplusplus) && __cplusplus >= 201402L
989 [[deprecated("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6")]]
990 #elif defined(__GNUC__) || defined(__clang__)
991 __attribute__ ((__deprecated__("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6")))
992 #elif defined(_MSC_VER)
993 __declspec(deprecated("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6"))
994 #endif
995 static CYTHON_INLINE int PyGILState_Check(void) {
996 return 0;
997 }
998 #else // PYPY_VERSION_NUM < 0x07030600
999 #endif // PYPY_VERSION_NUM < 0x07030600
1000 #else
1001 static CYTHON_INLINE int PyGILState_Check(void) {
1002 PyThreadState * tstate = _PyThreadState_Current;
1003 return tstate && (tstate == PyGILState_GetThisThreadState());
1004 }
1005 #endif
1006 #endif
1007 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030d0000 || defined(_PyDict_NewPresized)
1008 #define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n))
1009 #else
1010 #define __Pyx_PyDict_NewPresized(n) PyDict_New()
1011 #endif
1012 #if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION
1013 #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
1014 #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
1015 #else
1016 #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
1017 #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
1018 #endif
1019 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX > 0x030600B4 && PY_VERSION_HEX < 0x030d0000 && CYTHON_USE_UNICODE_INTERNALS
1020 #define __Pyx_PyDict_GetItemStrWithError(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash)
1021 static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStr(PyObject *dict, PyObject *name) {
1022 PyObject *res = __Pyx_PyDict_GetItemStrWithError(dict, name);
1023 if (res == NULL) PyErr_Clear();
1024 return res;
1025 }
1026 #elif PY_MAJOR_VERSION >= 3 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07020000)
1027 #define __Pyx_PyDict_GetItemStrWithError PyDict_GetItemWithError
1028 #define __Pyx_PyDict_GetItemStr PyDict_GetItem
1029 #else
1030 static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStrWithError(PyObject *dict, PyObject *name) {
1031 #if CYTHON_COMPILING_IN_PYPY
1032 return PyDict_GetItem(dict, name);
1033 #else
1034 PyDictEntry *ep;
1035 PyDictObject *mp = (PyDictObject*) dict;
1036 long hash = ((PyStringObject *) name)->ob_shash;
1037 assert(hash != -1);
1038 ep = (mp->ma_lookup)(mp, name, hash);
1039 if (ep == NULL) {
1040 return NULL;
1041 }
1042 return ep->me_value;
1043 #endif
1044 }
1045 #define __Pyx_PyDict_GetItemStr PyDict_GetItem
1046 #endif
1047 #if CYTHON_USE_TYPE_SLOTS
1048 #define __Pyx_PyType_GetFlags(tp) (((PyTypeObject *)tp)->tp_flags)
1049 #define __Pyx_PyType_HasFeature(type, feature) ((__Pyx_PyType_GetFlags(type) & (feature)) != 0)
1050 #define __Pyx_PyObject_GetIterNextFunc(obj) (Py_TYPE(obj)->tp_iternext)
1051 #else
1052 #define __Pyx_PyType_GetFlags(tp) (PyType_GetFlags((PyTypeObject *)tp))
1053 #define __Pyx_PyType_HasFeature(type, feature) PyType_HasFeature(type, feature)
1054 #define __Pyx_PyObject_GetIterNextFunc(obj) PyIter_Next
1055 #endif
1056 #if CYTHON_COMPILING_IN_LIMITED_API
1057 #define __Pyx_SetItemOnTypeDict(tp, k, v) PyObject_GenericSetAttr((PyObject*)tp, k, v)
1058 #else
1059 #define __Pyx_SetItemOnTypeDict(tp, k, v) PyDict_SetItem(tp->tp_dict, k, v)
1060 #endif
1061 #if CYTHON_USE_TYPE_SPECS && PY_VERSION_HEX >= 0x03080000
1062 #define __Pyx_PyHeapTypeObject_GC_Del(obj) {\
1063 PyTypeObject *type = Py_TYPE((PyObject*)obj);\
1064 assert(__Pyx_PyType_HasFeature(type, Py_TPFLAGS_HEAPTYPE));\
1065 PyObject_GC_Del(obj);\
1066 Py_DECREF(type);\
1067 }
1068 #else
1069 #define __Pyx_PyHeapTypeObject_GC_Del(obj) PyObject_GC_Del(obj)
1070 #endif
1071 #if CYTHON_COMPILING_IN_LIMITED_API
1072 #define CYTHON_PEP393_ENABLED 1
1073 #define __Pyx_PyUnicode_READY(op) (0)
1074 #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GetLength(u)
1075 #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_ReadChar(u, i)
1076 #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((void)u, 1114111U)
1077 #define __Pyx_PyUnicode_KIND(u) ((void)u, (0))
1078 #define __Pyx_PyUnicode_DATA(u) ((void*)u)
1079 #define __Pyx_PyUnicode_READ(k, d, i) ((void)k, PyUnicode_ReadChar((PyObject*)(d), i))
1080 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GetLength(u))
1081 #elif PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
1082 #define CYTHON_PEP393_ENABLED 1
1083 #if PY_VERSION_HEX >= 0x030C0000
1084 #define __Pyx_PyUnicode_READY(op) (0)
1085 #else
1086 #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\
1087 0 : _PyUnicode_Ready((PyObject *)(op)))
1088 #endif
1089 #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
1090 #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
1091 #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u)
1092 #define __Pyx_PyUnicode_KIND(u) ((int)PyUnicode_KIND(u))
1093 #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
1094 #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
1095 #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, (Py_UCS4) ch)
1096 #if PY_VERSION_HEX >= 0x030C0000
1097 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u))
1098 #else
1099 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000
1100 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length))
1101 #else
1102 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u)))
1103 #endif
1104 #endif
1105 #else
1106 #define CYTHON_PEP393_ENABLED 0
1107 #define PyUnicode_1BYTE_KIND 1
1108 #define PyUnicode_2BYTE_KIND 2
1109 #define PyUnicode_4BYTE_KIND 4
1110 #define __Pyx_PyUnicode_READY(op) (0)
1111 #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
1112 #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
1113 #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535U : 1114111U)
1114 #define __Pyx_PyUnicode_KIND(u) ((int)sizeof(Py_UNICODE))
1115 #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
1116 #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
1117 #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = (Py_UNICODE) ch)
1118 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u))
1119 #endif
1120 #if CYTHON_COMPILING_IN_PYPY
1121 #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b)
1122 #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b)
1123 #else
1124 #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b)
1125 #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\
1126 PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
1127 #endif
1128 #if CYTHON_COMPILING_IN_PYPY
1129 #if !defined(PyUnicode_DecodeUnicodeEscape)
1130 #define PyUnicode_DecodeUnicodeEscape(s, size, errors) PyUnicode_Decode(s, size, "unicode_escape", errors)
1131 #endif
1132 #if !defined(PyUnicode_Contains) || (PY_MAJOR_VERSION == 2 && PYPY_VERSION_NUM < 0x07030500)
1133 #undef PyUnicode_Contains
1134 #define PyUnicode_Contains(u, s) PySequence_Contains(u, s)
1135 #endif
1136 #if !defined(PyByteArray_Check)
1137 #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type)
1138 #endif
1139 #if !defined(PyObject_Format)
1140 #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt)
1141 #endif
1142 #endif
1143 #define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
1144 #define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyUnicode_Check(b) && !PyUnicode_CheckExact(b)))) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
1145 #if PY_MAJOR_VERSION >= 3
1146 #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b)
1147 #else
1148 #define __Pyx_PyString_Format(a, b) PyString_Format(a, b)
1149 #endif
1150 #if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII)
1151 #define PyObject_ASCII(o) PyObject_Repr(o)
1152 #endif
1153 #if PY_MAJOR_VERSION >= 3
1154 #define PyBaseString_Type PyUnicode_Type
1155 #define PyStringObject PyUnicodeObject
1156 #define PyString_Type PyUnicode_Type
1157 #define PyString_Check PyUnicode_Check
1158 #define PyString_CheckExact PyUnicode_CheckExact
1159 #ifndef PyObject_Unicode
1160 #define PyObject_Unicode PyObject_Str
1161 #endif
1162 #endif
1163 #if PY_MAJOR_VERSION >= 3
1164 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
1165 #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
1166 #else
1167 #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj))
1168 #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
1169 #endif
1170 #if CYTHON_COMPILING_IN_CPYTHON
1171 #define __Pyx_PySequence_ListKeepNew(obj)\
1172 (likely(PyList_CheckExact(obj) && Py_REFCNT(obj) == 1) ? __Pyx_NewRef(obj) : PySequence_List(obj))
1173 #else
1174 #define __Pyx_PySequence_ListKeepNew(obj) PySequence_List(obj)
1175 #endif
1176 #ifndef PySet_CheckExact
1177 #define PySet_CheckExact(obj) __Pyx_IS_TYPE(obj, &PySet_Type)
1178 #endif
1179 #if PY_VERSION_HEX >= 0x030900A4
1180 #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt)
1181 #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size)
1182 #else
1183 #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt)
1184 #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size)
1185 #endif
1186 #if CYTHON_ASSUME_SAFE_MACROS
1187 #define __Pyx_PySequence_ITEM(o, i) PySequence_ITEM(o, i)
1188 #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq)
1189 #define __Pyx_PyTuple_SET_ITEM(o, i, v) (PyTuple_SET_ITEM(o, i, v), (0))
1190 #define __Pyx_PyList_SET_ITEM(o, i, v) (PyList_SET_ITEM(o, i, v), (0))
1191 #define __Pyx_PyTuple_GET_SIZE(o) PyTuple_GET_SIZE(o)
1192 #define __Pyx_PyList_GET_SIZE(o) PyList_GET_SIZE(o)
1193 #define __Pyx_PySet_GET_SIZE(o) PySet_GET_SIZE(o)
1194 #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_GET_SIZE(o)
1195 #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_GET_SIZE(o)
1196 #else
1197 #define __Pyx_PySequence_ITEM(o, i) PySequence_GetItem(o, i)
1198 #define __Pyx_PySequence_SIZE(seq) PySequence_Size(seq)
1199 #define __Pyx_PyTuple_SET_ITEM(o, i, v) PyTuple_SetItem(o, i, v)
1200 #define __Pyx_PyList_SET_ITEM(o, i, v) PyList_SetItem(o, i, v)
1201 #define __Pyx_PyTuple_GET_SIZE(o) PyTuple_Size(o)
1202 #define __Pyx_PyList_GET_SIZE(o) PyList_Size(o)
1203 #define __Pyx_PySet_GET_SIZE(o) PySet_Size(o)
1204 #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_Size(o)
1205 #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_Size(o)
1206 #endif
1207 #if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1
1208 #define __Pyx_PyImport_AddModuleRef(name) PyImport_AddModuleRef(name)
1209 #else
1210 static CYTHON_INLINE PyObject *__Pyx_PyImport_AddModuleRef(const char *name) {
1211 PyObject *module = PyImport_AddModule(name);
1212 Py_XINCREF(module);
1213 return module;
1214 }
1215 #endif
1216 #if PY_MAJOR_VERSION >= 3
1217 #define PyIntObject PyLongObject
1218 #define PyInt_Type PyLong_Type
1219 #define PyInt_Check(op) PyLong_Check(op)
1220 #define PyInt_CheckExact(op) PyLong_CheckExact(op)
1221 #define __Pyx_Py3Int_Check(op) PyLong_Check(op)
1222 #define __Pyx_Py3Int_CheckExact(op) PyLong_CheckExact(op)
1223 #define PyInt_FromString PyLong_FromString
1224 #define PyInt_FromUnicode PyLong_FromUnicode
1225 #define PyInt_FromLong PyLong_FromLong
1226 #define PyInt_FromSize_t PyLong_FromSize_t
1227 #define PyInt_FromSsize_t PyLong_FromSsize_t
1228 #define PyInt_AsLong PyLong_AsLong
1229 #define PyInt_AS_LONG PyLong_AS_LONG
1230 #define PyInt_AsSsize_t PyLong_AsSsize_t
1231 #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
1232 #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
1233 #define PyNumber_Int PyNumber_Long
1234 #else
1235 #define __Pyx_Py3Int_Check(op) (PyLong_Check(op) || PyInt_Check(op))
1236 #define __Pyx_Py3Int_CheckExact(op) (PyLong_CheckExact(op) || PyInt_CheckExact(op))
1237 #endif
1238 #if PY_MAJOR_VERSION >= 3
1239 #define PyBoolObject PyLongObject
1240 #endif
1241 #if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
1242 #ifndef PyUnicode_InternFromString
1243 #define PyUnicode_InternFromString(s) PyUnicode_FromString(s)
1244 #endif
1245 #endif
1246 #if PY_VERSION_HEX < 0x030200A4
1247 typedef long Py_hash_t;
1248 #define __Pyx_PyInt_FromHash_t PyInt_FromLong
1249 #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsHash_t
1250 #else
1251 #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
1252 #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsSsize_t
1253 #endif
1254 #if CYTHON_USE_ASYNC_SLOTS
1255 #if PY_VERSION_HEX >= 0x030500B1
1256 #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods
1257 #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async)
1258 #else
1259 #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
1260 #endif
1261 #else
1262 #define __Pyx_PyType_AsAsync(obj) NULL
1263 #endif
1264 #ifndef __Pyx_PyAsyncMethodsStruct
1265 typedef struct {
1266 unaryfunc am_await;
1267 unaryfunc am_aiter;
1268 unaryfunc am_anext;
1269 } __Pyx_PyAsyncMethodsStruct;
1270 #endif
1271
1272 #if defined(_WIN32) || defined(WIN32) || defined(MS_WINDOWS)
1273 #if !defined(_USE_MATH_DEFINES)
1274 #define _USE_MATH_DEFINES
1275 #endif
1276 #endif
1277 #include <math.h>
1278 #ifdef NAN
1279 #define __PYX_NAN() ((float) NAN)
1280 #else
1281 static CYTHON_INLINE float __PYX_NAN() {
1282 float value;
1283 memset(&value, 0xFF, sizeof(value));
1284 return value;
1285 }
1286 #endif
1287 #if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL)
1288 #define __Pyx_truncl trunc
1289 #else
1290 #define __Pyx_truncl truncl
1291 #endif
1292
1293 #define __PYX_MARK_ERR_POS(f_index, lineno) \
1294 { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; }
1295 #define __PYX_ERR(f_index, lineno, Ln_error) \
1296 { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; }
1297
1298 #ifdef CYTHON_EXTERN_C
1299 #undef __PYX_EXTERN_C
1300 #define __PYX_EXTERN_C CYTHON_EXTERN_C
1301 #elif defined(__PYX_EXTERN_C)
1302 #ifdef _MSC_VER
1303 #pragma message ("Please do not define the '__PYX_EXTERN_C' macro externally. Use 'CYTHON_EXTERN_C' instead.")
1304 #else
1305 #warning Please do not define the '__PYX_EXTERN_C' macro externally. Use 'CYTHON_EXTERN_C' instead.
1306 #endif
1307 #else
1308 #ifdef __cplusplus
1309 #define __PYX_EXTERN_C extern "C"
1310 #else
1311 #define __PYX_EXTERN_C extern
1312 #endif
1313 #endif
1314
1315 #define __PYX_HAVE__pysam__libcvcf
1316 #define __PYX_HAVE_API__pysam__libcvcf
1317 /* Early includes */
1318 #include <string.h>
1319 #include <stdlib.h>
1320 #include <stdint.h>
1321 #include <stdio.h>
1322 #include "fcntl.h"
1323 #include "unistd.h"
1324 #include <sys/types.h>
1325 #include "stdarg.h"
1326 #include "htslib/kstring.h"
1327 #include "htslib_util.h"
1328 #include "htslib/hfile.h"
1329 #include "htslib/bgzf.h"
1330 #include "htslib/hts.h"
1331 #include "htslib/sam.h"
1332 #include "htslib/faidx.h"
1333 #include "htslib/tbx.h"
1334 #include "htslib/vcf.h"
1335 #include "htslib/vcfutils.h"
1336 #include "htslib/cram.h"
1337 #include "pysam_stream.h"
1338 #include <stddef.h>
1339 #include "pythread.h"
1340
1341 #if CYTHON_COMPILING_IN_PYPY
1342 #ifdef _MSC_VER
1343 #pragma message ("This module uses CPython specific internals of 'array.array', which are not available in PyPy.")
1344 #else
1345 #warning This module uses CPython specific internals of 'array.array', which are not available in PyPy.
1346 #endif
1347 #endif
1348
1349 #ifdef _OPENMP
1350 #include <omp.h>
1351 #endif /* _OPENMP */
1352
1353 #if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS)
1354 #define CYTHON_WITHOUT_ASSERTIONS
1355 #endif
1356
1357 typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding;
1358 const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
1359
1360 #define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
1361 #define __PYX_DEFAULT_STRING_ENCODING_IS_UTF8 0
1362 #define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT (PY_MAJOR_VERSION >= 3 && __PYX_DEFAULT_STRING_ENCODING_IS_UTF8)
1363 #define __PYX_DEFAULT_STRING_ENCODING ""
1364 #define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
1365 #define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
1366 #define __Pyx_uchar_cast(c) ((unsigned char)c)
1367 #define __Pyx_long_cast(x) ((long)x)
1368 #define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\
1369 (sizeof(type) < sizeof(Py_ssize_t)) ||\
1370 (sizeof(type) > sizeof(Py_ssize_t) &&\
1371 likely(v < (type)PY_SSIZE_T_MAX ||\
1372 v == (type)PY_SSIZE_T_MAX) &&\
1373 (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\
1374 v == (type)PY_SSIZE_T_MIN))) ||\
1375 (sizeof(type) == sizeof(Py_ssize_t) &&\
1376 (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\
1377 v == (type)PY_SSIZE_T_MAX))) )
1378 static CYTHON_INLINE int __Pyx_is_valid_index(Py_ssize_t i, Py_ssize_t limit) {
1379 return (size_t) i < (size_t) limit;
1380 }
1381 #if defined (__cplusplus) && __cplusplus >= 201103L
1382 #include <cstdlib>
1383 #define __Pyx_sst_abs(value) std::abs(value)
1384 #elif SIZEOF_INT >= SIZEOF_SIZE_T
1385 #define __Pyx_sst_abs(value) abs(value)
1386 #elif SIZEOF_LONG >= SIZEOF_SIZE_T
1387 #define __Pyx_sst_abs(value) labs(value)
1388 #elif defined (_MSC_VER)
1389 #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value))
1390 #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
1391 #define __Pyx_sst_abs(value) llabs(value)
1392 #elif defined (__GNUC__)
1393 #define __Pyx_sst_abs(value) __builtin_llabs(value)
1394 #else
1395 #define __Pyx_sst_abs(value) ((value<0) ? -value : value)
1396 #endif
1397 static CYTHON_INLINE Py_ssize_t __Pyx_ssize_strlen(const char *s);
1398 static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*);
1399 static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
1400 static CYTHON_INLINE PyObject* __Pyx_PyByteArray_FromString(const char*);
1401 #define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
1402 #define __Pyx_PyBytes_FromString PyBytes_FromString
1403 #define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
1404 static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
1405 #if PY_MAJOR_VERSION < 3
1406 #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
1407 #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
1408 #else
1409 #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
1410 #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
1411 #endif
1412 #define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s))
1413 #define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s))
1414 #define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s))
1415 #define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s))
1416 #define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s))
1417 #define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s))
1418 #define __Pyx_PyObject_AsWritableString(s) ((char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s))
1419 #define __Pyx_PyObject_AsWritableSString(s) ((signed char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s))
1420 #define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s))
1421 #define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s))
1422 #define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s))
1423 #define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s)
1424 #define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s)
1425 #define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s)
1426 #define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s)
1427 #define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
1428 #define __Pyx_PyUnicode_FromOrdinal(o) PyUnicode_FromOrdinal((int)o)
1429 #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
1430 #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj)
1431 #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
1432 static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b);
1433 static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
1434 static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*);
1435 static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
1436 #define __Pyx_PySequence_Tuple(obj)\
1437 (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj))
1438 static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
1439 static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
1440 static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*);
1441 #if CYTHON_ASSUME_SAFE_MACROS
1442 #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
1443 #else
1444 #define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
1445 #endif
1446 #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
1447 #if PY_MAJOR_VERSION >= 3
1448 #define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x))
1449 #else
1450 #define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x))
1451 #endif
1452 #if CYTHON_USE_PYLONG_INTERNALS
1453 #if PY_VERSION_HEX >= 0x030C00A7
1454 #ifndef _PyLong_SIGN_MASK
1455 #define _PyLong_SIGN_MASK 3
1456 #endif
1457 #ifndef _PyLong_NON_SIZE_BITS
1458 #define _PyLong_NON_SIZE_BITS 3
1459 #endif
1460 #define __Pyx_PyLong_Sign(x) (((PyLongObject*)x)->long_value.lv_tag & _PyLong_SIGN_MASK)
1461 #define __Pyx_PyLong_IsNeg(x) ((__Pyx_PyLong_Sign(x) & 2) != 0)
1462 #define __Pyx_PyLong_IsNonNeg(x) (!__Pyx_PyLong_IsNeg(x))
1463 #define __Pyx_PyLong_IsZero(x) (__Pyx_PyLong_Sign(x) & 1)
1464 #define __Pyx_PyLong_IsPos(x) (__Pyx_PyLong_Sign(x) == 0)
1465 #define __Pyx_PyLong_CompactValueUnsigned(x) (__Pyx_PyLong_Digits(x)[0])
1466 #define __Pyx_PyLong_DigitCount(x) ((Py_ssize_t) (((PyLongObject*)x)->long_value.lv_tag >> _PyLong_NON_SIZE_BITS))
1467 #define __Pyx_PyLong_SignedDigitCount(x)\
1468 ((1 - (Py_ssize_t) __Pyx_PyLong_Sign(x)) * __Pyx_PyLong_DigitCount(x))
1469 #if defined(PyUnstable_Long_IsCompact) && defined(PyUnstable_Long_CompactValue)
1470 #define __Pyx_PyLong_IsCompact(x) PyUnstable_Long_IsCompact((PyLongObject*) x)
1471 #define __Pyx_PyLong_CompactValue(x) PyUnstable_Long_CompactValue((PyLongObject*) x)
1472 #else
1473 #define __Pyx_PyLong_IsCompact(x) (((PyLongObject*)x)->long_value.lv_tag < (2 << _PyLong_NON_SIZE_BITS))
1474 #define __Pyx_PyLong_CompactValue(x) ((1 - (Py_ssize_t) __Pyx_PyLong_Sign(x)) * (Py_ssize_t) __Pyx_PyLong_Digits(x)[0])
1475 #endif
1476 typedef Py_ssize_t __Pyx_compact_pylong;
1477 typedef size_t __Pyx_compact_upylong;
1478 #else
1479 #define __Pyx_PyLong_IsNeg(x) (Py_SIZE(x) < 0)
1480 #define __Pyx_PyLong_IsNonNeg(x) (Py_SIZE(x) >= 0)
1481 #define __Pyx_PyLong_IsZero(x) (Py_SIZE(x) == 0)
1482 #define __Pyx_PyLong_IsPos(x) (Py_SIZE(x) > 0)
1483 #define __Pyx_PyLong_CompactValueUnsigned(x) ((Py_SIZE(x) == 0) ? 0 : __Pyx_PyLong_Digits(x)[0])
1484 #define __Pyx_PyLong_DigitCount(x) __Pyx_sst_abs(Py_SIZE(x))
1485 #define __Pyx_PyLong_SignedDigitCount(x) Py_SIZE(x)
1486 #define __Pyx_PyLong_IsCompact(x) (Py_SIZE(x) == 0 || Py_SIZE(x) == 1 || Py_SIZE(x) == -1)
1487 #define __Pyx_PyLong_CompactValue(x)\
1488 ((Py_SIZE(x) == 0) ? (sdigit) 0 : ((Py_SIZE(x) < 0) ? -(sdigit)__Pyx_PyLong_Digits(x)[0] : (sdigit)__Pyx_PyLong_Digits(x)[0]))
1489 typedef sdigit __Pyx_compact_pylong;
1490 typedef digit __Pyx_compact_upylong;
1491 #endif
1492 #if PY_VERSION_HEX >= 0x030C00A5
1493 #define __Pyx_PyLong_Digits(x) (((PyLongObject*)x)->long_value.ob_digit)
1494 #else
1495 #define __Pyx_PyLong_Digits(x) (((PyLongObject*)x)->ob_digit)
1496 #endif
1497 #endif
1498 #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
1499 #include <string.h>
1500 static int __Pyx_sys_getdefaultencoding_not_ascii;
1501 static int __Pyx_init_sys_getdefaultencoding_params(void) {
1502 PyObject* sys;
1503 PyObject* default_encoding = NULL;
1504 PyObject* ascii_chars_u = NULL;
1505 PyObject* ascii_chars_b = NULL;
1506 const char* default_encoding_c;
1507 sys = PyImport_ImportModule("sys");
1508 if (!sys) goto bad;
1509 default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
1510 Py_DECREF(sys);
1511 if (!default_encoding) goto bad;
1512 default_encoding_c = PyBytes_AsString(default_encoding);
1513 if (!default_encoding_c) goto bad;
1514 if (strcmp(default_encoding_c, "ascii") == 0) {
1515 __Pyx_sys_getdefaultencoding_not_ascii = 0;
1516 } else {
1517 char ascii_chars[128];
1518 int c;
1519 for (c = 0; c < 128; c++) {
1520 ascii_chars[c] = (char) c;
1521 }
1522 __Pyx_sys_getdefaultencoding_not_ascii = 1;
1523 ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
1524 if (!ascii_chars_u) goto bad;
1525 ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
1526 if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
1527 PyErr_Format(
1528 PyExc_ValueError,
1529 "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
1530 default_encoding_c);
1531 goto bad;
1532 }
1533 Py_DECREF(ascii_chars_u);
1534 Py_DECREF(ascii_chars_b);
1535 }
1536 Py_DECREF(default_encoding);
1537 return 0;
1538 bad:
1539 Py_XDECREF(default_encoding);
1540 Py_XDECREF(ascii_chars_u);
1541 Py_XDECREF(ascii_chars_b);
1542 return -1;
1543 }
1544 #endif
1545 #if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
1546 #define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
1547 #else
1548 #define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
1549 #if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
1550 #include <string.h>
1551 static char* __PYX_DEFAULT_STRING_ENCODING;
1552 static int __Pyx_init_sys_getdefaultencoding_params(void) {
1553 PyObject* sys;
1554 PyObject* default_encoding = NULL;
1555 char* default_encoding_c;
1556 sys = PyImport_ImportModule("sys");
1557 if (!sys) goto bad;
1558 default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
1559 Py_DECREF(sys);
1560 if (!default_encoding) goto bad;
1561 default_encoding_c = PyBytes_AsString(default_encoding);
1562 if (!default_encoding_c) goto bad;
1563 __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
1564 if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
1565 strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
1566 Py_DECREF(default_encoding);
1567 return 0;
1568 bad:
1569 Py_XDECREF(default_encoding);
1570 return -1;
1571 }
1572 #endif
1573 #endif
1574
1575
1576 /* Test for GCC > 2.95 */
1577 #if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
1578 #define likely(x) __builtin_expect(!!(x), 1)
1579 #define unlikely(x) __builtin_expect(!!(x), 0)
1580 #else /* !__GNUC__ or GCC < 2.95 */
1581 #define likely(x) (x)
1582 #define unlikely(x) (x)
1583 #endif /* __GNUC__ */
1584 static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; }
1585
1586 #if !CYTHON_USE_MODULE_STATE
1587 static PyObject *__pyx_m = NULL;
1588 #endif
1589 static int __pyx_lineno;
1590 static int __pyx_clineno = 0;
1591 static const char * __pyx_cfilenm = __FILE__;
1592 static const char *__pyx_filename;
1593
1594 /* #### Code section: filename_table ### */
1595
1596 static const char *__pyx_f[] = {
1597 "pysam/libcvcf.pyx",
1598 "<stringsource>",
1599 "contextvars.pxd",
1600 "array.pxd",
1601 "pysam/libchtslib.pxd",
1602 "pysam/libctabix.pxd",
1603 "pysam/libctabixproxies.pxd",
1604 "type.pxd",
1605 "bool.pxd",
1606 "complex.pxd",
1607 };
1608 /* #### Code section: utility_code_proto_before_types ### */
1609 /* ForceInitThreads.proto */
1610 #ifndef __PYX_FORCE_INIT_THREADS
1611 #define __PYX_FORCE_INIT_THREADS 0
1612 #endif
1613
1614 /* #### Code section: numeric_typedefs ### */
1615 /* #### Code section: complex_type_declarations ### */
1616 /* #### Code section: type_declarations ### */
1617
1618 /*--- Type declarations ---*/
1619 #ifndef _ARRAYARRAY_H
1620 struct arrayobject;
1621 typedef struct arrayobject arrayobject;
1622 #endif
1623 struct __pyx_obj_5pysam_10libchtslib_HTSFile;
1624 struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator;
1625 struct __pyx_obj_5pysam_9libctabix_TabixFile;
1626 struct __pyx_obj_5pysam_9libctabix_Parser;
1627 struct __pyx_obj_5pysam_9libctabix_asTuple;
1628 struct __pyx_obj_5pysam_9libctabix_asGTF;
1629 struct __pyx_obj_5pysam_9libctabix_asGFF3;
1630 struct __pyx_obj_5pysam_9libctabix_asBed;
1631 struct __pyx_obj_5pysam_9libctabix_asVCF;
1632 struct __pyx_obj_5pysam_9libctabix_TabixIterator;
1633 struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed;
1634 struct __pyx_obj_5pysam_9libctabix_GZIterator;
1635 struct __pyx_obj_5pysam_9libctabix_GZIteratorHead;
1636 struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed;
1637 struct __pyx_obj_5pysam_9libctabix_Tabixfile;
1638 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy;
1639 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxyIterator;
1640 struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy;
1641 struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy;
1642 struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy;
1643 struct __pyx_obj_5pysam_16libctabixproxies_BedProxy;
1644 struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy;
1645 struct __pyx_obj_5pysam_7libcvcf_VCFRecord;
1646 struct __pyx_obj_5pysam_7libcvcf_asVCFRecord;
1647 struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse;
1648 struct __pyx_opt_args_5pysam_16libctabixproxies_10TupleProxy_copy;
1649
1650 /* "pysam/libctabixproxies.pxd":23
1651 * cdef take(self, char * buffer, size_t nbytes)
1652 * cdef present(self, char * buffer, size_t nbytes)
1653 * cdef copy(self, char * buffer, size_t nbytes, bint reset=*) # <<<<<<<<<<<<<<
1654 * cdef update(self, char * buffer, size_t nbytes)
1655 *
1656 */
1657 struct __pyx_opt_args_5pysam_16libctabixproxies_10TupleProxy_copy {
1658 int __pyx_n;
1659 int reset;
1660 };
1661 struct __pyx_opt_args_7cpython_11contextvars_get_value;
1662 struct __pyx_opt_args_7cpython_11contextvars_get_value_no_default;
1663
1664 /* "cpython/contextvars.pxd":112
1665 *
1666 *
1667 * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<<
1668 * """Return a new reference to the value of the context variable,
1669 * or the default value of the context variable,
1670 */
1671 struct __pyx_opt_args_7cpython_11contextvars_get_value {
1672 int __pyx_n;
1673 PyObject *default_value;
1674 };
1675
1676 /* "cpython/contextvars.pxd":129
1677 *
1678 *
1679 * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<<
1680 * """Return a new reference to the value of the context variable,
1681 * or the provided default value if no such value was found.
1682 */
1683 struct __pyx_opt_args_7cpython_11contextvars_get_value_no_default {
1684 int __pyx_n;
1685 PyObject *default_value;
1686 };
1687 struct __pyx_opt_args_5pysam_9libcutils_parse_region;
1688 struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array;
1689 struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring;
1690 struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring;
1691 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str;
1692 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_bytes;
1693 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len;
1694 struct __pyx_opt_args_5pysam_9libcutils_force_str;
1695 struct __pyx_opt_args_5pysam_9libcutils_force_bytes;
1696 struct __pyx_opt_args_5pysam_9libcutils_decode_bytes;
1697
1698 /* "pysam/libcutils.pxd":8
1699 * from cpython cimport array as c_array
1700 *
1701 * cpdef parse_region(contig=*, start=*, stop=*, region=*, reference=*, end=*) # <<<<<<<<<<<<<<
1702 *
1703 * cdef int libc_whence_from_io(int whence)
1704 */
1705 struct __pyx_opt_args_5pysam_9libcutils_parse_region {
1706 int __pyx_n;
1707 PyObject *contig;
1708 PyObject *start;
1709 PyObject *stop;
1710 PyObject *region;
1711 PyObject *reference;
1712 PyObject *end;
1713 };
1714
1715 /* "pysam/libcutils.pxd":15
1716 * # Utility functions for quality string conversions
1717 *
1718 * cpdef c_array.array qualitystring_to_array(input_str, int offset=*) # <<<<<<<<<<<<<<
1719 * cpdef array_to_qualitystring(c_array.array arr, int offset=*)
1720 * cpdef qualities_to_qualitystring(qualities, int offset=*)
1721 */
1722 struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array {
1723 int __pyx_n;
1724 int offset;
1725 };
1726
1727 /* "pysam/libcutils.pxd":16
1728 *
1729 * cpdef c_array.array qualitystring_to_array(input_str, int offset=*)
1730 * cpdef array_to_qualitystring(c_array.array arr, int offset=*) # <<<<<<<<<<<<<<
1731 * cpdef qualities_to_qualitystring(qualities, int offset=*)
1732 *
1733 */
1734 struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring {
1735 int __pyx_n;
1736 int offset;
1737 };
1738
1739 /* "pysam/libcutils.pxd":17
1740 * cpdef c_array.array qualitystring_to_array(input_str, int offset=*)
1741 * cpdef array_to_qualitystring(c_array.array arr, int offset=*)
1742 * cpdef qualities_to_qualitystring(qualities, int offset=*) # <<<<<<<<<<<<<<
1743 *
1744 * ########################################################################
1745 */
1746 struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring {
1747 int __pyx_n;
1748 int offset;
1749 };
1750
1751 /* "pysam/libcutils.pxd":29
1752 * ## Python 3 compatibility functions
1753 * ########################################################################
1754 * cdef charptr_to_str(const char *s, encoding=*, errors=*) # <<<<<<<<<<<<<<
1755 * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*)
1756 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
1757 */
1758 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str {
1759 int __pyx_n;
1760 PyObject *encoding;
1761 PyObject *errors;
1762 };
1763
1764 /* "pysam/libcutils.pxd":30
1765 * ########################################################################
1766 * cdef charptr_to_str(const char *s, encoding=*, errors=*)
1767 * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*) # <<<<<<<<<<<<<<
1768 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
1769 * cdef force_str(object s, encoding=*, errors=*)
1770 */
1771 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_bytes {
1772 int __pyx_n;
1773 PyObject *encoding;
1774 PyObject *errors;
1775 };
1776
1777 /* "pysam/libcutils.pxd":31
1778 * cdef charptr_to_str(const char *s, encoding=*, errors=*)
1779 * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*)
1780 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) # <<<<<<<<<<<<<<
1781 * cdef force_str(object s, encoding=*, errors=*)
1782 * cdef bytes force_bytes(object s, encoding=*, errors=*)
1783 */
1784 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len {
1785 int __pyx_n;
1786 PyObject *encoding;
1787 PyObject *errors;
1788 };
1789
1790 /* "pysam/libcutils.pxd":32
1791 * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*)
1792 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
1793 * cdef force_str(object s, encoding=*, errors=*) # <<<<<<<<<<<<<<
1794 * cdef bytes force_bytes(object s, encoding=*, errors=*)
1795 * cdef decode_bytes(bytes s, encoding=*, errors=*)
1796 */
1797 struct __pyx_opt_args_5pysam_9libcutils_force_str {
1798 int __pyx_n;
1799 PyObject *encoding;
1800 PyObject *errors;
1801 };
1802
1803 /* "pysam/libcutils.pxd":33
1804 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
1805 * cdef force_str(object s, encoding=*, errors=*)
1806 * cdef bytes force_bytes(object s, encoding=*, errors=*) # <<<<<<<<<<<<<<
1807 * cdef decode_bytes(bytes s, encoding=*, errors=*)
1808 * cdef bytes encode_filename(object filename)
1809 */
1810 struct __pyx_opt_args_5pysam_9libcutils_force_bytes {
1811 int __pyx_n;
1812 PyObject *encoding;
1813 PyObject *errors;
1814 };
1815
1816 /* "pysam/libcutils.pxd":34
1817 * cdef force_str(object s, encoding=*, errors=*)
1818 * cdef bytes force_bytes(object s, encoding=*, errors=*)
1819 * cdef decode_bytes(bytes s, encoding=*, errors=*) # <<<<<<<<<<<<<<
1820 * cdef bytes encode_filename(object filename)
1821 * cdef from_string_and_size(const char *s, size_t length)
1822 */
1823 struct __pyx_opt_args_5pysam_9libcutils_decode_bytes {
1824 int __pyx_n;
1825 PyObject *encoding;
1826 PyObject *errors;
1827 };
1828
1829 /* "pysam/libchtslib.pxd":2706
1830 *
1831 *
1832 * cdef class HTSFile(object): # <<<<<<<<<<<<<<
1833 * cdef htsFile *htsfile # pointer to htsFile structure
1834 * cdef int64_t start_offset # BGZF offset of first record
1835 */
1836 struct __pyx_obj_5pysam_10libchtslib_HTSFile {
1837 PyObject_HEAD
1838 struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile *__pyx_vtab;
1839 htsFile *htsfile;
1840 int64_t start_offset;
1841 PyObject *filename;
1842 PyObject *mode;
1843 PyObject *threads;
1844 PyObject *index_filename;
1845 int is_stream;
1846 int is_remote;
1847 int duplicate_filehandle;
1848 };
1849
1850
1851 /* "pysam/libctabix.pxd":48
1852 *
1853 *
1854 * cdef class tabix_file_iterator: # <<<<<<<<<<<<<<
1855 * cdef BGZF * fh
1856 * cdef kstream_t * kstream
1857 */
1858 struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator {
1859 PyObject_HEAD
1860 struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator *__pyx_vtab;
1861 BGZF *fh;
1862 kstream_t *kstream;
1863 kstring_t buffer;
1864 size_t size;
1865 struct __pyx_obj_5pysam_9libctabix_Parser *parser;
1866 int fd;
1867 int duplicated_fd;
1868 PyObject *infile;
1869 };
1870
1871
1872 /* "pysam/libctabix.pxd":61
1873 *
1874 *
1875 * cdef class TabixFile(HTSFile): # <<<<<<<<<<<<<<
1876 * # pointer to index structure
1877 * cdef tbx_t * index
1878 */
1879 struct __pyx_obj_5pysam_9libctabix_TabixFile {
1880 struct __pyx_obj_5pysam_10libchtslib_HTSFile __pyx_base;
1881 tbx_t *index;
1882 PyObject *filename_index;
1883 struct __pyx_obj_5pysam_9libctabix_Parser *parser;
1884 PyObject *encoding;
1885 };
1886
1887
1888 /* "pysam/libctabix.pxd":72
1889 *
1890 *
1891 * cdef class Parser: # <<<<<<<<<<<<<<
1892 * cdef encoding
1893 * cdef parse(self, char * buffer, int len)
1894 */
1895 struct __pyx_obj_5pysam_9libctabix_Parser {
1896 PyObject_HEAD
1897 struct __pyx_vtabstruct_5pysam_9libctabix_Parser *__pyx_vtab;
1898 PyObject *encoding;
1899 };
1900
1901
1902 /* "pysam/libctabix.pxd":77
1903 *
1904 *
1905 * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
1906 * cdef parse(self, char * buffer, int len)
1907 *
1908 */
1909 struct __pyx_obj_5pysam_9libctabix_asTuple {
1910 struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base;
1911 };
1912
1913
1914 /* "pysam/libctabix.pxd":81
1915 *
1916 *
1917 * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
1918 * pass
1919 *
1920 */
1921 struct __pyx_obj_5pysam_9libctabix_asGTF {
1922 struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base;
1923 };
1924
1925
1926 /* "pysam/libctabix.pxd":85
1927 *
1928 *
1929 * cdef class asGFF3(Parser): # <<<<<<<<<<<<<<
1930 * pass
1931 *
1932 */
1933 struct __pyx_obj_5pysam_9libctabix_asGFF3 {
1934 struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base;
1935 };
1936
1937
1938 /* "pysam/libctabix.pxd":89
1939 *
1940 *
1941 * cdef class asBed(Parser): # <<<<<<<<<<<<<<
1942 * pass
1943 *
1944 */
1945 struct __pyx_obj_5pysam_9libctabix_asBed {
1946 struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base;
1947 };
1948
1949
1950 /* "pysam/libctabix.pxd":93
1951 *
1952 *
1953 * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
1954 * pass
1955 *
1956 */
1957 struct __pyx_obj_5pysam_9libctabix_asVCF {
1958 struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base;
1959 };
1960
1961
1962 /* "pysam/libctabix.pxd":97
1963 *
1964 *
1965 * cdef class TabixIterator: # <<<<<<<<<<<<<<
1966 * cdef hts_itr_t * iterator
1967 * cdef TabixFile tabixfile
1968 */
1969 struct __pyx_obj_5pysam_9libctabix_TabixIterator {
1970 PyObject_HEAD
1971 struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator *__pyx_vtab;
1972 hts_itr_t *iterator;
1973 struct __pyx_obj_5pysam_9libctabix_TabixFile *tabixfile;
1974 kstring_t buffer;
1975 PyObject *encoding;
1976 };
1977
1978
1979 /* "pysam/libctabix.pxd":105
1980 *
1981 *
1982 * cdef class TabixIteratorParsed(TabixIterator): # <<<<<<<<<<<<<<
1983 * cdef Parser parser
1984 *
1985 */
1986 struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed {
1987 struct __pyx_obj_5pysam_9libctabix_TabixIterator __pyx_base;
1988 struct __pyx_obj_5pysam_9libctabix_Parser *parser;
1989 };
1990
1991
1992 /* "pysam/libctabix.pxd":109
1993 *
1994 *
1995 * cdef class GZIterator: # <<<<<<<<<<<<<<
1996 * cdef object _filename
1997 * cdef BGZF * gzipfile
1998 */
1999 struct __pyx_obj_5pysam_9libctabix_GZIterator {
2000 PyObject_HEAD
2001 struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator *__pyx_vtab;
2002 PyObject *_filename;
2003 BGZF *gzipfile;
2004 kstream_t *kstream;
2005 kstring_t buffer;
2006 PyObject *encoding;
2007 };
2008
2009
2010 /* "pysam/libctabix.pxd":118
2011 *
2012 *
2013 * cdef class GZIteratorHead(GZIterator): # <<<<<<<<<<<<<<
2014 * pass
2015 *
2016 */
2017 struct __pyx_obj_5pysam_9libctabix_GZIteratorHead {
2018 struct __pyx_obj_5pysam_9libctabix_GZIterator __pyx_base;
2019 };
2020
2021
2022 /* "pysam/libctabix.pxd":122
2023 *
2024 *
2025 * cdef class GZIteratorParsed(GZIterator): # <<<<<<<<<<<<<<
2026 * cdef Parser parser
2027 *
2028 */
2029 struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed {
2030 struct __pyx_obj_5pysam_9libctabix_GZIterator __pyx_base;
2031 struct __pyx_obj_5pysam_9libctabix_Parser *parser;
2032 };
2033
2034
2035 /* "pysam/libctabix.pxd":127
2036 *
2037 * # Compatibility Layer for pysam < 0.8
2038 * cdef class Tabixfile(TabixFile): # <<<<<<<<<<<<<<
2039 * pass
2040 */
2041 struct __pyx_obj_5pysam_9libctabix_Tabixfile {
2042 struct __pyx_obj_5pysam_9libctabix_TabixFile __pyx_base;
2043 };
2044
2045
2046 /* "pysam/libctabixproxies.pxd":5
2047 * from libc.stdint cimport uint8_t, int32_t, uint32_t, int64_t, uint64_t
2048 *
2049 * cdef class TupleProxy: # <<<<<<<<<<<<<<
2050 *
2051 * cdef:
2052 */
2053 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy {
2054 PyObject_HEAD
2055 struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy *__pyx_vtab;
2056 char *data;
2057 char **fields;
2058 int nfields;
2059 int nbytes;
2060 int offset;
2061 int is_modified;
2062 PyObject *encoding;
2063 };
2064
2065
2066 /* "pysam/libctabixproxies.pxd":27
2067 *
2068 *
2069 * cdef class TupleProxyIterator: # <<<<<<<<<<<<<<
2070 * cdef TupleProxy proxy
2071 * cdef int index
2072 */
2073 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxyIterator {
2074 PyObject_HEAD
2075 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *proxy;
2076 int index;
2077 };
2078
2079
2080 /* "pysam/libctabixproxies.pxd":32
2081 *
2082 *
2083 * cdef class NamedTupleProxy(TupleProxy): # <<<<<<<<<<<<<<
2084 * pass
2085 *
2086 */
2087 struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy {
2088 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy __pyx_base;
2089 };
2090
2091
2092 /* "pysam/libctabixproxies.pxd":36
2093 *
2094 *
2095 * cdef class GTFProxy(NamedTupleProxy): # <<<<<<<<<<<<<<
2096 * cdef object attribute_dict
2097 * cpdef int getMaxFields(self)
2098 */
2099 struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy {
2100 struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base;
2101 PyObject *attribute_dict;
2102 };
2103
2104
2105 /* "pysam/libctabixproxies.pxd":42
2106 *
2107 *
2108 * cdef class GFF3Proxy(GTFProxy): # <<<<<<<<<<<<<<
2109 * pass
2110 *
2111 */
2112 struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy {
2113 struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy __pyx_base;
2114 };
2115
2116
2117 /* "pysam/libctabixproxies.pxd":46
2118 *
2119 *
2120 * cdef class BedProxy(NamedTupleProxy): # <<<<<<<<<<<<<<
2121 *
2122 * cdef:
2123 */
2124 struct __pyx_obj_5pysam_16libctabixproxies_BedProxy {
2125 struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base;
2126 char *contig;
2127 uint32_t start;
2128 uint32_t end;
2129 int bedfields;
2130 };
2131
2132
2133 /* "pysam/libctabixproxies.pxd":58
2134 * cdef update(self, char * buffer, size_t nbytes)
2135 *
2136 * cdef class VCFProxy(NamedTupleProxy) : # <<<<<<<<<<<<<<
2137 *
2138 * cdef:
2139 */
2140 struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy {
2141 struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base;
2142 char *contig;
2143 uint32_t pos;
2144 };
2145
2146
2147 /* "pysam/libcvcf.pyx":104
2148 * ###########################################################################################################
2149 *
2150 * cdef class VCFRecord(libctabixproxies.TupleProxy): # <<<<<<<<<<<<<<
2151 * '''vcf record.
2152 *
2153 */
2154 struct __pyx_obj_5pysam_7libcvcf_VCFRecord {
2155 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy __pyx_base;
2156 PyObject *vcf;
2157 char *contig;
2158 uint32_t pos;
2159 };
2160
2161
2162 /* "pysam/libcvcf.pyx":241
2163 *
2164 *
2165 * cdef class asVCFRecord(libctabix.Parser): # <<<<<<<<<<<<<<
2166 * '''converts a :term:`tabix row` into a VCF record.'''
2167 * cdef vcffile
2168 */
2169 struct __pyx_obj_5pysam_7libcvcf_asVCFRecord {
2170 struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base;
2171 PyObject *vcffile;
2172 };
2173
2174
2175 /* "pysam/libcvcf.pyx":929
2176 * return line
2177 *
2178 * def _parse(self, line, stream): # <<<<<<<<<<<<<<
2179 * # deal with files with header only
2180 * if line.startswith("##"): return
2181 */
2182 struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse {
2183 PyObject_HEAD
2184 PyObject *__pyx_v_d;
2185 PyObject *__pyx_v_line;
2186 PyObject *__pyx_v_self;
2187 PyObject *__pyx_v_stream;
2188 PyObject *__pyx_t_0;
2189 Py_ssize_t __pyx_t_1;
2190 PyObject *(*__pyx_t_2)(PyObject *);
2191 };
2192
2193
2194
2195 /* "pysam/libchtslib.pxd":2706
2196 *
2197 *
2198 * cdef class HTSFile(object): # <<<<<<<<<<<<<<
2199 * cdef htsFile *htsfile # pointer to htsFile structure
2200 * cdef int64_t start_offset # BGZF offset of first record
2201 */
2202
2203 struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile {
2204 htsFile *(*_open_htsfile)(struct __pyx_obj_5pysam_10libchtslib_HTSFile *);
2205 };
2206 static struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile *__pyx_vtabptr_5pysam_10libchtslib_HTSFile;
2207
2208
2209 /* "pysam/libctabix.pxd":48
2210 *
2211 *
2212 * cdef class tabix_file_iterator: # <<<<<<<<<<<<<<
2213 * cdef BGZF * fh
2214 * cdef kstream_t * kstream
2215 */
2216
2217 struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator {
2218 PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *);
2219 };
2220 static struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator *__pyx_vtabptr_5pysam_9libctabix_tabix_file_iterator;
2221
2222
2223 /* "pysam/libctabix.pxd":61
2224 *
2225 *
2226 * cdef class TabixFile(HTSFile): # <<<<<<<<<<<<<<
2227 * # pointer to index structure
2228 * cdef tbx_t * index
2229 */
2230
2231 struct __pyx_vtabstruct_5pysam_9libctabix_TabixFile {
2232 struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile __pyx_base;
2233 };
2234 static struct __pyx_vtabstruct_5pysam_9libctabix_TabixFile *__pyx_vtabptr_5pysam_9libctabix_TabixFile;
2235
2236
2237 /* "pysam/libctabix.pxd":72
2238 *
2239 *
2240 * cdef class Parser: # <<<<<<<<<<<<<<
2241 * cdef encoding
2242 * cdef parse(self, char * buffer, int len)
2243 */
2244
2245 struct __pyx_vtabstruct_5pysam_9libctabix_Parser {
2246 PyObject *(*parse)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int);
2247 };
2248 static struct __pyx_vtabstruct_5pysam_9libctabix_Parser *__pyx_vtabptr_5pysam_9libctabix_Parser;
2249
2250
2251 /* "pysam/libctabix.pxd":77
2252 *
2253 *
2254 * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
2255 * cdef parse(self, char * buffer, int len)
2256 *
2257 */
2258
2259 struct __pyx_vtabstruct_5pysam_9libctabix_asTuple {
2260 struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base;
2261 };
2262 static struct __pyx_vtabstruct_5pysam_9libctabix_asTuple *__pyx_vtabptr_5pysam_9libctabix_asTuple;
2263
2264
2265 /* "pysam/libctabix.pxd":81
2266 *
2267 *
2268 * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
2269 * pass
2270 *
2271 */
2272
2273 struct __pyx_vtabstruct_5pysam_9libctabix_asGTF {
2274 struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base;
2275 };
2276 static struct __pyx_vtabstruct_5pysam_9libctabix_asGTF *__pyx_vtabptr_5pysam_9libctabix_asGTF;
2277
2278
2279 /* "pysam/libctabix.pxd":85
2280 *
2281 *
2282 * cdef class asGFF3(Parser): # <<<<<<<<<<<<<<
2283 * pass
2284 *
2285 */
2286
2287 struct __pyx_vtabstruct_5pysam_9libctabix_asGFF3 {
2288 struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base;
2289 };
2290 static struct __pyx_vtabstruct_5pysam_9libctabix_asGFF3 *__pyx_vtabptr_5pysam_9libctabix_asGFF3;
2291
2292
2293 /* "pysam/libctabix.pxd":89
2294 *
2295 *
2296 * cdef class asBed(Parser): # <<<<<<<<<<<<<<
2297 * pass
2298 *
2299 */
2300
2301 struct __pyx_vtabstruct_5pysam_9libctabix_asBed {
2302 struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base;
2303 };
2304 static struct __pyx_vtabstruct_5pysam_9libctabix_asBed *__pyx_vtabptr_5pysam_9libctabix_asBed;
2305
2306
2307 /* "pysam/libctabix.pxd":93
2308 *
2309 *
2310 * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
2311 * pass
2312 *
2313 */
2314
2315 struct __pyx_vtabstruct_5pysam_9libctabix_asVCF {
2316 struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base;
2317 };
2318 static struct __pyx_vtabstruct_5pysam_9libctabix_asVCF *__pyx_vtabptr_5pysam_9libctabix_asVCF;
2319
2320
2321 /* "pysam/libctabix.pxd":97
2322 *
2323 *
2324 * cdef class TabixIterator: # <<<<<<<<<<<<<<
2325 * cdef hts_itr_t * iterator
2326 * cdef TabixFile tabixfile
2327 */
2328
2329 struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator {
2330 int (*__pyx___cnext__)(struct __pyx_obj_5pysam_9libctabix_TabixIterator *);
2331 };
2332 static struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator *__pyx_vtabptr_5pysam_9libctabix_TabixIterator;
2333
2334
2335 /* "pysam/libctabix.pxd":105
2336 *
2337 *
2338 * cdef class TabixIteratorParsed(TabixIterator): # <<<<<<<<<<<<<<
2339 * cdef Parser parser
2340 *
2341 */
2342
2343 struct __pyx_vtabstruct_5pysam_9libctabix_TabixIteratorParsed {
2344 struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator __pyx_base;
2345 };
2346 static struct __pyx_vtabstruct_5pysam_9libctabix_TabixIteratorParsed *__pyx_vtabptr_5pysam_9libctabix_TabixIteratorParsed;
2347
2348
2349 /* "pysam/libctabix.pxd":109
2350 *
2351 *
2352 * cdef class GZIterator: # <<<<<<<<<<<<<<
2353 * cdef object _filename
2354 * cdef BGZF * gzipfile
2355 */
2356
2357 struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator {
2358 int (*__pyx___cnext__)(struct __pyx_obj_5pysam_9libctabix_GZIterator *);
2359 };
2360 static struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator *__pyx_vtabptr_5pysam_9libctabix_GZIterator;
2361
2362
2363 /* "pysam/libctabix.pxd":118
2364 *
2365 *
2366 * cdef class GZIteratorHead(GZIterator): # <<<<<<<<<<<<<<
2367 * pass
2368 *
2369 */
2370
2371 struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorHead {
2372 struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator __pyx_base;
2373 };
2374 static struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorHead *__pyx_vtabptr_5pysam_9libctabix_GZIteratorHead;
2375
2376
2377 /* "pysam/libctabix.pxd":122
2378 *
2379 *
2380 * cdef class GZIteratorParsed(GZIterator): # <<<<<<<<<<<<<<
2381 * cdef Parser parser
2382 *
2383 */
2384
2385 struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorParsed {
2386 struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator __pyx_base;
2387 };
2388 static struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorParsed *__pyx_vtabptr_5pysam_9libctabix_GZIteratorParsed;
2389
2390
2391 /* "pysam/libctabix.pxd":127
2392 *
2393 * # Compatibility Layer for pysam < 0.8
2394 * cdef class Tabixfile(TabixFile): # <<<<<<<<<<<<<<
2395 * pass
2396 */
2397
2398 struct __pyx_vtabstruct_5pysam_9libctabix_Tabixfile {
2399 struct __pyx_vtabstruct_5pysam_9libctabix_TabixFile __pyx_base;
2400 };
2401 static struct __pyx_vtabstruct_5pysam_9libctabix_Tabixfile *__pyx_vtabptr_5pysam_9libctabix_Tabixfile;
2402
2403
2404 /* "pysam/libctabixproxies.pxd":5
2405 * from libc.stdint cimport uint8_t, int32_t, uint32_t, int64_t, uint64_t
2406 *
2407 * cdef class TupleProxy: # <<<<<<<<<<<<<<
2408 *
2409 * cdef:
2410 */
2411
2412 struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy {
2413 int (*getMaxFields)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, int __pyx_skip_dispatch);
2414 int (*getMinFields)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, int __pyx_skip_dispatch);
2415 PyObject *(*take)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t);
2416 PyObject *(*present)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t);
2417 PyObject *(*copy)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t, struct __pyx_opt_args_5pysam_16libctabixproxies_10TupleProxy_copy *__pyx_optional_args);
2418 PyObject *(*update)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t);
2419 };
2420 static struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy *__pyx_vtabptr_5pysam_16libctabixproxies_TupleProxy;
2421
2422
2423 /* "pysam/libctabixproxies.pxd":32
2424 *
2425 *
2426 * cdef class NamedTupleProxy(TupleProxy): # <<<<<<<<<<<<<<
2427 * pass
2428 *
2429 */
2430
2431 struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy {
2432 struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy __pyx_base;
2433 };
2434 static struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy *__pyx_vtabptr_5pysam_16libctabixproxies_NamedTupleProxy;
2435
2436
2437 /* "pysam/libctabixproxies.pxd":36
2438 *
2439 *
2440 * cdef class GTFProxy(NamedTupleProxy): # <<<<<<<<<<<<<<
2441 * cdef object attribute_dict
2442 * cpdef int getMaxFields(self)
2443 */
2444
2445 struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy {
2446 struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base;
2447 };
2448 static struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy *__pyx_vtabptr_5pysam_16libctabixproxies_GTFProxy;
2449
2450
2451 /* "pysam/libctabixproxies.pxd":42
2452 *
2453 *
2454 * cdef class GFF3Proxy(GTFProxy): # <<<<<<<<<<<<<<
2455 * pass
2456 *
2457 */
2458
2459 struct __pyx_vtabstruct_5pysam_16libctabixproxies_GFF3Proxy {
2460 struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy __pyx_base;
2461 };
2462 static struct __pyx_vtabstruct_5pysam_16libctabixproxies_GFF3Proxy *__pyx_vtabptr_5pysam_16libctabixproxies_GFF3Proxy;
2463
2464
2465 /* "pysam/libctabixproxies.pxd":46
2466 *
2467 *
2468 * cdef class BedProxy(NamedTupleProxy): # <<<<<<<<<<<<<<
2469 *
2470 * cdef:
2471 */
2472
2473 struct __pyx_vtabstruct_5pysam_16libctabixproxies_BedProxy {
2474 struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base;
2475 };
2476 static struct __pyx_vtabstruct_5pysam_16libctabixproxies_BedProxy *__pyx_vtabptr_5pysam_16libctabixproxies_BedProxy;
2477
2478
2479 /* "pysam/libctabixproxies.pxd":58
2480 * cdef update(self, char * buffer, size_t nbytes)
2481 *
2482 * cdef class VCFProxy(NamedTupleProxy) : # <<<<<<<<<<<<<<
2483 *
2484 * cdef:
2485 */
2486
2487 struct __pyx_vtabstruct_5pysam_16libctabixproxies_VCFProxy {
2488 struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base;
2489 };
2490 static struct __pyx_vtabstruct_5pysam_16libctabixproxies_VCFProxy *__pyx_vtabptr_5pysam_16libctabixproxies_VCFProxy;
2491
2492
2493 /* "pysam/libcvcf.pyx":104
2494 * ###########################################################################################################
2495 *
2496 * cdef class VCFRecord(libctabixproxies.TupleProxy): # <<<<<<<<<<<<<<
2497 * '''vcf record.
2498 *
2499 */
2500
2501 struct __pyx_vtabstruct_5pysam_7libcvcf_VCFRecord {
2502 struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy __pyx_base;
2503 };
2504 static struct __pyx_vtabstruct_5pysam_7libcvcf_VCFRecord *__pyx_vtabptr_5pysam_7libcvcf_VCFRecord;
2505
2506
2507 /* "pysam/libcvcf.pyx":241
2508 *
2509 *
2510 * cdef class asVCFRecord(libctabix.Parser): # <<<<<<<<<<<<<<
2511 * '''converts a :term:`tabix row` into a VCF record.'''
2512 * cdef vcffile
2513 */
2514
2515 struct __pyx_vtabstruct_5pysam_7libcvcf_asVCFRecord {
2516 struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base;
2517 };
2518 static struct __pyx_vtabstruct_5pysam_7libcvcf_asVCFRecord *__pyx_vtabptr_5pysam_7libcvcf_asVCFRecord;
2519 /* #### Code section: utility_code_proto ### */
2520
2521 /* --- Runtime support code (head) --- */
2522 /* Refnanny.proto */
2523 #ifndef CYTHON_REFNANNY
2524 #define CYTHON_REFNANNY 0
2525 #endif
2526 #if CYTHON_REFNANNY
2527 typedef struct {
2528 void (*INCREF)(void*, PyObject*, Py_ssize_t);
2529 void (*DECREF)(void*, PyObject*, Py_ssize_t);
2530 void (*GOTREF)(void*, PyObject*, Py_ssize_t);
2531 void (*GIVEREF)(void*, PyObject*, Py_ssize_t);
2532 void* (*SetupContext)(const char*, Py_ssize_t, const char*);
2533 void (*FinishContext)(void**);
2534 } __Pyx_RefNannyAPIStruct;
2535 static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
2536 static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname);
2537 #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
2538 #ifdef WITH_THREAD
2539 #define __Pyx_RefNannySetupContext(name, acquire_gil)\
2540 if (acquire_gil) {\
2541 PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\
2542 __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__));\
2543 PyGILState_Release(__pyx_gilstate_save);\
2544 } else {\
2545 __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__));\
2546 }
2547 #define __Pyx_RefNannyFinishContextNogil() {\
2548 PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\
2549 __Pyx_RefNannyFinishContext();\
2550 PyGILState_Release(__pyx_gilstate_save);\
2551 }
2552 #else
2553 #define __Pyx_RefNannySetupContext(name, acquire_gil)\
2554 __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__))
2555 #define __Pyx_RefNannyFinishContextNogil() __Pyx_RefNannyFinishContext()
2556 #endif
2557 #define __Pyx_RefNannyFinishContextNogil() {\
2558 PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\
2559 __Pyx_RefNannyFinishContext();\
2560 PyGILState_Release(__pyx_gilstate_save);\
2561 }
2562 #define __Pyx_RefNannyFinishContext()\
2563 __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
2564 #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), (__LINE__))
2565 #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), (__LINE__))
2566 #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), (__LINE__))
2567 #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), (__LINE__))
2568 #define __Pyx_XINCREF(r) do { if((r) == NULL); else {__Pyx_INCREF(r); }} while(0)
2569 #define __Pyx_XDECREF(r) do { if((r) == NULL); else {__Pyx_DECREF(r); }} while(0)
2570 #define __Pyx_XGOTREF(r) do { if((r) == NULL); else {__Pyx_GOTREF(r); }} while(0)
2571 #define __Pyx_XGIVEREF(r) do { if((r) == NULL); else {__Pyx_GIVEREF(r);}} while(0)
2572 #else
2573 #define __Pyx_RefNannyDeclarations
2574 #define __Pyx_RefNannySetupContext(name, acquire_gil)
2575 #define __Pyx_RefNannyFinishContextNogil()
2576 #define __Pyx_RefNannyFinishContext()
2577 #define __Pyx_INCREF(r) Py_INCREF(r)
2578 #define __Pyx_DECREF(r) Py_DECREF(r)
2579 #define __Pyx_GOTREF(r)
2580 #define __Pyx_GIVEREF(r)
2581 #define __Pyx_XINCREF(r) Py_XINCREF(r)
2582 #define __Pyx_XDECREF(r) Py_XDECREF(r)
2583 #define __Pyx_XGOTREF(r)
2584 #define __Pyx_XGIVEREF(r)
2585 #endif
2586 #define __Pyx_Py_XDECREF_SET(r, v) do {\
2587 PyObject *tmp = (PyObject *) r;\
2588 r = v; Py_XDECREF(tmp);\
2589 } while (0)
2590 #define __Pyx_XDECREF_SET(r, v) do {\
2591 PyObject *tmp = (PyObject *) r;\
2592 r = v; __Pyx_XDECREF(tmp);\
2593 } while (0)
2594 #define __Pyx_DECREF_SET(r, v) do {\
2595 PyObject *tmp = (PyObject *) r;\
2596 r = v; __Pyx_DECREF(tmp);\
2597 } while (0)
2598 #define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
2599 #define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
2600
2601 /* PyErrExceptionMatches.proto */
2602 #if CYTHON_FAST_THREAD_STATE
2603 #define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err)
2604 static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err);
2605 #else
2606 #define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err)
2607 #endif
2608
2609 /* PyThreadStateGet.proto */
2610 #if CYTHON_FAST_THREAD_STATE
2611 #define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate;
2612 #define __Pyx_PyThreadState_assign __pyx_tstate = __Pyx_PyThreadState_Current;
2613 #if PY_VERSION_HEX >= 0x030C00A6
2614 #define __Pyx_PyErr_Occurred() (__pyx_tstate->current_exception != NULL)
2615 #define __Pyx_PyErr_CurrentExceptionType() (__pyx_tstate->current_exception ? (PyObject*) Py_TYPE(__pyx_tstate->current_exception) : (PyObject*) NULL)
2616 #else
2617 #define __Pyx_PyErr_Occurred() (__pyx_tstate->curexc_type != NULL)
2618 #define __Pyx_PyErr_CurrentExceptionType() (__pyx_tstate->curexc_type)
2619 #endif
2620 #else
2621 #define __Pyx_PyThreadState_declare
2622 #define __Pyx_PyThreadState_assign
2623 #define __Pyx_PyErr_Occurred() (PyErr_Occurred() != NULL)
2624 #define __Pyx_PyErr_CurrentExceptionType() PyErr_Occurred()
2625 #endif
2626
2627 /* PyErrFetchRestore.proto */
2628 #if CYTHON_FAST_THREAD_STATE
2629 #define __Pyx_PyErr_Clear() __Pyx_ErrRestore(NULL, NULL, NULL)
2630 #define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb)
2631 #define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb)
2632 #define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb)
2633 #define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb)
2634 static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb);
2635 static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
2636 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A6
2637 #define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL))
2638 #else
2639 #define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc)
2640 #endif
2641 #else
2642 #define __Pyx_PyErr_Clear() PyErr_Clear()
2643 #define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc)
2644 #define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb)
2645 #define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb)
2646 #define __Pyx_ErrRestoreInState(tstate, type, value, tb) PyErr_Restore(type, value, tb)
2647 #define __Pyx_ErrFetchInState(tstate, type, value, tb) PyErr_Fetch(type, value, tb)
2648 #define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb)
2649 #define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb)
2650 #endif
2651
2652 /* PyObjectGetAttrStr.proto */
2653 #if CYTHON_USE_TYPE_SLOTS
2654 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name);
2655 #else
2656 #define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
2657 #endif
2658
2659 /* PyObjectGetAttrStrNoError.proto */
2660 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name);
2661
2662 /* GetBuiltinName.proto */
2663 static PyObject *__Pyx_GetBuiltinName(PyObject *name);
2664
2665 /* TupleAndListFromArray.proto */
2666 #if CYTHON_COMPILING_IN_CPYTHON
2667 static CYTHON_INLINE PyObject* __Pyx_PyList_FromArray(PyObject *const *src, Py_ssize_t n);
2668 static CYTHON_INLINE PyObject* __Pyx_PyTuple_FromArray(PyObject *const *src, Py_ssize_t n);
2669 #endif
2670
2671 /* IncludeStringH.proto */
2672 #include <string.h>
2673
2674 /* BytesEquals.proto */
2675 static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals);
2676
2677 /* UnicodeEquals.proto */
2678 static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals);
2679
2680 /* fastcall.proto */
2681 #if CYTHON_AVOID_BORROWED_REFS
2682 #define __Pyx_Arg_VARARGS(args, i) PySequence_GetItem(args, i)
2683 #elif CYTHON_ASSUME_SAFE_MACROS
2684 #define __Pyx_Arg_VARARGS(args, i) PyTuple_GET_ITEM(args, i)
2685 #else
2686 #define __Pyx_Arg_VARARGS(args, i) PyTuple_GetItem(args, i)
2687 #endif
2688 #if CYTHON_AVOID_BORROWED_REFS
2689 #define __Pyx_Arg_NewRef_VARARGS(arg) __Pyx_NewRef(arg)
2690 #define __Pyx_Arg_XDECREF_VARARGS(arg) Py_XDECREF(arg)
2691 #else
2692 #define __Pyx_Arg_NewRef_VARARGS(arg) arg
2693 #define __Pyx_Arg_XDECREF_VARARGS(arg)
2694 #endif
2695 #define __Pyx_NumKwargs_VARARGS(kwds) PyDict_Size(kwds)
2696 #define __Pyx_KwValues_VARARGS(args, nargs) NULL
2697 #define __Pyx_GetKwValue_VARARGS(kw, kwvalues, s) __Pyx_PyDict_GetItemStrWithError(kw, s)
2698 #define __Pyx_KwargsAsDict_VARARGS(kw, kwvalues) PyDict_Copy(kw)
2699 #if CYTHON_METH_FASTCALL
2700 #define __Pyx_Arg_FASTCALL(args, i) args[i]
2701 #define __Pyx_NumKwargs_FASTCALL(kwds) PyTuple_GET_SIZE(kwds)
2702 #define __Pyx_KwValues_FASTCALL(args, nargs) ((args) + (nargs))
2703 static CYTHON_INLINE PyObject * __Pyx_GetKwValue_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues, PyObject *s);
2704 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000
2705 CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues);
2706 #else
2707 #define __Pyx_KwargsAsDict_FASTCALL(kw, kwvalues) _PyStack_AsDict(kwvalues, kw)
2708 #endif
2709 #define __Pyx_Arg_NewRef_FASTCALL(arg) arg /* no-op, __Pyx_Arg_FASTCALL is direct and this needs
2710 to have the same reference counting */
2711 #define __Pyx_Arg_XDECREF_FASTCALL(arg)
2712 #else
2713 #define __Pyx_Arg_FASTCALL __Pyx_Arg_VARARGS
2714 #define __Pyx_NumKwargs_FASTCALL __Pyx_NumKwargs_VARARGS
2715 #define __Pyx_KwValues_FASTCALL __Pyx_KwValues_VARARGS
2716 #define __Pyx_GetKwValue_FASTCALL __Pyx_GetKwValue_VARARGS
2717 #define __Pyx_KwargsAsDict_FASTCALL __Pyx_KwargsAsDict_VARARGS
2718 #define __Pyx_Arg_NewRef_FASTCALL(arg) __Pyx_Arg_NewRef_VARARGS(arg)
2719 #define __Pyx_Arg_XDECREF_FASTCALL(arg) __Pyx_Arg_XDECREF_VARARGS(arg)
2720 #endif
2721 #if CYTHON_COMPILING_IN_CPYTHON && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
2722 #define __Pyx_ArgsSlice_VARARGS(args, start, stop) __Pyx_PyTuple_FromArray(&__Pyx_Arg_VARARGS(args, start), stop - start)
2723 #define __Pyx_ArgsSlice_FASTCALL(args, start, stop) __Pyx_PyTuple_FromArray(&__Pyx_Arg_FASTCALL(args, start), stop - start)
2724 #else
2725 #define __Pyx_ArgsSlice_VARARGS(args, start, stop) PyTuple_GetSlice(args, start, stop)
2726 #define __Pyx_ArgsSlice_FASTCALL(args, start, stop) PyTuple_GetSlice(args, start, stop)
2727 #endif
2728
2729 /* RaiseArgTupleInvalid.proto */
2730 static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
2731 Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found);
2732
2733 /* RaiseDoubleKeywords.proto */
2734 static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
2735
2736 /* ParseKeywords.proto */
2737 static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject *const *kwvalues,
2738 PyObject **argnames[],
2739 PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,
2740 const char* function_name);
2741
2742 /* PyDictVersioning.proto */
2743 #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS
2744 #define __PYX_DICT_VERSION_INIT ((PY_UINT64_T) -1)
2745 #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag)
2746 #define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)\
2747 (version_var) = __PYX_GET_DICT_VERSION(dict);\
2748 (cache_var) = (value);
2749 #define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) {\
2750 static PY_UINT64_T __pyx_dict_version = 0;\
2751 static PyObject *__pyx_dict_cached_value = NULL;\
2752 if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\
2753 (VAR) = __pyx_dict_cached_value;\
2754 } else {\
2755 (VAR) = __pyx_dict_cached_value = (LOOKUP);\
2756 __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\
2757 }\
2758 }
2759 static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj);
2760 static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj);
2761 static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version);
2762 #else
2763 #define __PYX_GET_DICT_VERSION(dict) (0)
2764 #define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)
2765 #define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) (VAR) = (LOOKUP);
2766 #endif
2767
2768 /* GetModuleGlobalName.proto */
2769 #if CYTHON_USE_DICT_VERSIONS
2770 #define __Pyx_GetModuleGlobalName(var, name) do {\
2771 static PY_UINT64_T __pyx_dict_version = 0;\
2772 static PyObject *__pyx_dict_cached_value = NULL;\
2773 (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\
2774 (likely(__pyx_dict_cached_value) ? __Pyx_NewRef(__pyx_dict_cached_value) : __Pyx_GetBuiltinName(name)) :\
2775 __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\
2776 } while(0)
2777 #define __Pyx_GetModuleGlobalNameUncached(var, name) do {\
2778 PY_UINT64_T __pyx_dict_version;\
2779 PyObject *__pyx_dict_cached_value;\
2780 (var) = __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\
2781 } while(0)
2782 static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value);
2783 #else
2784 #define __Pyx_GetModuleGlobalName(var, name) (var) = __Pyx__GetModuleGlobalName(name)
2785 #define __Pyx_GetModuleGlobalNameUncached(var, name) (var) = __Pyx__GetModuleGlobalName(name)
2786 static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name);
2787 #endif
2788
2789 /* PyFunctionFastCall.proto */
2790 #if CYTHON_FAST_PYCALL
2791 #if !CYTHON_VECTORCALL
2792 #define __Pyx_PyFunction_FastCall(func, args, nargs)\
2793 __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL)
2794 static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs);
2795 #endif
2796 #define __Pyx_BUILD_ASSERT_EXPR(cond)\
2797 (sizeof(char [1 - 2*!(cond)]) - 1)
2798 #ifndef Py_MEMBER_SIZE
2799 #define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member)
2800 #endif
2801 #if !CYTHON_VECTORCALL
2802 #if PY_VERSION_HEX >= 0x03080000
2803 #include "frameobject.h"
2804 #if PY_VERSION_HEX >= 0x030b00a6 && !CYTHON_COMPILING_IN_LIMITED_API
2805 #ifndef Py_BUILD_CORE
2806 #define Py_BUILD_CORE 1
2807 #endif
2808 #include "internal/pycore_frame.h"
2809 #endif
2810 #define __Pxy_PyFrame_Initialize_Offsets()
2811 #define __Pyx_PyFrame_GetLocalsplus(frame) ((frame)->f_localsplus)
2812 #else
2813 static size_t __pyx_pyframe_localsplus_offset = 0;
2814 #include "frameobject.h"
2815 #define __Pxy_PyFrame_Initialize_Offsets()\
2816 ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\
2817 (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus)))
2818 #define __Pyx_PyFrame_GetLocalsplus(frame)\
2819 (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset))
2820 #endif
2821 #endif
2822 #endif
2823
2824 /* PyObjectCall.proto */
2825 #if CYTHON_COMPILING_IN_CPYTHON
2826 static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
2827 #else
2828 #define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
2829 #endif
2830
2831 /* PyObjectCallMethO.proto */
2832 #if CYTHON_COMPILING_IN_CPYTHON
2833 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
2834 #endif
2835
2836 /* PyObjectFastCall.proto */
2837 #define __Pyx_PyObject_FastCall(func, args, nargs) __Pyx_PyObject_FastCallDict(func, args, (size_t)(nargs), NULL)
2838 static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs);
2839
2840 /* GetItemInt.proto */
2841 #define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
2842 (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
2843 __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\
2844 (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\
2845 __Pyx_GetItemInt_Generic(o, to_py_func(i))))
2846 #define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
2847 (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
2848 __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\
2849 (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
2850 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
2851 int wraparound, int boundscheck);
2852 #define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
2853 (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
2854 __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\
2855 (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
2856 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
2857 int wraparound, int boundscheck);
2858 static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
2859 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
2860 int is_list, int wraparound, int boundscheck);
2861
2862 /* PyObjectCallOneArg.proto */
2863 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);
2864
2865 /* PyIntBinop.proto */
2866 #if !CYTHON_COMPILING_IN_PYPY
2867 static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check);
2868 #else
2869 #define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace, zerodivision_check)\
2870 (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2))
2871 #endif
2872
2873 /* GetTopmostException.proto */
2874 #if CYTHON_USE_EXC_INFO_STACK && CYTHON_FAST_THREAD_STATE
2875 static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate);
2876 #endif
2877
2878 /* SaveResetException.proto */
2879 #if CYTHON_FAST_THREAD_STATE
2880 #define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb)
2881 static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
2882 #define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb)
2883 static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb);
2884 #else
2885 #define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb)
2886 #define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb)
2887 #endif
2888
2889 /* GetException.proto */
2890 #if CYTHON_FAST_THREAD_STATE
2891 #define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb)
2892 static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
2893 #else
2894 static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb);
2895 #endif
2896
2897 /* RaiseException.proto */
2898 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause);
2899
2900 /* ListAppend.proto */
2901 #if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS
2902 static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
2903 PyListObject* L = (PyListObject*) list;
2904 Py_ssize_t len = Py_SIZE(list);
2905 if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) {
2906 Py_INCREF(x);
2907 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000
2908 L->ob_item[len] = x;
2909 #else
2910 PyList_SET_ITEM(list, len, x);
2911 #endif
2912 __Pyx_SET_SIZE(list, len + 1);
2913 return 0;
2914 }
2915 return PyList_Append(list, x);
2916 }
2917 #else
2918 #define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
2919 #endif
2920
2921 /* pybytes_as_double.proto */
2922 static double __Pyx_SlowPyString_AsDouble(PyObject *obj);
2923 static double __Pyx__PyBytes_AsDouble(PyObject *obj, const char* start, Py_ssize_t length);
2924 static CYTHON_INLINE double __Pyx_PyBytes_AsDouble(PyObject *obj) {
2925 char* as_c_string;
2926 Py_ssize_t size;
2927 #if CYTHON_ASSUME_SAFE_MACROS
2928 as_c_string = PyBytes_AS_STRING(obj);
2929 size = PyBytes_GET_SIZE(obj);
2930 #else
2931 if (PyBytes_AsStringAndSize(obj, &as_c_string, &size) < 0) {
2932 return (double)-1;
2933 }
2934 #endif
2935 return __Pyx__PyBytes_AsDouble(obj, as_c_string, size);
2936 }
2937 static CYTHON_INLINE double __Pyx_PyByteArray_AsDouble(PyObject *obj) {
2938 char* as_c_string;
2939 Py_ssize_t size;
2940 #if CYTHON_ASSUME_SAFE_MACROS
2941 as_c_string = PyByteArray_AS_STRING(obj);
2942 size = PyByteArray_GET_SIZE(obj);
2943 #else
2944 as_c_string = PyByteArray_AsString(obj);
2945 if (as_c_string == NULL) {
2946 return (double)-1;
2947 }
2948 size = PyByteArray_Size(obj);
2949 #endif
2950 return __Pyx__PyBytes_AsDouble(obj, as_c_string, size);
2951 }
2952
2953 /* pyunicode_as_double.proto */
2954 #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY && CYTHON_ASSUME_SAFE_MACROS
2955 static const char* __Pyx__PyUnicode_AsDouble_Copy(const void* data, const int kind, char* buffer, Py_ssize_t start, Py_ssize_t end) {
2956 int last_was_punctuation;
2957 Py_ssize_t i;
2958 last_was_punctuation = 1;
2959 for (i=start; i <= end; i++) {
2960 Py_UCS4 chr = PyUnicode_READ(kind, data, i);
2961 int is_punctuation = (chr == '_') | (chr == '.');
2962 *buffer = (char)chr;
2963 buffer += (chr != '_');
2964 if (unlikely(chr > 127)) goto parse_failure;
2965 if (unlikely(last_was_punctuation & is_punctuation)) goto parse_failure;
2966 last_was_punctuation = is_punctuation;
2967 }
2968 if (unlikely(last_was_punctuation)) goto parse_failure;
2969 *buffer = '\0';
2970 return buffer;
2971 parse_failure:
2972 return NULL;
2973 }
2974 static double __Pyx__PyUnicode_AsDouble_inf_nan(const void* data, int kind, Py_ssize_t start, Py_ssize_t length) {
2975 int matches = 1;
2976 Py_UCS4 chr;
2977 Py_UCS4 sign = PyUnicode_READ(kind, data, start);
2978 int is_signed = (sign == '-') | (sign == '+');
2979 start += is_signed;
2980 length -= is_signed;
2981 switch (PyUnicode_READ(kind, data, start)) {
2982 #ifdef Py_NAN
2983 case 'n':
2984 case 'N':
2985 if (unlikely(length != 3)) goto parse_failure;
2986 chr = PyUnicode_READ(kind, data, start+1);
2987 matches &= (chr == 'a') | (chr == 'A');
2988 chr = PyUnicode_READ(kind, data, start+2);
2989 matches &= (chr == 'n') | (chr == 'N');
2990 if (unlikely(!matches)) goto parse_failure;
2991 return (sign == '-') ? -Py_NAN : Py_NAN;
2992 #endif
2993 case 'i':
2994 case 'I':
2995 if (unlikely(length < 3)) goto parse_failure;
2996 chr = PyUnicode_READ(kind, data, start+1);
2997 matches &= (chr == 'n') | (chr == 'N');
2998 chr = PyUnicode_READ(kind, data, start+2);
2999 matches &= (chr == 'f') | (chr == 'F');
3000 if (likely(length == 3 && matches))
3001 return (sign == '-') ? -Py_HUGE_VAL : Py_HUGE_VAL;
3002 if (unlikely(length != 8)) goto parse_failure;
3003 chr = PyUnicode_READ(kind, data, start+3);
3004 matches &= (chr == 'i') | (chr == 'I');
3005 chr = PyUnicode_READ(kind, data, start+4);
3006 matches &= (chr == 'n') | (chr == 'N');
3007 chr = PyUnicode_READ(kind, data, start+5);
3008 matches &= (chr == 'i') | (chr == 'I');
3009 chr = PyUnicode_READ(kind, data, start+6);
3010 matches &= (chr == 't') | (chr == 'T');
3011 chr = PyUnicode_READ(kind, data, start+7);
3012 matches &= (chr == 'y') | (chr == 'Y');
3013 if (unlikely(!matches)) goto parse_failure;
3014 return (sign == '-') ? -Py_HUGE_VAL : Py_HUGE_VAL;
3015 case '.': case '0': case '1': case '2': case '3': case '4': case '5': case '6': case '7': case '8': case '9':
3016 break;
3017 default:
3018 goto parse_failure;
3019 }
3020 return 0.0;
3021 parse_failure:
3022 return -1.0;
3023 }
3024 static double __Pyx_PyUnicode_AsDouble_WithSpaces(PyObject *obj) {
3025 double value;
3026 const char *last;
3027 char *end;
3028 Py_ssize_t start, length = PyUnicode_GET_LENGTH(obj);
3029 const int kind = PyUnicode_KIND(obj);
3030 const void* data = PyUnicode_DATA(obj);
3031 start = 0;
3032 while (Py_UNICODE_ISSPACE(PyUnicode_READ(kind, data, start)))
3033 start++;
3034 while (start < length - 1 && Py_UNICODE_ISSPACE(PyUnicode_READ(kind, data, length - 1)))
3035 length--;
3036 length -= start;
3037 if (unlikely(length <= 0)) goto fallback;
3038 value = __Pyx__PyUnicode_AsDouble_inf_nan(data, kind, start, length);
3039 if (unlikely(value == -1.0)) goto fallback;
3040 if (value != 0.0) return value;
3041 if (length < 40) {
3042 char number[40];
3043 last = __Pyx__PyUnicode_AsDouble_Copy(data, kind, number, start, start + length);
3044 if (unlikely(!last)) goto fallback;
3045 value = PyOS_string_to_double(number, &end, NULL);
3046 } else {
3047 char *number = (char*) PyMem_Malloc((length + 1) * sizeof(char));
3048 if (unlikely(!number)) goto fallback;
3049 last = __Pyx__PyUnicode_AsDouble_Copy(data, kind, number, start, start + length);
3050 if (unlikely(!last)) {
3051 PyMem_Free(number);
3052 goto fallback;
3053 }
3054 value = PyOS_string_to_double(number, &end, NULL);
3055 PyMem_Free(number);
3056 }
3057 if (likely(end == last) || (value == (double)-1 && PyErr_Occurred())) {
3058 return value;
3059 }
3060 fallback:
3061 return __Pyx_SlowPyString_AsDouble(obj);
3062 }
3063 #endif
3064 static CYTHON_INLINE double __Pyx_PyUnicode_AsDouble(PyObject *obj) {
3065 #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY && CYTHON_ASSUME_SAFE_MACROS
3066 if (unlikely(__Pyx_PyUnicode_READY(obj) == -1))
3067 return (double)-1;
3068 if (likely(PyUnicode_IS_ASCII(obj))) {
3069 const char *s;
3070 Py_ssize_t length;
3071 s = PyUnicode_AsUTF8AndSize(obj, &length);
3072 return __Pyx__PyBytes_AsDouble(obj, s, length);
3073 }
3074 return __Pyx_PyUnicode_AsDouble_WithSpaces(obj);
3075 #else
3076 return __Pyx_SlowPyString_AsDouble(obj);
3077 #endif
3078 }
3079
3080 /* pynumber_float.proto */
3081 static CYTHON_INLINE PyObject* __Pyx__PyNumber_Float(PyObject* obj);
3082 #define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : __Pyx__PyNumber_Float(x))
3083
3084 /* PyObject_Unicode.proto */
3085 #if PY_MAJOR_VERSION >= 3
3086 #define __Pyx_PyObject_Unicode(obj)\
3087 (likely(PyUnicode_CheckExact(obj)) ? __Pyx_NewRef(obj) : PyObject_Str(obj))
3088 #else
3089 #define __Pyx_PyObject_Unicode(obj)\
3090 (likely(PyUnicode_CheckExact(obj)) ? __Pyx_NewRef(obj) : PyObject_Unicode(obj))
3091 #endif
3092
3093 /* RaiseUnboundLocalError.proto */
3094 static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
3095
3096 /* ObjectGetItem.proto */
3097 #if CYTHON_USE_TYPE_SLOTS
3098 static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject *key);
3099 #else
3100 #define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key)
3101 #endif
3102
3103 /* GCCDiagnostics.proto */
3104 #if !defined(__INTEL_COMPILER) && defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6))
3105 #define __Pyx_HAS_GCC_DIAGNOSTIC
3106 #endif
3107
3108 /* BuildPyUnicode.proto */
3109 static PyObject* __Pyx_PyUnicode_BuildFromAscii(Py_ssize_t ulength, char* chars, int clength,
3110 int prepend_sign, char padding_char);
3111
3112 /* CIntToPyUnicode.proto */
3113 static CYTHON_INLINE PyObject* __Pyx_PyUnicode_From_Py_ssize_t(Py_ssize_t value, Py_ssize_t width, char padding_char, char format_char);
3114
3115 /* PyObjectFormatAndDecref.proto */
3116 static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatSimpleAndDecref(PyObject* s, PyObject* f);
3117 static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatAndDecref(PyObject* s, PyObject* f);
3118
3119 /* JoinPyUnicode.proto */
3120 static PyObject* __Pyx_PyUnicode_Join(PyObject* value_tuple, Py_ssize_t value_count, Py_ssize_t result_ulength,
3121 Py_UCS4 max_char);
3122
3123 /* PyIntCompare.proto */
3124 static CYTHON_INLINE int __Pyx_PyInt_BoolEqObjC(PyObject *op1, PyObject *op2, long intval, long inplace);
3125
3126 /* PyIntCompare.proto */
3127 static CYTHON_INLINE int __Pyx_PyInt_BoolNeObjC(PyObject *op1, PyObject *op2, long intval, long inplace);
3128
3129 /* DictGetItem.proto */
3130 #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
3131 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key);
3132 #define __Pyx_PyObject_Dict_GetItem(obj, name)\
3133 (likely(PyDict_CheckExact(obj)) ?\
3134 __Pyx_PyDict_GetItem(obj, name) : PyObject_GetItem(obj, name))
3135 #else
3136 #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
3137 #define __Pyx_PyObject_Dict_GetItem(obj, name) PyObject_GetItem(obj, name)
3138 #endif
3139
3140 /* SliceObject.proto */
3141 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
3142 PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
3143 PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
3144 int has_cstart, int has_cstop, int wraparound);
3145
3146 /* KeywordStringCheck.proto */
3147 static int __Pyx_CheckKeywordStrings(PyObject *kw, const char* function_name, int kw_allowed);
3148
3149 /* GetAttr3.proto */
3150 static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *);
3151
3152 /* RaiseUnexpectedTypeError.proto */
3153 static int __Pyx_RaiseUnexpectedTypeError(const char *expected, PyObject *obj);
3154
3155 /* IterFinish.proto */
3156 static CYTHON_INLINE int __Pyx_IterFinish(void);
3157
3158 /* PyObjectCallNoArg.proto */
3159 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
3160
3161 /* PyObjectGetMethod.proto */
3162 static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method);
3163
3164 /* PyObjectCallMethod0.proto */
3165 static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name);
3166
3167 /* RaiseNeedMoreValuesToUnpack.proto */
3168 static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
3169
3170 /* RaiseTooManyValuesToUnpack.proto */
3171 static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
3172
3173 /* UnpackItemEndCheck.proto */
3174 static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected);
3175
3176 /* RaiseNoneIterError.proto */
3177 static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
3178
3179 /* UnpackTupleError.proto */
3180 static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index);
3181
3182 /* UnpackTuple2.proto */
3183 #define __Pyx_unpack_tuple2(tuple, value1, value2, is_tuple, has_known_size, decref_tuple)\
3184 (likely(is_tuple || PyTuple_Check(tuple)) ?\
3185 (likely(has_known_size || PyTuple_GET_SIZE(tuple) == 2) ?\
3186 __Pyx_unpack_tuple2_exact(tuple, value1, value2, decref_tuple) :\
3187 (__Pyx_UnpackTupleError(tuple, 2), -1)) :\
3188 __Pyx_unpack_tuple2_generic(tuple, value1, value2, has_known_size, decref_tuple))
3189 static CYTHON_INLINE int __Pyx_unpack_tuple2_exact(
3190 PyObject* tuple, PyObject** value1, PyObject** value2, int decref_tuple);
3191 static int __Pyx_unpack_tuple2_generic(
3192 PyObject* tuple, PyObject** value1, PyObject** value2, int has_known_size, int decref_tuple);
3193
3194 /* dict_iter.proto */
3195 static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name,
3196 Py_ssize_t* p_orig_length, int* p_is_dict);
3197 static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos,
3198 PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict);
3199
3200 /* PyObjectSetAttrStr.proto */
3201 #if CYTHON_USE_TYPE_SLOTS
3202 #define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o, n, NULL)
3203 static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value);
3204 #else
3205 #define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n)
3206 #define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v)
3207 #endif
3208
3209 /* PySequenceContains.proto */
3210 static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) {
3211 int result = PySequence_Contains(seq, item);
3212 return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
3213 }
3214
3215 /* unicode_tailmatch.proto */
3216 static int __Pyx_PyUnicode_Tailmatch(
3217 PyObject* s, PyObject* substr, Py_ssize_t start, Py_ssize_t end, int direction);
3218
3219 /* PyUnicode_Substring.proto */
3220 static CYTHON_INLINE PyObject* __Pyx_PyUnicode_Substring(
3221 PyObject* text, Py_ssize_t start, Py_ssize_t stop);
3222
3223 /* PyIntBinop.proto */
3224 #if !CYTHON_COMPILING_IN_PYPY
3225 static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check);
3226 #else
3227 #define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace, zerodivision_check)\
3228 (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2))
3229 #endif
3230
3231 /* PyDictContains.proto */
3232 static CYTHON_INLINE int __Pyx_PyDict_ContainsTF(PyObject* item, PyObject* dict, int eq) {
3233 int result = PyDict_Contains(dict, item);
3234 return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
3235 }
3236
3237 /* ListCompAppend.proto */
3238 #if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS
3239 static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
3240 PyListObject* L = (PyListObject*) list;
3241 Py_ssize_t len = Py_SIZE(list);
3242 if (likely(L->allocated > len)) {
3243 Py_INCREF(x);
3244 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000
3245 L->ob_item[len] = x;
3246 #else
3247 PyList_SET_ITEM(list, len, x);
3248 #endif
3249 __Pyx_SET_SIZE(list, len + 1);
3250 return 0;
3251 }
3252 return PyList_Append(list, x);
3253 }
3254 #else
3255 #define __Pyx_ListComp_Append(L,x) PyList_Append(L,x)
3256 #endif
3257
3258 /* UnicodeConcatInPlace.proto */
3259 # if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
3260 #if CYTHON_REFNANNY
3261 #define __Pyx_PyUnicode_ConcatInPlace(left, right) __Pyx_PyUnicode_ConcatInPlaceImpl(&left, right, __pyx_refnanny)
3262 #else
3263 #define __Pyx_PyUnicode_ConcatInPlace(left, right) __Pyx_PyUnicode_ConcatInPlaceImpl(&left, right)
3264 #endif
3265 static CYTHON_INLINE PyObject *__Pyx_PyUnicode_ConcatInPlaceImpl(PyObject **p_left, PyObject *right
3266 #if CYTHON_REFNANNY
3267 , void* __pyx_refnanny
3268 #endif
3269 );
3270 #else
3271 #define __Pyx_PyUnicode_ConcatInPlace __Pyx_PyUnicode_Concat
3272 #endif
3273 #define __Pyx_PyUnicode_ConcatInPlaceSafe(left, right) ((unlikely((left) == Py_None) || unlikely((right) == Py_None)) ?\
3274 PyNumber_InPlaceAdd(left, right) : __Pyx_PyUnicode_ConcatInPlace(left, right))
3275
3276 /* DivInt[Py_ssize_t].proto */
3277 static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t);
3278
3279 /* SliceTupleAndList.proto */
3280 #if CYTHON_COMPILING_IN_CPYTHON
3281 static CYTHON_INLINE PyObject* __Pyx_PyList_GetSlice(PyObject* src, Py_ssize_t start, Py_ssize_t stop);
3282 static CYTHON_INLINE PyObject* __Pyx_PyTuple_GetSlice(PyObject* src, Py_ssize_t start, Py_ssize_t stop);
3283 #else
3284 #define __Pyx_PyList_GetSlice(seq, start, stop) PySequence_GetSlice(seq, start, stop)
3285 #define __Pyx_PyTuple_GetSlice(seq, start, stop) PySequence_GetSlice(seq, start, stop)
3286 #endif
3287
3288 /* AssertionsEnabled.proto */
3289 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
3290 #define __Pyx_init_assertions_enabled() (0)
3291 #define __pyx_assertions_enabled() (1)
3292 #elif CYTHON_COMPILING_IN_LIMITED_API || (CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030C0000)
3293 static int __pyx_assertions_enabled_flag;
3294 #define __pyx_assertions_enabled() (__pyx_assertions_enabled_flag)
3295 static int __Pyx_init_assertions_enabled(void) {
3296 PyObject *builtins, *debug, *debug_str;
3297 int flag;
3298 builtins = PyEval_GetBuiltins();
3299 if (!builtins) goto bad;
3300 debug_str = PyUnicode_FromStringAndSize("__debug__", 9);
3301 if (!debug_str) goto bad;
3302 debug = PyObject_GetItem(builtins, debug_str);
3303 Py_DECREF(debug_str);
3304 if (!debug) goto bad;
3305 flag = PyObject_IsTrue(debug);
3306 Py_DECREF(debug);
3307 if (flag == -1) goto bad;
3308 __pyx_assertions_enabled_flag = flag;
3309 return 0;
3310 bad:
3311 __pyx_assertions_enabled_flag = 1;
3312 return -1;
3313 }
3314 #else
3315 #define __Pyx_init_assertions_enabled() (0)
3316 #define __pyx_assertions_enabled() (!Py_OptimizeFlag)
3317 #endif
3318
3319 /* PyObjectCall2Args.proto */
3320 static CYTHON_INLINE PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2);
3321
3322 /* PyObjectCallMethod1.proto */
3323 static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg);
3324
3325 /* append.proto */
3326 static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x);
3327
3328 /* PyIntBinop.proto */
3329 #if !CYTHON_COMPILING_IN_PYPY
3330 static PyObject* __Pyx_PyInt_FloorDivideObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check);
3331 #else
3332 #define __Pyx_PyInt_FloorDivideObjC(op1, op2, intval, inplace, zerodivision_check)\
3333 (inplace ? PyNumber_InPlaceFloorDivide(op1, op2) : PyNumber_FloorDivide(op1, op2))
3334 #endif
3335
3336 /* PyIntBinop.proto */
3337 #if !CYTHON_COMPILING_IN_PYPY
3338 static PyObject* __Pyx_PyInt_RemainderObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check);
3339 #else
3340 #define __Pyx_PyInt_RemainderObjC(op1, op2, intval, inplace, zerodivision_check)\
3341 (inplace ? PyNumber_InPlaceRemainder(op1, op2) : PyNumber_Remainder(op1, op2))
3342 #endif
3343
3344 /* SetItemInt.proto */
3345 #define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
3346 (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
3347 __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) :\
3348 (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) :\
3349 __Pyx_SetItemInt_Generic(o, to_py_func(i), v)))
3350 static int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v);
3351 static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
3352 int is_list, int wraparound, int boundscheck);
3353
3354 /* PyUnicodeContains.proto */
3355 static CYTHON_INLINE int __Pyx_PyUnicode_ContainsTF(PyObject* substring, PyObject* text, int eq) {
3356 int result = PyUnicode_Contains(text, substring);
3357 return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
3358 }
3359
3360 /* pyobject_as_double.proto */
3361 static double __Pyx__PyObject_AsDouble(PyObject* obj);
3362 #if CYTHON_COMPILING_IN_PYPY
3363 #define __Pyx_PyObject_AsDouble(obj)\
3364 (likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) :\
3365 likely(PyInt_CheckExact(obj)) ?\
3366 PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj))
3367 #else
3368 #define __Pyx_PyObject_AsDouble(obj)\
3369 ((likely(PyFloat_CheckExact(obj))) ? PyFloat_AS_DOUBLE(obj) :\
3370 likely(PyLong_CheckExact(obj)) ?\
3371 PyLong_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj))
3372 #endif
3373
3374 /* PySequenceMultiply.proto */
3375 #define __Pyx_PySequence_Multiply_Left(mul, seq) __Pyx_PySequence_Multiply(seq, mul)
3376 static CYTHON_INLINE PyObject* __Pyx_PySequence_Multiply(PyObject *seq, Py_ssize_t mul);
3377
3378 /* pep479.proto */
3379 static void __Pyx_Generator_Replace_StopIteration(int in_async_gen);
3380
3381 /* Import.proto */
3382 static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
3383
3384 /* ImportFrom.proto */
3385 static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);
3386
3387 /* GetAttr.proto */
3388 static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *);
3389
3390 /* HasAttr.proto */
3391 static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *);
3392
3393 /* CallNextTpDealloc.proto */
3394 static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc);
3395
3396 /* CallNextTpTraverse.proto */
3397 static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse);
3398
3399 /* CallNextTpClear.proto */
3400 static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear);
3401
3402 /* TypeImport.proto */
3403 #ifndef __PYX_HAVE_RT_ImportType_proto_3_0_11
3404 #define __PYX_HAVE_RT_ImportType_proto_3_0_11
3405 #if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L
3406 #include <stdalign.h>
3407 #endif
3408 #if (defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L) || __cplusplus >= 201103L
3409 #define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) alignof(s)
3410 #else
3411 #define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) sizeof(void*)
3412 #endif
3413 enum __Pyx_ImportType_CheckSize_3_0_11 {
3414 __Pyx_ImportType_CheckSize_Error_3_0_11 = 0,
3415 __Pyx_ImportType_CheckSize_Warn_3_0_11 = 1,
3416 __Pyx_ImportType_CheckSize_Ignore_3_0_11 = 2
3417 };
3418 static PyTypeObject *__Pyx_ImportType_3_0_11(PyObject* module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_11 check_size);
3419 #endif
3420
3421 /* GetVTable.proto */
3422 static void* __Pyx_GetVtable(PyTypeObject *type);
3423
3424 /* IncludeStructmemberH.proto */
3425 #include <structmember.h>
3426
3427 /* FixUpExtensionType.proto */
3428 #if CYTHON_USE_TYPE_SPECS
3429 static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject *type);
3430 #endif
3431
3432 /* ValidateBasesTuple.proto */
3433 #if CYTHON_COMPILING_IN_CPYTHON || CYTHON_COMPILING_IN_LIMITED_API || CYTHON_USE_TYPE_SPECS
3434 static int __Pyx_validate_bases_tuple(const char *type_name, Py_ssize_t dictoffset, PyObject *bases);
3435 #endif
3436
3437 /* PyType_Ready.proto */
3438 CYTHON_UNUSED static int __Pyx_PyType_Ready(PyTypeObject *t);
3439
3440 /* PyObject_GenericGetAttrNoDict.proto */
3441 #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
3442 static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name);
3443 #else
3444 #define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr
3445 #endif
3446
3447 /* PyObject_GenericGetAttr.proto */
3448 #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
3449 static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name);
3450 #else
3451 #define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr
3452 #endif
3453
3454 /* SetVTable.proto */
3455 static int __Pyx_SetVtable(PyTypeObject* typeptr , void* vtable);
3456
3457 /* MergeVTables.proto */
3458 #if !CYTHON_COMPILING_IN_LIMITED_API
3459 static int __Pyx_MergeVtables(PyTypeObject *type);
3460 #endif
3461
3462 /* SetupReduce.proto */
3463 #if !CYTHON_COMPILING_IN_LIMITED_API
3464 static int __Pyx_setup_reduce(PyObject* type_obj);
3465 #endif
3466
3467 /* ImportDottedModule.proto */
3468 static PyObject *__Pyx_ImportDottedModule(PyObject *name, PyObject *parts_tuple);
3469 #if PY_MAJOR_VERSION >= 3
3470 static PyObject *__Pyx_ImportDottedModule_WalkParts(PyObject *module, PyObject *name, PyObject *parts_tuple);
3471 #endif
3472
3473 /* FetchSharedCythonModule.proto */
3474 static PyObject *__Pyx_FetchSharedCythonABIModule(void);
3475
3476 /* FetchCommonType.proto */
3477 #if !CYTHON_USE_TYPE_SPECS
3478 static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type);
3479 #else
3480 static PyTypeObject* __Pyx_FetchCommonTypeFromSpec(PyObject *module, PyType_Spec *spec, PyObject *bases);
3481 #endif
3482
3483 /* PyMethodNew.proto */
3484 #if CYTHON_COMPILING_IN_LIMITED_API
3485 static PyObject *__Pyx_PyMethod_New(PyObject *func, PyObject *self, PyObject *typ) {
3486 PyObject *typesModule=NULL, *methodType=NULL, *result=NULL;
3487 CYTHON_UNUSED_VAR(typ);
3488 if (!self)
3489 return __Pyx_NewRef(func);
3490 typesModule = PyImport_ImportModule("types");
3491 if (!typesModule) return NULL;
3492 methodType = PyObject_GetAttrString(typesModule, "MethodType");
3493 Py_DECREF(typesModule);
3494 if (!methodType) return NULL;
3495 result = PyObject_CallFunctionObjArgs(methodType, func, self, NULL);
3496 Py_DECREF(methodType);
3497 return result;
3498 }
3499 #elif PY_MAJOR_VERSION >= 3
3500 static PyObject *__Pyx_PyMethod_New(PyObject *func, PyObject *self, PyObject *typ) {
3501 CYTHON_UNUSED_VAR(typ);
3502 if (!self)
3503 return __Pyx_NewRef(func);
3504 return PyMethod_New(func, self);
3505 }
3506 #else
3507 #define __Pyx_PyMethod_New PyMethod_New
3508 #endif
3509
3510 /* PyVectorcallFastCallDict.proto */
3511 #if CYTHON_METH_FASTCALL
3512 static CYTHON_INLINE PyObject *__Pyx_PyVectorcall_FastCallDict(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw);
3513 #endif
3514
3515 /* CythonFunctionShared.proto */
3516 #define __Pyx_CyFunction_USED
3517 #define __Pyx_CYFUNCTION_STATICMETHOD 0x01
3518 #define __Pyx_CYFUNCTION_CLASSMETHOD 0x02
3519 #define __Pyx_CYFUNCTION_CCLASS 0x04
3520 #define __Pyx_CYFUNCTION_COROUTINE 0x08
3521 #define __Pyx_CyFunction_GetClosure(f)\
3522 (((__pyx_CyFunctionObject *) (f))->func_closure)
3523 #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
3524 #define __Pyx_CyFunction_GetClassObj(f)\
3525 (((__pyx_CyFunctionObject *) (f))->func_classobj)
3526 #else
3527 #define __Pyx_CyFunction_GetClassObj(f)\
3528 ((PyObject*) ((PyCMethodObject *) (f))->mm_class)
3529 #endif
3530 #define __Pyx_CyFunction_SetClassObj(f, classobj)\
3531 __Pyx__CyFunction_SetClassObj((__pyx_CyFunctionObject *) (f), (classobj))
3532 #define __Pyx_CyFunction_Defaults(type, f)\
3533 ((type *)(((__pyx_CyFunctionObject *) (f))->defaults))
3534 #define __Pyx_CyFunction_SetDefaultsGetter(f, g)\
3535 ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g)
3536 typedef struct {
3537 #if CYTHON_COMPILING_IN_LIMITED_API
3538 PyObject_HEAD
3539 PyObject *func;
3540 #elif PY_VERSION_HEX < 0x030900B1
3541 PyCFunctionObject func;
3542 #else
3543 PyCMethodObject func;
3544 #endif
3545 #if CYTHON_BACKPORT_VECTORCALL
3546 __pyx_vectorcallfunc func_vectorcall;
3547 #endif
3548 #if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API
3549 PyObject *func_weakreflist;
3550 #endif
3551 PyObject *func_dict;
3552 PyObject *func_name;
3553 PyObject *func_qualname;
3554 PyObject *func_doc;
3555 PyObject *func_globals;
3556 PyObject *func_code;
3557 PyObject *func_closure;
3558 #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
3559 PyObject *func_classobj;
3560 #endif
3561 void *defaults;
3562 int defaults_pyobjects;
3563 size_t defaults_size;
3564 int flags;
3565 PyObject *defaults_tuple;
3566 PyObject *defaults_kwdict;
3567 PyObject *(*defaults_getter)(PyObject *);
3568 PyObject *func_annotations;
3569 PyObject *func_is_coroutine;
3570 } __pyx_CyFunctionObject;
3571 #undef __Pyx_CyOrPyCFunction_Check
3572 #define __Pyx_CyFunction_Check(obj) __Pyx_TypeCheck(obj, __pyx_CyFunctionType)
3573 #define __Pyx_CyOrPyCFunction_Check(obj) __Pyx_TypeCheck2(obj, __pyx_CyFunctionType, &PyCFunction_Type)
3574 #define __Pyx_CyFunction_CheckExact(obj) __Pyx_IS_TYPE(obj, __pyx_CyFunctionType)
3575 static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc);
3576 #undef __Pyx_IsSameCFunction
3577 #define __Pyx_IsSameCFunction(func, cfunc) __Pyx__IsSameCyOrCFunction(func, cfunc)
3578 static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject* op, PyMethodDef *ml,
3579 int flags, PyObject* qualname,
3580 PyObject *closure,
3581 PyObject *module, PyObject *globals,
3582 PyObject* code);
3583 static CYTHON_INLINE void __Pyx__CyFunction_SetClassObj(__pyx_CyFunctionObject* f, PyObject* classobj);
3584 static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m,
3585 size_t size,
3586 int pyobjects);
3587 static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
3588 PyObject *tuple);
3589 static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m,
3590 PyObject *dict);
3591 static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m,
3592 PyObject *dict);
3593 static int __pyx_CyFunction_init(PyObject *module);
3594 #if CYTHON_METH_FASTCALL
3595 static PyObject * __Pyx_CyFunction_Vectorcall_NOARGS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames);
3596 static PyObject * __Pyx_CyFunction_Vectorcall_O(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames);
3597 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames);
3598 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames);
3599 #if CYTHON_BACKPORT_VECTORCALL
3600 #define __Pyx_CyFunction_func_vectorcall(f) (((__pyx_CyFunctionObject*)f)->func_vectorcall)
3601 #else
3602 #define __Pyx_CyFunction_func_vectorcall(f) (((PyCFunctionObject*)f)->vectorcall)
3603 #endif
3604 #endif
3605
3606 /* CythonFunction.proto */
3607 static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml,
3608 int flags, PyObject* qualname,
3609 PyObject *closure,
3610 PyObject *module, PyObject *globals,
3611 PyObject* code);
3612
3613 /* Py3UpdateBases.proto */
3614 static PyObject* __Pyx_PEP560_update_bases(PyObject *bases);
3615
3616 /* CalculateMetaclass.proto */
3617 static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases);
3618
3619 /* SetNameInClass.proto */
3620 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && PY_VERSION_HEX < 0x030d0000
3621 #define __Pyx_SetNameInClass(ns, name, value)\
3622 (likely(PyDict_CheckExact(ns)) ? _PyDict_SetItem_KnownHash(ns, name, value, ((PyASCIIObject *) name)->hash) : PyObject_SetItem(ns, name, value))
3623 #elif CYTHON_COMPILING_IN_CPYTHON
3624 #define __Pyx_SetNameInClass(ns, name, value)\
3625 (likely(PyDict_CheckExact(ns)) ? PyDict_SetItem(ns, name, value) : PyObject_SetItem(ns, name, value))
3626 #else
3627 #define __Pyx_SetNameInClass(ns, name, value) PyObject_SetItem(ns, name, value)
3628 #endif
3629
3630 /* PyObjectLookupSpecial.proto */
3631 #if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS
3632 #define __Pyx_PyObject_LookupSpecialNoError(obj, attr_name) __Pyx__PyObject_LookupSpecial(obj, attr_name, 0)
3633 #define __Pyx_PyObject_LookupSpecial(obj, attr_name) __Pyx__PyObject_LookupSpecial(obj, attr_name, 1)
3634 static CYTHON_INLINE PyObject* __Pyx__PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name, int with_error);
3635 #else
3636 #define __Pyx_PyObject_LookupSpecialNoError(o,n) __Pyx_PyObject_GetAttrStrNoError(o,n)
3637 #define __Pyx_PyObject_LookupSpecial(o,n) __Pyx_PyObject_GetAttrStr(o,n)
3638 #endif
3639
3640 /* Py3ClassCreate.proto */
3641 static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname,
3642 PyObject *mkw, PyObject *modname, PyObject *doc);
3643 static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, PyObject *dict,
3644 PyObject *mkw, int calculate_metaclass, int allow_py2_metaclass);
3645
3646 /* CLineInTraceback.proto */
3647 #ifdef CYTHON_CLINE_IN_TRACEBACK
3648 #define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0)
3649 #else
3650 static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line);
3651 #endif
3652
3653 /* CodeObjectCache.proto */
3654 #if !CYTHON_COMPILING_IN_LIMITED_API
3655 typedef struct {
3656 PyCodeObject* code_object;
3657 int code_line;
3658 } __Pyx_CodeObjectCacheEntry;
3659 struct __Pyx_CodeObjectCache {
3660 int count;
3661 int max_count;
3662 __Pyx_CodeObjectCacheEntry* entries;
3663 };
3664 static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
3665 static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
3666 static PyCodeObject *__pyx_find_code_object(int code_line);
3667 static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
3668 #endif
3669
3670 /* AddTraceback.proto */
3671 static void __Pyx_AddTraceback(const char *funcname, int c_line,
3672 int py_line, const char *filename);
3673
3674 /* ArrayAPI.proto */
3675 #ifndef _ARRAYARRAY_H
3676 #define _ARRAYARRAY_H
3677 typedef struct arraydescr {
3678 int typecode;
3679 int itemsize;
3680 PyObject * (*getitem)(struct arrayobject *, Py_ssize_t);
3681 int (*setitem)(struct arrayobject *, Py_ssize_t, PyObject *);
3682 #if PY_MAJOR_VERSION >= 3
3683 char *formats;
3684 #endif
3685 } arraydescr;
3686 struct arrayobject {
3687 PyObject_HEAD
3688 Py_ssize_t ob_size;
3689 union {
3690 char *ob_item;
3691 float *as_floats;
3692 double *as_doubles;
3693 int *as_ints;
3694 unsigned int *as_uints;
3695 unsigned char *as_uchars;
3696 signed char *as_schars;
3697 char *as_chars;
3698 unsigned long *as_ulongs;
3699 long *as_longs;
3700 #if PY_MAJOR_VERSION >= 3
3701 unsigned long long *as_ulonglongs;
3702 long long *as_longlongs;
3703 #endif
3704 short *as_shorts;
3705 unsigned short *as_ushorts;
3706 Py_UNICODE *as_pyunicodes;
3707 void *as_voidptr;
3708 } data;
3709 Py_ssize_t allocated;
3710 struct arraydescr *ob_descr;
3711 PyObject *weakreflist;
3712 #if PY_MAJOR_VERSION >= 3
3713 int ob_exports;
3714 #endif
3715 };
3716 #ifndef NO_NEWARRAY_INLINE
3717 static CYTHON_INLINE PyObject * newarrayobject(PyTypeObject *type, Py_ssize_t size,
3718 struct arraydescr *descr) {
3719 arrayobject *op;
3720 size_t nbytes;
3721 if (size < 0) {
3722 PyErr_BadInternalCall();
3723 return NULL;
3724 }
3725 nbytes = size * descr->itemsize;
3726 if (nbytes / descr->itemsize != (size_t)size) {
3727 return PyErr_NoMemory();
3728 }
3729 op = (arrayobject *) type->tp_alloc(type, 0);
3730 if (op == NULL) {
3731 return NULL;
3732 }
3733 op->ob_descr = descr;
3734 op->allocated = size;
3735 op->weakreflist = NULL;
3736 __Pyx_SET_SIZE(op, size);
3737 if (size <= 0) {
3738 op->data.ob_item = NULL;
3739 }
3740 else {
3741 op->data.ob_item = PyMem_NEW(char, nbytes);
3742 if (op->data.ob_item == NULL) {
3743 Py_DECREF(op);
3744 return PyErr_NoMemory();
3745 }
3746 }
3747 return (PyObject *) op;
3748 }
3749 #else
3750 PyObject* newarrayobject(PyTypeObject *type, Py_ssize_t size,
3751 struct arraydescr *descr);
3752 #endif
3753 static CYTHON_INLINE int resize(arrayobject *self, Py_ssize_t n) {
3754 void *items = (void*) self->data.ob_item;
3755 PyMem_Resize(items, char, (size_t)(n * self->ob_descr->itemsize));
3756 if (items == NULL) {
3757 PyErr_NoMemory();
3758 return -1;
3759 }
3760 self->data.ob_item = (char*) items;
3761 __Pyx_SET_SIZE(self, n);
3762 self->allocated = n;
3763 return 0;
3764 }
3765 static CYTHON_INLINE int resize_smart(arrayobject *self, Py_ssize_t n) {
3766 void *items = (void*) self->data.ob_item;
3767 Py_ssize_t newsize;
3768 if (n < self->allocated && n*4 > self->allocated) {
3769 __Pyx_SET_SIZE(self, n);
3770 return 0;
3771 }
3772 newsize = n + (n / 2) + 1;
3773 if (newsize <= n) {
3774 PyErr_NoMemory();
3775 return -1;
3776 }
3777 PyMem_Resize(items, char, (size_t)(newsize * self->ob_descr->itemsize));
3778 if (items == NULL) {
3779 PyErr_NoMemory();
3780 return -1;
3781 }
3782 self->data.ob_item = (char*) items;
3783 __Pyx_SET_SIZE(self, n);
3784 self->allocated = newsize;
3785 return 0;
3786 }
3787 #endif
3788
3789 /* CIntFromPy.proto */
3790 static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
3791
3792 /* CIntToPy.proto */
3793 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
3794
3795 /* CIntToPy.proto */
3796 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value);
3797
3798 /* CIntFromPy.proto */
3799 static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
3800
3801 /* FormatTypeName.proto */
3802 #if CYTHON_COMPILING_IN_LIMITED_API
3803 typedef PyObject *__Pyx_TypeName;
3804 #define __Pyx_FMT_TYPENAME "%U"
3805 static __Pyx_TypeName __Pyx_PyType_GetName(PyTypeObject* tp);
3806 #define __Pyx_DECREF_TypeName(obj) Py_XDECREF(obj)
3807 #else
3808 typedef const char *__Pyx_TypeName;
3809 #define __Pyx_FMT_TYPENAME "%.200s"
3810 #define __Pyx_PyType_GetName(tp) ((tp)->tp_name)
3811 #define __Pyx_DECREF_TypeName(obj)
3812 #endif
3813
3814 /* FastTypeChecks.proto */
3815 #if CYTHON_COMPILING_IN_CPYTHON
3816 #define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type)
3817 #define __Pyx_TypeCheck2(obj, type1, type2) __Pyx_IsAnySubtype2(Py_TYPE(obj), (PyTypeObject *)type1, (PyTypeObject *)type2)
3818 static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b);
3819 static CYTHON_INLINE int __Pyx_IsAnySubtype2(PyTypeObject *cls, PyTypeObject *a, PyTypeObject *b);
3820 static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type);
3821 static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2);
3822 #else
3823 #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
3824 #define __Pyx_TypeCheck2(obj, type1, type2) (PyObject_TypeCheck(obj, (PyTypeObject *)type1) || PyObject_TypeCheck(obj, (PyTypeObject *)type2))
3825 #define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type)
3826 #define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2))
3827 #endif
3828 #define __Pyx_PyErr_ExceptionMatches2(err1, err2) __Pyx_PyErr_GivenExceptionMatches2(__Pyx_PyErr_CurrentExceptionType(), err1, err2)
3829 #define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception)
3830
3831 /* SwapException.proto */
3832 #if CYTHON_FAST_THREAD_STATE
3833 #define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb)
3834 static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
3835 #else
3836 static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb);
3837 #endif
3838
3839 /* CoroutineBase.proto */
3840 struct __pyx_CoroutineObject;
3841 typedef PyObject *(*__pyx_coroutine_body_t)(struct __pyx_CoroutineObject *, PyThreadState *, PyObject *);
3842 #if CYTHON_USE_EXC_INFO_STACK
3843 #define __Pyx_ExcInfoStruct _PyErr_StackItem
3844 #else
3845 typedef struct {
3846 PyObject *exc_type;
3847 PyObject *exc_value;
3848 PyObject *exc_traceback;
3849 } __Pyx_ExcInfoStruct;
3850 #endif
3851 typedef struct __pyx_CoroutineObject {
3852 PyObject_HEAD
3853 __pyx_coroutine_body_t body;
3854 PyObject *closure;
3855 __Pyx_ExcInfoStruct gi_exc_state;
3856 PyObject *gi_weakreflist;
3857 PyObject *classobj;
3858 PyObject *yieldfrom;
3859 PyObject *gi_name;
3860 PyObject *gi_qualname;
3861 PyObject *gi_modulename;
3862 PyObject *gi_code;
3863 PyObject *gi_frame;
3864 int resume_label;
3865 char is_running;
3866 } __pyx_CoroutineObject;
3867 static __pyx_CoroutineObject *__Pyx__Coroutine_New(
3868 PyTypeObject *type, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure,
3869 PyObject *name, PyObject *qualname, PyObject *module_name);
3870 static __pyx_CoroutineObject *__Pyx__Coroutine_NewInit(
3871 __pyx_CoroutineObject *gen, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure,
3872 PyObject *name, PyObject *qualname, PyObject *module_name);
3873 static CYTHON_INLINE void __Pyx_Coroutine_ExceptionClear(__Pyx_ExcInfoStruct *self);
3874 static int __Pyx_Coroutine_clear(PyObject *self);
3875 static PyObject *__Pyx_Coroutine_Send(PyObject *self, PyObject *value);
3876 static PyObject *__Pyx_Coroutine_Close(PyObject *self);
3877 static PyObject *__Pyx_Coroutine_Throw(PyObject *gen, PyObject *args);
3878 #if CYTHON_USE_EXC_INFO_STACK
3879 #define __Pyx_Coroutine_SwapException(self)
3880 #define __Pyx_Coroutine_ResetAndClearException(self) __Pyx_Coroutine_ExceptionClear(&(self)->gi_exc_state)
3881 #else
3882 #define __Pyx_Coroutine_SwapException(self) {\
3883 __Pyx_ExceptionSwap(&(self)->gi_exc_state.exc_type, &(self)->gi_exc_state.exc_value, &(self)->gi_exc_state.exc_traceback);\
3884 __Pyx_Coroutine_ResetFrameBackpointer(&(self)->gi_exc_state);\
3885 }
3886 #define __Pyx_Coroutine_ResetAndClearException(self) {\
3887 __Pyx_ExceptionReset((self)->gi_exc_state.exc_type, (self)->gi_exc_state.exc_value, (self)->gi_exc_state.exc_traceback);\
3888 (self)->gi_exc_state.exc_type = (self)->gi_exc_state.exc_value = (self)->gi_exc_state.exc_traceback = NULL;\
3889 }
3890 #endif
3891 #if CYTHON_FAST_THREAD_STATE
3892 #define __Pyx_PyGen_FetchStopIterationValue(pvalue)\
3893 __Pyx_PyGen__FetchStopIterationValue(__pyx_tstate, pvalue)
3894 #else
3895 #define __Pyx_PyGen_FetchStopIterationValue(pvalue)\
3896 __Pyx_PyGen__FetchStopIterationValue(__Pyx_PyThreadState_Current, pvalue)
3897 #endif
3898 static int __Pyx_PyGen__FetchStopIterationValue(PyThreadState *tstate, PyObject **pvalue);
3899 static CYTHON_INLINE void __Pyx_Coroutine_ResetFrameBackpointer(__Pyx_ExcInfoStruct *exc_state);
3900
3901 /* PatchModuleWithCoroutine.proto */
3902 static PyObject* __Pyx_Coroutine_patch_module(PyObject* module, const char* py_code);
3903
3904 /* PatchGeneratorABC.proto */
3905 static int __Pyx_patch_abc(void);
3906
3907 /* Generator.proto */
3908 #define __Pyx_Generator_USED
3909 #define __Pyx_Generator_CheckExact(obj) __Pyx_IS_TYPE(obj, __pyx_GeneratorType)
3910 #define __Pyx_Generator_New(body, code, closure, name, qualname, module_name)\
3911 __Pyx__Coroutine_New(__pyx_GeneratorType, body, code, closure, name, qualname, module_name)
3912 static PyObject *__Pyx_Generator_Next(PyObject *self);
3913 static int __pyx_Generator_init(PyObject *module);
3914
3915 /* CheckBinaryVersion.proto */
3916 static unsigned long __Pyx_get_runtime_version(void);
3917 static int __Pyx_check_binary_version(unsigned long ct_version, unsigned long rt_version, int allow_newer);
3918
3919 /* FunctionImport.proto */
3920 static int __Pyx_ImportFunction_3_0_11(PyObject *module, const char *funcname, void (**f)(void), const char *sig);
3921
3922 /* InitStrings.proto */
3923 static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);
3924
3925 /* #### Code section: module_declarations ### */
3926 static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4real_real(PyComplexObject *__pyx_v_self); /* proto*/
3927 static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4imag_imag(PyComplexObject *__pyx_v_self); /* proto*/
3928 static PyObject *__pyx_f_5pysam_7libcvcf_9VCFRecord_update(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes); /* proto*/
3929 static PyObject *__pyx_f_5pysam_7libcvcf_11asVCFRecord_parse(struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto*/
3930
3931 /* Module declarations from "libc.string" */
3932
3933 /* Module declarations from "libc.stdlib" */
3934
3935 /* Module declarations from "libc.stdint" */
3936
3937 /* Module declarations from "libc.stdio" */
3938
3939 /* Module declarations from "posix.types" */
3940
3941 /* Module declarations from "pysam.libchtslib" */
3942
3943 /* Module declarations from "pysam.libctabix" */
3944
3945 /* Module declarations from "pysam.libctabixproxies" */
3946
3947 /* Module declarations from "cython" */
3948
3949 /* Module declarations from "cpython.version" */
3950
3951 /* Module declarations from "__builtin__" */
3952
3953 /* Module declarations from "cpython.type" */
3954
3955 /* Module declarations from "cpython.object" */
3956
3957 /* Module declarations from "cpython.ref" */
3958
3959 /* Module declarations from "cpython.exc" */
3960
3961 /* Module declarations from "cpython.module" */
3962
3963 /* Module declarations from "cpython.mem" */
3964
3965 /* Module declarations from "cpython.tuple" */
3966
3967 /* Module declarations from "cpython.list" */
3968
3969 /* Module declarations from "cpython.sequence" */
3970
3971 /* Module declarations from "cpython.mapping" */
3972
3973 /* Module declarations from "cpython.iterator" */
3974
3975 /* Module declarations from "cpython.number" */
3976
3977 /* Module declarations from "cpython.int" */
3978
3979 /* Module declarations from "__builtin__" */
3980
3981 /* Module declarations from "cpython.bool" */
3982
3983 /* Module declarations from "cpython.long" */
3984
3985 /* Module declarations from "cpython.float" */
3986
3987 /* Module declarations from "__builtin__" */
3988
3989 /* Module declarations from "cpython.complex" */
3990
3991 /* Module declarations from "cpython.string" */
3992
3993 /* Module declarations from "libc.stddef" */
3994
3995 /* Module declarations from "cpython.unicode" */
3996
3997 /* Module declarations from "cpython.pyport" */
3998
3999 /* Module declarations from "cpython.dict" */
4000
4001 /* Module declarations from "cpython.instance" */
4002
4003 /* Module declarations from "cpython.function" */
4004
4005 /* Module declarations from "cpython.method" */
4006
4007 /* Module declarations from "cpython.weakref" */
4008
4009 /* Module declarations from "cpython.getargs" */
4010
4011 /* Module declarations from "cpython.pythread" */
4012
4013 /* Module declarations from "cpython.pystate" */
4014
4015 /* Module declarations from "cpython.cobject" */
4016
4017 /* Module declarations from "cpython.oldbuffer" */
4018
4019 /* Module declarations from "cpython.set" */
4020
4021 /* Module declarations from "cpython.buffer" */
4022
4023 /* Module declarations from "cpython.bytes" */
4024
4025 /* Module declarations from "cpython.pycapsule" */
4026
4027 /* Module declarations from "cpython.contextvars" */
4028
4029 /* Module declarations from "cpython" */
4030
4031 /* Module declarations from "array" */
4032
4033 /* Module declarations from "cpython.array" */
4034 static CYTHON_INLINE int __pyx_f_7cpython_5array_extend_buffer(arrayobject *, char *, Py_ssize_t); /*proto*/
4035
4036 /* Module declarations from "pysam.libcutils" */
4037 static PyObject *(*__pyx_f_5pysam_9libcutils_force_str)(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_str *__pyx_optional_args); /*proto*/
4038
4039 /* Module declarations from "pysam.libcvcf" */
4040 static PyObject *__pyx_f_5pysam_7libcvcf___pyx_unpickle_asVCFRecord__set_state(struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *, PyObject *); /*proto*/
4041 /* #### Code section: typeinfo ### */
4042 /* #### Code section: before_global_var ### */
4043 #define __Pyx_MODULE_NAME "pysam.libcvcf"
4044 extern int __pyx_module_is_main_pysam__libcvcf;
4045 int __pyx_module_is_main_pysam__libcvcf = 0;
4046
4047 /* Implementation of "pysam.libcvcf" */
4048 /* #### Code section: global_var ### */
4049 static PyObject *__pyx_builtin_object;
4050 static PyObject *__pyx_builtin_ValueError;
4051 static PyObject *__pyx_builtin_range;
4052 static PyObject *__pyx_builtin_TypeError;
4053 static PyObject *__pyx_builtin_enumerate;
4054 static PyObject *__pyx_builtin_map;
4055 static PyObject *__pyx_builtin_AssertionError;
4056 static PyObject *__pyx_builtin_min;
4057 static PyObject *__pyx_builtin_zip;
4058 static PyObject *__pyx_builtin_StopIteration;
4059 static PyObject *__pyx_builtin_KeyError;
4060 static PyObject *__pyx_builtin_NotImplementedError;
4061 static PyObject *__pyx_builtin_MemoryError;
4062 /* #### Code section: string_decls ### */
4063 static const char __pyx_k_[] = "";
4064 static const char __pyx_k_0[] = "0";
4065 static const char __pyx_k_A[] = "A";
4066 static const char __pyx_k_D[] = "D";
4067 static const char __pyx_k_G[] = "G";
4068 static const char __pyx_k_I[] = "I";
4069 static const char __pyx_k_N[] = "N";
4070 static const char __pyx_k_a[] = "a";
4071 static const char __pyx_k_c[] = "c";
4072 static const char __pyx_k_d[] = "d";
4073 static const char __pyx_k_f[] = "f";
4074 static const char __pyx_k_i[] = "i";
4075 static const char __pyx_k_k[] = "k";
4076 static const char __pyx_k_l[] = "l";
4077 static const char __pyx_k_n[] = "n";
4078 static const char __pyx_k_r[] = "r";
4079 static const char __pyx_k_s[] = "s";
4080 static const char __pyx_k_t[] = "t";
4081 static const char __pyx_k_v[] = "v";
4082 static const char __pyx_k_x[] = "x";
4083 static const char __pyx_k_y[] = "y";
4084 static const char __pyx_k_DP[] = "DP";
4085 static const char __pyx_k_EC[] = "EC";
4086 static const char __pyx_k_FT[] = "FT";
4087 static const char __pyx_k_GL[] = "GL";
4088 static const char __pyx_k_GP[] = "GP";
4089 static const char __pyx_k_GQ[] = "GQ";
4090 static const char __pyx_k_GT[] = "GT";
4091 static const char __pyx_k_HQ[] = "HQ";
4092 static const char __pyx_k_ID[] = "ID=";
4093 static const char __pyx_k_MQ[] = "MQ";
4094 static const char __pyx_k_PL[] = "PL";
4095 static const char __pyx_k_PQ[] = "PQ";
4096 static const char __pyx_k_PS[] = "PS";
4097 static const char __pyx_k__2[] = ",";
4098 static const char __pyx_k__3[] = ":";
4099 static const char __pyx_k__4[] = "-";
4100 static const char __pyx_k__5[] = ".";
4101 static const char __pyx_k__6[] = ";";
4102 static const char __pyx_k__7[] = "=";
4103 static const char __pyx_k__8[] = ")";
4104 static const char __pyx_k_fa[] = "fa";
4105 static const char __pyx_k_gc[] = "gc";
4106 static const char __pyx_k_id[] = "id=";
4107 static const char __pyx_k_na[] = "na";
4108 static const char __pyx_k_re[] = "re";
4109 static const char __pyx_k_ALT[] = "ALT";
4110 static const char __pyx_k_GLE[] = "GLE";
4111 static const char __pyx_k_POS[] = "POS";
4112 static const char __pyx_k_REF[] = "REF";
4113 static const char __pyx_k_VCF[] = "VCF";
4114 static const char __pyx_k__10[] = ": '";
4115 static const char __pyx_k__11[] = "'\n";
4116 static const char __pyx_k__12[] = " ";
4117 static const char __pyx_k__13[] = ": ";
4118 static const char __pyx_k__14[] = "\n";
4119 static const char __pyx_k__15[] = "<";
4120 static const char __pyx_k__16[] = ">";
4121 static const char __pyx_k__19[] = "\"";
4122 static const char __pyx_k__23[] = "##";
4123 static const char __pyx_k__24[] = "#";
4124 static const char __pyx_k__25[] = "\t";
4125 static const char __pyx_k__27[] = "|";
4126 static const char __pyx_k__33[] = "*";
4127 static const char __pyx_k__34[] = "[|/\\\\]";
4128 static const char __pyx_k_add[] = "add";
4129 static const char __pyx_k_all[] = "__all__";
4130 static const char __pyx_k_alt[] = "alt";
4131 static const char __pyx_k_del[] = "__del__";
4132 static const char __pyx_k_doc[] = "__doc__";
4133 static const char __pyx_k_end[] = "end";
4134 static const char __pyx_k_err[] = "err";
4135 static const char __pyx_k_fmt[] = "fmt";
4136 static const char __pyx_k_for[] = " for ";
4137 static const char __pyx_k_get[] = "get";
4138 static const char __pyx_k_got[] = "), got ";
4139 static const char __pyx_k_gts[] = "gts";
4140 static const char __pyx_k_idx[] = "idx";
4141 static const char __pyx_k_key[] = "key";
4142 static const char __pyx_k_map[] = "map";
4143 static const char __pyx_k_min[] = "min";
4144 static const char __pyx_k_new[] = "__new__";
4145 static const char __pyx_k_nmb[] = "nmb";
4146 static const char __pyx_k_opt[] = "opt";
4147 static const char __pyx_k_pos[] = "pos";
4148 static const char __pyx_k_ref[] = "ref";
4149 static const char __pyx_k_sys[] = "sys";
4150 static const char __pyx_k_var[] = "var";
4151 static const char __pyx_k_vcf[] = "vcf";
4152 static const char __pyx_k_zip[] = "zip";
4153 static const char __pyx_k_Flag[] = "Flag";
4154 static const char __pyx_k_ID_2[] = "ID";
4155 static const char __pyx_k_INFO[] = "INFO";
4156 static const char __pyx_k_PASS[] = "PASS";
4157 static const char __pyx_k_QUAL[] = "QUAL";
4158 static const char __pyx_k_Type[] = "Type=";
4159 static const char __pyx_k__139[] = "?";
4160 static const char __pyx_k_addn[] = "addn";
4161 static const char __pyx_k_alt1[] = "alt1";
4162 static const char __pyx_k_alt2[] = "alt2";
4163 static const char __pyx_k_args[] = "args";
4164 static const char __pyx_k_cols[] = "cols";
4165 static const char __pyx_k_copy[] = "_copy";
4166 static const char __pyx_k_data[] = "data";
4167 static const char __pyx_k_dict[] = "__dict__";
4168 static const char __pyx_k_elts[] = "elts";
4169 static const char __pyx_k_find[] = "find";
4170 static const char __pyx_k_id_2[] = "id";
4171 static const char __pyx_k_info[] = "_info";
4172 static const char __pyx_k_init[] = "__init__";
4173 static const char __pyx_k_join[] = "join";
4174 static const char __pyx_k_keys[] = "keys";
4175 static const char __pyx_k_last[] = "last";
4176 static const char __pyx_k_left[] = "left";
4177 static const char __pyx_k_line[] = "line";
4178 static const char __pyx_k_main[] = "__main__";
4179 static const char __pyx_k_name[] = "__name__";
4180 static const char __pyx_k_pos1[] = "pos1";
4181 static const char __pyx_k_pos2[] = "pos2";
4182 static const char __pyx_k_qual[] = "qual";
4183 static const char __pyx_k_ref1[] = "ref1";
4184 static const char __pyx_k_ref2[] = "ref2";
4185 static const char __pyx_k_rest[] = "rest";
4186 static const char __pyx_k_self[] = "self";
4187 static const char __pyx_k_send[] = "send";
4188 static const char __pyx_k_spec[] = "__spec__";
4189 static const char __pyx_k_test[] = "__test__";
4190 static const char __pyx_k_type[] = "type";
4191 static const char __pyx_k_ACGTN[] = "ACGTN";
4192 static const char __pyx_k_CHROM[] = "CHROM";
4193 static const char __pyx_k_Error[] = "Error";
4194 static const char __pyx_k_Float[] = "Float";
4195 static const char __pyx_k_addns[] = "addns";
4196 static const char __pyx_k_ascii[] = "ascii";
4197 static const char __pyx_k_blurp[] = "blurp";
4198 static const char __pyx_k_chrom[] = "chrom";
4199 static const char __pyx_k_close[] = "close";
4200 static const char __pyx_k_descr[] = "descr";
4201 static const char __pyx_k_error[] = "error";
4202 static const char __pyx_k_faref[] = "faref";
4203 static const char __pyx_k_fetch[] = "fetch";
4204 static const char __pyx_k_first[] = "first";
4205 static const char __pyx_k_found[] = "(found ";
4206 static const char __pyx_k_ielts[] = "ielts";
4207 static const char __pyx_k_label[] = "label";
4208 static const char __pyx_k_lines[] = "lines";
4209 static const char __pyx_k_match[] = "match";
4210 static const char __pyx_k_parse[] = "_parse";
4211 static const char __pyx_k_pysam[] = "pysam";
4212 static const char __pyx_k_range[] = "range";
4213 static const char __pyx_k_sdata[] = "sdata";
4214 static const char __pyx_k_split[] = "split";
4215 static const char __pyx_k_start[] = "start";
4216 static const char __pyx_k_state[] = "state";
4217 static const char __pyx_k_strip[] = "strip";
4218 static const char __pyx_k_super[] = "super";
4219 static const char __pyx_k_throw[] = "throw";
4220 static const char __pyx_k_upper[] = "upper";
4221 static const char __pyx_k_value[] = "value";
4222 static const char __pyx_k_write[] = "write";
4223 static const char __pyx_k_FILTER[] = "FILTER";
4224 static const char __pyx_k_FORMAT[] = "FORMAT";
4225 static const char __pyx_k_GTdata[] = "GTdata";
4226 static const char __pyx_k_Number[] = "Number=";
4227 static const char __pyx_k_String[] = "String";
4228 static const char __pyx_k_Type_2[] = "Type";
4229 static const char __pyx_k_allele[] = "allele";
4230 static const char __pyx_k_append[] = "append";
4231 static const char __pyx_k_bisect[] = "bisect";
4232 static const char __pyx_k_copy_2[] = "copy";
4233 static const char __pyx_k_dict_2[] = "_dict";
4234 static const char __pyx_k_dict_3[] = "dict";
4235 static const char __pyx_k_enable[] = "enable";
4236 static const char __pyx_k_errors[] = "_errors";
4237 static const char __pyx_k_filter[] = "_filter";
4238 static const char __pyx_k_format[] = "format";
4239 static const char __pyx_k_header[] = "_header";
4240 static const char __pyx_k_import[] = "__import__";
4241 static const char __pyx_k_info_2[] = "info";
4242 static const char __pyx_k_line_2[] = "_line";
4243 static const char __pyx_k_lineno[] = "_lineno";
4244 static const char __pyx_k_module[] = "__module__";
4245 static const char __pyx_k_number[] = "number";
4246 static const char __pyx_k_object[] = "object";
4247 static const char __pyx_k_output[] = "(output)";
4248 static const char __pyx_k_parser[] = "parser";
4249 static const char __pyx_k_pickle[] = "pickle";
4250 static const char __pyx_k_record[] = "record";
4251 static const char __pyx_k_reduce[] = "__reduce__";
4252 static const char __pyx_k_region[] = "region";
4253 static const char __pyx_k_result[] = "result";
4254 static const char __pyx_k_sample[] = "sample";
4255 static const char __pyx_k_stream[] = "stream";
4256 static const char __pyx_k_string[] = "string";
4257 static const char __pyx_k_update[] = "update";
4258 static const char __pyx_k_values[] = "values";
4259 static const char __pyx_k_ACGTN_2[] = "^[ACGTN]+$";
4260 static const char __pyx_k_Integer[] = "Integer";
4261 static const char __pyx_k_VCFv3_3[] = "VCFv3.3";
4262 static const char __pyx_k_VCFv4_0[] = "VCFv4.0";
4263 static const char __pyx_k_VCFv4_1[] = "VCFv4.1";
4264 static const char __pyx_k_VCFv4_2[] = "VCFv4.2";
4265 static const char __pyx_k_Warning[] = "Warning";
4266 static const char __pyx_k_alleles[] = "#alleles";
4267 static const char __pyx_k_compile[] = "compile";
4268 static const char __pyx_k_connect[] = "connect";
4269 static const char __pyx_k_disable[] = "disable";
4270 static const char __pyx_k_errwarn[] = "errwarn";
4271 static const char __pyx_k_getinfo[] = "getinfo";
4272 static const char __pyx_k_in_line[] = " in line ";
4273 static const char __pyx_k_lines_2[] = "_lines";
4274 static const char __pyx_k_longest[] = "longest";
4275 static const char __pyx_k_missing[] = "missing";
4276 static const char __pyx_k_movable[] = "movable";
4277 static const char __pyx_k_newalts[] = "newalts";
4278 static const char __pyx_k_parse_2[] = "parse";
4279 static const char __pyx_k_prepare[] = "__prepare__";
4280 static const char __pyx_k_regions[] = "regions";
4281 static const char __pyx_k_replace[] = "replace";
4282 static const char __pyx_k_samples[] = "_samples";
4283 static const char __pyx_k_setinfo[] = "setinfo";
4284 static const char __pyx_k_vcffile[] = "vcffile";
4285 static const char __pyx_k_version[] = "_version";
4286 static const char __pyx_k_GTstring[] = "GTstring";
4287 static const char __pyx_k_Genotype[] = "Genotype";
4288 static const char __pyx_k_KeyError[] = "KeyError";
4289 static const char __pyx_k_Number_2[] = "Number";
4290 static const char __pyx_k_VCF_says[] = ", VCF says ";
4291 static const char __pyx_k_deepcopy[] = "deepcopy";
4292 static const char __pyx_k_encoding[] = "encoding";
4293 static const char __pyx_k_endswith[] = "endswith";
4294 static const char __pyx_k_expected[] = "; expected ";
4295 static const char __pyx_k_filename[] = "filename";
4296 static const char __pyx_k_filter_2[] = "filter";
4297 static const char __pyx_k_format_2[] = "_format";
4298 static const char __pyx_k_getstate[] = "__getstate__";
4299 static const char __pyx_k_gtsRegEx[] = "gtsRegEx";
4300 static const char __pyx_k_header_2[] = "header";
4301 static const char __pyx_k_headings[] = "headings";
4302 static const char __pyx_k_inregion[] = "inregion";
4303 static const char __pyx_k_operator[] = "operator";
4304 static const char __pyx_k_output_2[] = "output";
4305 static const char __pyx_k_pyx_type[] = "__pyx_type";
4306 static const char __pyx_k_qualname[] = "__qualname__";
4307 static const char __pyx_k_required[] = "_required";
4308 static const char __pyx_k_sequence[] = "sequence";
4309 static const char __pyx_k_set_name[] = "__set_name__";
4310 static const char __pyx_k_setstate[] = "__setstate__";
4311 static const char __pyx_k_shortest[] = "shortest";
4312 static const char __pyx_k_validate[] = "validate";
4313 static const char __pyx_k_Character[] = "Character";
4314 static const char __pyx_k_NT_NUMBER[] = "NT_NUMBER";
4315 static const char __pyx_k_Phase_set[] = "Phase set";
4316 static const char __pyx_k_Tabixfile[] = "Tabixfile";
4317 static const char __pyx_k_TypeError[] = "TypeError";
4318 static const char __pyx_k_VCFRecord[] = "VCFRecord";
4319 static const char __pyx_k_VCF___del[] = "VCF.__del__";
4320 static const char __pyx_k_VCF_close[] = "VCF.close";
4321 static const char __pyx_k_VCF_error[] = "VCF.error";
4322 static const char __pyx_k_VCF_fetch[] = "VCF.fetch";
4323 static const char __pyx_k_VCF_parse[] = "VCF.parse";
4324 static const char __pyx_k_VCF_write[] = "VCF.write";
4325 static const char __pyx_k_WRONG_REF[] = "WRONG_REF";
4326 static const char __pyx_k_convertGT[] = "convertGT";
4327 static const char __pyx_k_enumerate[] = "enumerate";
4328 static const char __pyx_k_genotypes[] = "#genotypes";
4329 static const char __pyx_k_getfilter[] = "getfilter";
4330 static const char __pyx_k_getformat[] = "getformat";
4331 static const char __pyx_k_getheader[] = "getheader";
4332 static const char __pyx_k_isenabled[] = "isenabled";
4333 static const char __pyx_k_last_line[] = "last_line";
4334 static const char __pyx_k_leftalign[] = "leftalign";
4335 static const char __pyx_k_lineparse[] = "lineparse";
4336 static const char __pyx_k_metaclass[] = "__metaclass__";
4337 static const char __pyx_k_pyx_state[] = "__pyx_state";
4338 static const char __pyx_k_reduce_ex[] = "__reduce_ex__";
4339 static const char __pyx_k_reference[] = "reference";
4340 static const char __pyx_k_regions_2[] = "_regions";
4341 static const char __pyx_k_samples_2[] = " samples (";
4342 static const char __pyx_k_samples_3[] = "samples";
4343 static const char __pyx_k_separator[] = "separator";
4344 static const char __pyx_k_setfilter[] = "setfilter";
4345 static const char __pyx_k_setformat[] = "setformat";
4346 static const char __pyx_k_setheader[] = "setheader";
4347 static const char __pyx_k_tabixfile[] = "tabixfile";
4348 static const char __pyx_k_version_2[] = "version";
4349 static const char __pyx_k_warnerror[] = "warnerror";
4350 static const char __pyx_k_NT_ALLELES[] = "NT_ALLELES";
4351 static const char __pyx_k_NT_UNKNOWN[] = "NT_UNKNOWN";
4352 static const char __pyx_k_VCF___init[] = "VCF.__init__";
4353 static const char __pyx_k_VCF__parse[] = "VCF._parse";
4354 static const char __pyx_k_ValueError[] = "ValueError";
4355 static const char __pyx_k_errorlabel[] = "errorlabel";
4356 static const char __pyx_k_expected_2[] = ", expected ";
4357 static const char __pyx_k_expected_3[] = "expected ";
4358 static const char __pyx_k_expected_4[] = "expected";
4359 static const char __pyx_k_fileformat[] = "fileformat";
4360 static const char __pyx_k_formatdict[] = "formatdict";
4361 static const char __pyx_k_getsamples[] = "getsamples";
4362 static const char __pyx_k_itemgetter[] = "itemgetter";
4363 static const char __pyx_k_itervalues[] = "itervalues";
4364 static const char __pyx_k_namedtuple[] = "namedtuple";
4365 static const char __pyx_k_numbertype[] = "numbertype";
4366 static const char __pyx_k_parse_data[] = "parse_data";
4367 static const char __pyx_k_pyx_result[] = "__pyx_result";
4368 static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
4369 static const char __pyx_k_required_2[] = "required";
4370 static const char __pyx_k_setregions[] = "setregions";
4371 static const char __pyx_k_setsamples[] = "setsamples";
4372 static const char __pyx_k_setversion[] = "setversion";
4373 static const char __pyx_k_startswith[] = "startswith";
4374 static const char __pyx_k_write_data[] = "write_data";
4375 static const char __pyx_k_Description[] = "Description=";
4376 static const char __pyx_k_MISSING_REF[] = "MISSING_REF";
4377 static const char __pyx_k_MemoryError[] = "MemoryError";
4378 static const char __pyx_k_PickleError[] = "PickleError";
4379 static const char __pyx_k_V33_BAD_REF[] = "V33_BAD_REF";
4380 static const char __pyx_k_VCF_connect[] = "VCF.connect";
4381 static const char __pyx_k_VCF_getinfo[] = "VCF.getinfo";
4382 static const char __pyx_k_VCF_setinfo[] = "VCF.setinfo";
4383 static const char __pyx_k_alleleRegEx[] = "alleleRegEx";
4384 static const char __pyx_k_asVCFRecord[] = "asVCFRecord";
4385 static const char __pyx_k_collections[] = "collections";
4386 static const char __pyx_k_defaultdict[] = "defaultdict";
4387 static const char __pyx_k_deletion_is[] = "(deletion is ";
4388 static const char __pyx_k_description[] = "description";
4389 static const char __pyx_k_errorstring[] = "errorstring";
4390 static const char __pyx_k_ignoreerror[] = "ignoreerror";
4391 static const char __pyx_k_leftalign_2[] = "_leftalign";
4392 static const char __pyx_k_mro_entries[] = "__mro_entries__";
4393 static const char __pyx_k_reference_2[] = "_reference";
4394 static const char __pyx_k_warn_errors[] = "_warn_errors";
4395 static const char __pyx_k_writeheader[] = "writeheader";
4396 static const char __pyx_k_BAD_GENOTYPE[] = "BAD_GENOTYPE";
4397 static const char __pyx_k_NT_GENOTYPES[] = "NT_GENOTYPES";
4398 static const char __pyx_k_VCF_inregion[] = "VCF.inregion";
4399 static const char __pyx_k_VCF_validate[] = "VCF.validate";
4400 static const char __pyx_k_get_expected[] = "get_expected";
4401 static const char __pyx_k_get_sequence[] = "get_sequence";
4402 static const char __pyx_k_initializing[] = "_initializing";
4403 static const char __pyx_k_is_coroutine[] = "_is_coroutine";
4404 static const char __pyx_k_missingvalue[] = "missingvalue";
4405 static const char __pyx_k_parse_format[] = "parse_format";
4406 static const char __pyx_k_parse_header[] = "parse_header";
4407 static const char __pyx_k_pyx_checksum[] = "__pyx_checksum";
4408 static const char __pyx_k_reference_is[] = "(reference is ";
4409 static const char __pyx_k_setreference[] = "setreference";
4410 static const char __pyx_k_stringsource[] = "<stringsource>";
4411 static const char __pyx_k_use_setstate[] = "use_setstate";
4412 static const char __pyx_k_write_header[] = "write_header";
4413 static const char __pyx_k_Description_2[] = "Description";
4414 static const char __pyx_k_NT_NR_ALLELES[] = "NT_NR_ALLELES";
4415 static const char __pyx_k_StopIteration[] = "StopIteration";
4416 static const char __pyx_k_Undefined_tag[] = "(Undefined tag)";
4417 static const char __pyx_k_VCF_convertGT[] = "VCF.convertGT";
4418 static const char __pyx_k_VCF_getfilter[] = "VCF.getfilter";
4419 static const char __pyx_k_VCF_getformat[] = "VCF.getformat";
4420 static const char __pyx_k_VCF_getheader[] = "VCF.getheader";
4421 static const char __pyx_k_VCF_setfilter[] = "VCF.setfilter";
4422 static const char __pyx_k_VCF_setformat[] = "VCF.setformat";
4423 static const char __pyx_k_VCF_setheader[] = "VCF.setheader";
4424 static const char __pyx_k_VCF_warnerror[] = "VCF.warnerror";
4425 static const char __pyx_k_class_getitem[] = "__class_getitem__";
4426 static const char __pyx_k_compare_calls[] = "compare_calls";
4427 static const char __pyx_k_convertGTback[] = "convertGTback";
4428 static const char __pyx_k_datagenerator[] = "datagenerator";
4429 static const char __pyx_k_format_format[] = "format_format";
4430 static const char __pyx_k_init_subclass[] = "__init_subclass__";
4431 static const char __pyx_k_parse_heading[] = "parse_heading";
4432 static const char __pyx_k_parse_regions[] = "parse_regions";
4433 static const char __pyx_k_pysam_libcvcf[] = "pysam.libcvcf";
4434 static const char __pyx_k_reduce_cython[] = "__reduce_cython__";
4435 static const char __pyx_k_sample2column[] = "_sample2column";
4436 static const char __pyx_k_write_heading[] = "write_heading";
4437 static const char __pyx_k_AssertionError[] = "AssertionError";
4438 static const char __pyx_k_V33_BAD_ALLELE[] = "V33_BAD_ALLELE";
4439 static const char __pyx_k_V40_BAD_ALLELE[] = "V40_BAD_ALLELE";
4440 static const char __pyx_k_VCF_getsamples[] = "VCF.getsamples";
4441 static const char __pyx_k_VCF_parse_data[] = "VCF.parse_data";
4442 static const char __pyx_k_VCF_setregions[] = "VCF.setregions";
4443 static const char __pyx_k_VCF_setsamples[] = "VCF.setsamples";
4444 static const char __pyx_k_VCF_setversion[] = "VCF.setversion";
4445 static const char __pyx_k_VCF_write_data[] = "VCF.write_data";
4446 static const char __pyx_k_add_definition[] = "_add_definition";
4447 static const char __pyx_k_have_deletions[] = "have_deletions";
4448 static const char __pyx_k_ignored_errors[] = "_ignored_errors";
4449 static const char __pyx_k_nonref_alleles[] = "#nonref_alleles";
4450 static const char __pyx_k_parameters_got[] = " parameters, got ";
4451 static const char __pyx_k_parse_header_2[] = "_parse_header";
4452 static const char __pyx_k_reference_is_2[] = ", reference is ";
4453 static const char __pyx_k_Phasing_quality[] = "Phasing quality";
4454 static const char __pyx_k_VCFRecord_error[] = "VCFRecord.error";
4455 static const char __pyx_k_VCF_ignoreerror[] = "VCF.ignoreerror";
4456 static const char __pyx_k_VCF_writeheader[] = "VCF.writeheader";
4457 static const char __pyx_k_faref_leftflank[] = "faref_leftflank";
4458 static const char __pyx_k_fileformat_VCFv[] = "##fileformat=VCFv";
4459 static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError";
4460 static const char __pyx_k_setstate_cython[] = "__setstate_cython__";
4461 static const char __pyx_k_Genotype_Quality[] = "Genotype Quality";
4462 static const char __pyx_k_POS_NOT_POSITIVE[] = "POS_NOT_POSITIVE";
4463 static const char __pyx_k_VCF_get_expected[] = "VCF.get_expected";
4464 static const char __pyx_k_VCF_parse_format[] = "VCF.parse_format";
4465 static const char __pyx_k_VCF_parse_header[] = "VCF.parse_header";
4466 static const char __pyx_k_VCF_setreference[] = "VCF.setreference";
4467 static const char __pyx_k_VCF_write_header[] = "VCF.write_header";
4468 static const char __pyx_k_parse_formatdata[] = "parse_formatdata";
4469 static const char __pyx_k_phased_genotypes[] = "#phased_genotypes";
4470 static const char __pyx_k_ERROR_INFO_STRING[] = "ERROR_INFO_STRING";
4471 static const char __pyx_k_ERROR_UNKNOWN_KEY[] = "ERROR_UNKNOWN_KEY";
4472 static const char __pyx_k_Haplotype_Quality[] = "Haplotype Quality";
4473 static const char __pyx_k_POS_NOT_NUMERICAL[] = "POS_NOT_NUMERICAL";
4474 static const char __pyx_k_VCF__parse_header[] = "VCF._parse_header";
4475 static const char __pyx_k_VCF_compare_calls[] = "VCF.compare_calls";
4476 static const char __pyx_k_VCF_convertGTback[] = "VCF.convertGTback";
4477 static const char __pyx_k_VCF_format_format[] = "VCF.format_format";
4478 static const char __pyx_k_VCF_parse_heading[] = "VCF.parse_heading";
4479 static const char __pyx_k_VCF_write_heading[] = "VCF.write_heading";
4480 static const char __pyx_k_format_formatdata[] = "format_formatdata";
4481 static const char __pyx_k_pysam_libcvcf_pyx[] = "pysam/libcvcf.pyx";
4482 static const char __pyx_k_values_in_element[] = " values in element ";
4483 static const char __pyx_k_FILTER_NOT_DEFINED[] = "FILTER_NOT_DEFINED";
4484 static const char __pyx_k_FORMAT_NOT_DEFINED[] = "FORMAT_NOT_DEFINED";
4485 static const char __pyx_k_QUAL_NOT_NUMERICAL[] = "QUAL_NOT_NUMERICAL";
4486 static const char __pyx_k_ZERO_LENGTH_ALLELE[] = "ZERO_LENGTH_ALLELE";
4487 static const char __pyx_k_asyncio_coroutines[] = "asyncio.coroutines";
4488 static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
4489 static const char __pyx_k_ERROR_TRAILING_DATA[] = "ERROR_TRAILING_DATA";
4490 static const char __pyx_k_NT_PHASED_GENOTYPES[] = "NT_PHASED_GENOTYPES";
4491 static const char __pyx_k_NotImplementedError[] = "NotImplementedError";
4492 static const char __pyx_k_RMS_mapping_quality[] = "RMS mapping quality";
4493 static const char __pyx_k_UNKNOWN_CHAR_IN_REF[] = "UNKNOWN_CHAR_IN_REF";
4494 static const char __pyx_k_VCF__add_definition[] = "VCF._add_definition";
4495 static const char __pyx_k_needs_to_be_checked[] = "needs to be checked";
4496 static const char __pyx_k_sth_entry_not_found[] = "(%sth entry not found)";
4497 static const char __pyx_k_BAD_NUMBER_OF_VALUES[] = "BAD_NUMBER_OF_VALUES";
4498 static const char __pyx_k_ERROR_FLAG_HAS_VALUE[] = "ERROR_FLAG_HAS_VALUE";
4499 static const char __pyx_k_Genotype_likelihoods[] = "Genotype likelihoods";
4500 static const char __pyx_k_VCF_parse_formatdata[] = "VCF.parse_formatdata";
4501 static const char __pyx_k_enter_default_format[] = "enter_default_format";
4502 static const char __pyx_k_BAD_NUMBER_OF_COLUMNS[] = "BAD_NUMBER_OF_COLUMNS";
4503 static const char __pyx_k_ERROR_FORMAT_NOT_CHAR[] = "ERROR_FORMAT_NOT_CHAR";
4504 static const char __pyx_k_FORMAT_MISSING_QUOTES[] = "FORMAT_MISSING_QUOTES";
4505 static const char __pyx_k_UNKNOWN_FORMAT_STRING[] = "UNKNOWN_FORMAT_STRING";
4506 static const char __pyx_k_VCF_format_formatdata[] = "VCF.format_formatdata";
4507 static const char __pyx_k_Invalid_error_string_s[] = "Invalid error string: %s";
4508 static const char __pyx_k_Sample_Genotype_Filter[] = "Sample Genotype Filter";
4509 static const char __pyx_k_V33_UNMATCHED_DELETION[] = "V33_UNMATCHED_DELETION";
4510 static const char __pyx_k_BADLY_FORMATTED_HEADING[] = "BADLY_FORMATTED_HEADING";
4511 static const char __pyx_k_ZERO_FOR_NON_FLAG_FIELD[] = "ZERO_FOR_NON_FLAG_FIELD";
4512 static const char __pyx_k_BAD_NUMBER_OF_PARAMETERS[] = "BAD_NUMBER_OF_PARAMETERS";
4513 static const char __pyx_k_ERROR_FORMAT_NOT_INTEGER[] = "ERROR_FORMAT_NOT_INTEGER";
4514 static const char __pyx_k_VCF_enter_default_format[] = "VCF.enter_default_format";
4515 static const char __pyx_k_pyx_unpickle_asVCFRecord[] = "__pyx_unpickle_asVCFRecord";
4516 static const char __pyx_k_VCFRecord___reduce_cython[] = "VCFRecord.__reduce_cython__";
4517 static const char __pyx_k_ERROR_FORMAT_NOT_NUMERICAL[] = "ERROR_FORMAT_NOT_NUMERICAL";
4518 static const char __pyx_k_V40_MISSING_ANGLE_BRACKETS[] = "V40_MISSING_ANGLE_BRACKETS";
4519 static const char __pyx_k_VCFRecord___setstate_cython[] = "VCFRecord.__setstate_cython__";
4520 static const char __pyx_k_WRONG_REF_Wrong_reference_s[] = "WRONG_REF:Wrong reference %s";
4521 static const char __pyx_k_asVCFRecord___reduce_cython[] = "asVCFRecord.__reduce_cython__";
4522 static const char __pyx_k_Conditional_genotype_quality[] = "Conditional genotype quality";
4523 static const char __pyx_k_BADLY_FORMATTED_FORMAT_STRING[] = "BADLY_FORMATTED_FORMAT_STRING";
4524 static const char __pyx_k_HEADING_NOT_SEPARATED_BY_TABS[] = "HEADING_NOT_SEPARATED_BY_TABS";
4525 static const char __pyx_k_MISSING_INDEL_ALLELE_REF_BASE[] = "MISSING_INDEL_ALLELE_REF_BASE";
4526 static const char __pyx_k_asVCFRecord___setstate_cython[] = "asVCFRecord.__setstate_cython__";
4527 static const char __pyx_k_BADLY_FORMATTED_HEADING_Did_not[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s";
4528 static const char __pyx_k_ERROR_FORMAT_NOT_CHAR_Eexpected[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string";
4529 static const char __pyx_k_ERROR_UNKNOWN_KEY_Unknown_key_s[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)";
4530 static const char __pyx_k_Expected_alternate_allel_counts[] = "Expected alternate allel counts";
4531 static const char __pyx_k_FILTER_NOT_DEFINED_Identifier_s[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header";
4532 static const char __pyx_k_FORMAT_NOT_DEFINED_Identifier_s[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header";
4533 static const char __pyx_k_POS_NOT_POSITIVE_Position_field[] = "POS_NOT_POSITIVE:Position field must be >0";
4534 static const char __pyx_k_Read_depth_at_this_position_for[] = "Read depth at this position for this sample";
4535 static const char __pyx_k_Unknown_number_type_encountered[] = "Unknown number type encountered: %s";
4536 static const char __pyx_k_V33_BAD_ALLELE_Cannot_interpret[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF";
4537 static const char __pyx_k_V33_BAD_REF_Reference_should_be[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF";
4538 static const char __pyx_k_V40_BAD_ALLELE_Bad_allele_found[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)";
4539 static const char __pyx_k_BADLY_FORMATTED_FORMAT_STRING_Fo[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string";
4540 static const char __pyx_k_BAD_CHR_TAG_Error_calculating_ch[] = "BAD_CHR_TAG:Error calculating chr tag for %s";
4541 static const char __pyx_k_BAD_GENOTYPE_Cannot_parse_genoty[] = "BAD_GENOTYPE:Cannot parse genotype (%s)";
4542 static const char __pyx_k_BAD_NUMBER_OF_COLUMNS_Wrong_numb[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)";
4543 static const char __pyx_k_BAD_NUMBER_OF_PARAMETERS_Found_u[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)";
4544 static const char __pyx_k_BAD_NUMBER_OF_VALUES_Found_too_m[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)";
4545 static const char __pyx_k_Can_only_handle_v3_3_and_v4_0_VC[] = "Can only handle v3.3 and v4.0 VCF files";
4546 static const char __pyx_k_Don_t_understand_region_string_s[] = "Don't understand region string '%s'";
4547 static const char __pyx_k_ERROR_FLAG_HAS_VALUE_Flag_fields[] = "ERROR_FLAG_HAS_VALUE:Flag fields should not have a value";
4548 static const char __pyx_k_ERROR_FORMAT_NOT_INTEGER_Expecte[] = "ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s";
4549 static const char __pyx_k_ERROR_FORMAT_NOT_NUMERICAL_Expec[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s";
4550 static const char __pyx_k_ERROR_INFO_STRING_Error_while_pa[] = "ERROR_INFO_STRING:Error while parsing info field";
4551 static const char __pyx_k_ERROR_TRAILING_DATA_Numerical_fi[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data";
4552 static const char __pyx_k_FORMAT_MISSING_QUOTES_Descriptio[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes";
4553 static const char __pyx_k_Genotype_posterior_probabilities[] = "Genotype posterior probabilities";
4554 static const char __pyx_k_HEADING_NOT_SEPARATED_BY_TABS_He[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs";
4555 static const char __pyx_k_Incompatible_checksums_0x_x_vs_0[] = "Incompatible checksums (0x%x vs (0xe48d6d5, 0xcc3d7cd, 0x1c28f48) = (encoding, vcffile))";
4556 static const char __pyx_k_MISSING_INDEL_ALLELE_REF_BASE_In[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base";
4557 static const char __pyx_k_MISSING_REF_Reference_allele_mis[] = "MISSING_REF:Reference allele missing";
4558 static const char __pyx_k_POS_NOT_NUMERICAL_Position_colum[] = "POS_NOT_NUMERICAL:Position column is not numerical";
4559 static const char __pyx_k_Phred_scaled_genotype_likelihood[] = "Phred-scaled genotype likelihoods";
4560 static const char __pyx_k_QUAL_NOT_NUMERICAL_Quality_field[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'";
4561 static const char __pyx_k_Required_key_s_not_found_in_data[] = "Required key %s not found in data";
4562 static const char __pyx_k_UNKNOWN_CHAR_IN_REF_Unknown_char[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field";
4563 static const char __pyx_k_UNKNOWN_FORMAT_STRING_Unknown_fi[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
4564 static const char __pyx_k_V33_UNMATCHED_DELETION_Deleted_s[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)";
4565 static const char __pyx_k_V40_FORMAT_MUST_HAVE_NAMED_FIELD[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS";
4566 static const char __pyx_k_V40_MISSING_ANGLE_BRACKETS_Forma[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets";
4567 static const char __pyx_k_ZERO_FOR_NON_FLAG_FIELD_number_s[] = "ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'";
4568 static const char __pyx_k_ZERO_LENGTH_ALLELE_Found_zero_le[] = "ZERO_LENGTH_ALLELE:Found zero-length allele";
4569 static const char __pyx_k_id_numbertype_number_type_descri[] = "id numbertype number type description missingvalue";
4570 static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__";
4571 static const char __pyx_k_V40_FORMAT_MUST_HAVE_NAMED_FIELD_2[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields";
4572 /* #### Code section: decls ### */
4573 static int __pyx_pf_7cpython_5array_5array___getbuffer__(arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info, CYTHON_UNUSED int __pyx_v_flags); /* proto */
4574 static void __pyx_pf_7cpython_5array_5array_2__releasebuffer__(CYTHON_UNUSED arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
4575 static PyObject *__pyx_pf_5pysam_7libcvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_fa); /* proto */
4576 static PyObject *__pyx_pf_5pysam_7libcvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string); /* proto */
4577 static int __pyx_pf_5pysam_7libcvcf_9VCFRecord___init__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */
4578 static int __pyx_pf_5pysam_7libcvcf_9VCFRecord_2__cinit__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */
4579 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_4error(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */
4580 static Py_ssize_t __pyx_pf_5pysam_7libcvcf_9VCFRecord_6__len__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self); /* proto */
4581 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_6contig___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self); /* proto */
4582 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_3pos___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self); /* proto */
4583 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_2id___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self); /* proto */
4584 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_3ref___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self); /* proto */
4585 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_3alt___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self); /* proto */
4586 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_4qual___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self); /* proto */
4587 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_6filter___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self); /* proto */
4588 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_4info___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self); /* proto */
4589 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_6format___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self); /* proto */
4590 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_7samples___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self); /* proto */
4591 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_8__getitem__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_key); /* proto */
4592 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_10__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self); /* proto */
4593 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_12__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
4594 static int __pyx_pf_5pysam_7libcvcf_11asVCFRecord___init__(struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v_vcffile); /* proto */
4595 static PyObject *__pyx_pf_5pysam_7libcvcf_11asVCFRecord_2__reduce_cython__(struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *__pyx_v_self); /* proto */
4596 static PyObject *__pyx_pf_5pysam_7libcvcf_11asVCFRecord_4__setstate_cython__(struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */
4597 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v__copy, PyObject *__pyx_v_reference, PyObject *__pyx_v_regions, PyObject *__pyx_v_lines, PyObject *__pyx_v_leftalign); /* proto */
4598 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */
4599 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_format, PyObject *__pyx_v_filter); /* proto */
4600 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fmt, PyObject *__pyx_v_filter); /* proto */
4601 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_alt); /* proto */
4602 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_key, PyObject *__pyx_v_data, PyObject *__pyx_v_line); /* proto */
4603 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_data, PyObject *__pyx_v_format, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_separator); /* proto */
4604 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
4605 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */
4606 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
4607 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */
4608 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
4609 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_GTstring); /* proto */
4610 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_GTdata); /* proto */
4611 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_line); /* proto */
4612 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_pos); /* proto */
4613 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_lineparse); /* proto */
4614 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_data); /* proto */
4615 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
4616 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_stream); /* proto */
4617 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
4618 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_samples); /* proto */
4619 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
4620 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_header); /* proto */
4621 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
4622 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_info); /* proto */
4623 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
4624 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format); /* proto */
4625 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
4626 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filter); /* proto */
4627 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_version); /* proto */
4628 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_regions); /* proto */
4629 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_ref); /* proto */
4630 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */
4631 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */
4632 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
4633 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_datagenerator); /* proto */
4634 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
4635 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_pos1, PyObject *__pyx_v_ref1, PyObject *__pyx_v_alt1, PyObject *__pyx_v_pos2, PyObject *__pyx_v_ref2, PyObject *__pyx_v_alt2); /* proto */
4636 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_encoding); /* proto */
4637 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_81__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
4638 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_83close(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
4639 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_85fetch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
4640 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_87validate(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_record); /* proto */
4641 static PyObject *__pyx_pf_5pysam_7libcvcf_4__pyx_unpickle_asVCFRecord(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */
4642 static PyObject *__pyx_tp_new_5pysam_7libcvcf_VCFRecord(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
4643 static PyObject *__pyx_tp_new_5pysam_7libcvcf_asVCFRecord(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
4644 static PyObject *__pyx_tp_new_5pysam_7libcvcf___pyx_scope_struct___parse(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
4645 /* #### Code section: late_includes ### */
4646 /* #### Code section: module_state ### */
4647 typedef struct {
4648 PyObject *__pyx_d;
4649 PyObject *__pyx_b;
4650 PyObject *__pyx_cython_runtime;
4651 PyObject *__pyx_empty_tuple;
4652 PyObject *__pyx_empty_bytes;
4653 PyObject *__pyx_empty_unicode;
4654 #ifdef __Pyx_CyFunction_USED
4655 PyTypeObject *__pyx_CyFunctionType;
4656 #endif
4657 #ifdef __Pyx_FusedFunction_USED
4658 PyTypeObject *__pyx_FusedFunctionType;
4659 #endif
4660 #ifdef __Pyx_Generator_USED
4661 PyTypeObject *__pyx_GeneratorType;
4662 #endif
4663 #ifdef __Pyx_IterableCoroutine_USED
4664 PyTypeObject *__pyx_IterableCoroutineType;
4665 #endif
4666 #ifdef __Pyx_Coroutine_USED
4667 PyTypeObject *__pyx_CoroutineAwaitType;
4668 #endif
4669 #ifdef __Pyx_Coroutine_USED
4670 PyTypeObject *__pyx_CoroutineType;
4671 #endif
4672 #if CYTHON_USE_MODULE_STATE
4673 #endif
4674 #if CYTHON_USE_MODULE_STATE
4675 #endif
4676 #if CYTHON_USE_MODULE_STATE
4677 #endif
4678 #if CYTHON_USE_MODULE_STATE
4679 #endif
4680 #if CYTHON_USE_MODULE_STATE
4681 #endif
4682 #if CYTHON_USE_MODULE_STATE
4683 #endif
4684 PyTypeObject *__pyx_ptype_5pysam_10libchtslib_HTSFile;
4685 #if CYTHON_USE_MODULE_STATE
4686 #endif
4687 PyTypeObject *__pyx_ptype_5pysam_9libctabix_tabix_file_iterator;
4688 PyTypeObject *__pyx_ptype_5pysam_9libctabix_TabixFile;
4689 PyTypeObject *__pyx_ptype_5pysam_9libctabix_Parser;
4690 PyTypeObject *__pyx_ptype_5pysam_9libctabix_asTuple;
4691 PyTypeObject *__pyx_ptype_5pysam_9libctabix_asGTF;
4692 PyTypeObject *__pyx_ptype_5pysam_9libctabix_asGFF3;
4693 PyTypeObject *__pyx_ptype_5pysam_9libctabix_asBed;
4694 PyTypeObject *__pyx_ptype_5pysam_9libctabix_asVCF;
4695 PyTypeObject *__pyx_ptype_5pysam_9libctabix_TabixIterator;
4696 PyTypeObject *__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed;
4697 PyTypeObject *__pyx_ptype_5pysam_9libctabix_GZIterator;
4698 PyTypeObject *__pyx_ptype_5pysam_9libctabix_GZIteratorHead;
4699 PyTypeObject *__pyx_ptype_5pysam_9libctabix_GZIteratorParsed;
4700 PyTypeObject *__pyx_ptype_5pysam_9libctabix_Tabixfile;
4701 #if CYTHON_USE_MODULE_STATE
4702 #endif
4703 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_TupleProxy;
4704 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator;
4705 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy;
4706 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_GTFProxy;
4707 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy;
4708 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_BedProxy;
4709 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_VCFProxy;
4710 #if CYTHON_USE_MODULE_STATE
4711 #endif
4712 #if CYTHON_USE_MODULE_STATE
4713 #endif
4714 #if CYTHON_USE_MODULE_STATE
4715 #endif
4716 #if CYTHON_USE_MODULE_STATE
4717 #endif
4718 PyTypeObject *__pyx_ptype_7cpython_4type_type;
4719 #if CYTHON_USE_MODULE_STATE
4720 #endif
4721 #if CYTHON_USE_MODULE_STATE
4722 #endif
4723 #if CYTHON_USE_MODULE_STATE
4724 #endif
4725 #if CYTHON_USE_MODULE_STATE
4726 #endif
4727 #if CYTHON_USE_MODULE_STATE
4728 #endif
4729 #if CYTHON_USE_MODULE_STATE
4730 #endif
4731 #if CYTHON_USE_MODULE_STATE
4732 #endif
4733 #if CYTHON_USE_MODULE_STATE
4734 #endif
4735 #if CYTHON_USE_MODULE_STATE
4736 #endif
4737 #if CYTHON_USE_MODULE_STATE
4738 #endif
4739 #if CYTHON_USE_MODULE_STATE
4740 #endif
4741 #if CYTHON_USE_MODULE_STATE
4742 #endif
4743 #if CYTHON_USE_MODULE_STATE
4744 #endif
4745 #if CYTHON_USE_MODULE_STATE
4746 #endif
4747 PyTypeObject *__pyx_ptype_7cpython_4bool_bool;
4748 #if CYTHON_USE_MODULE_STATE
4749 #endif
4750 #if CYTHON_USE_MODULE_STATE
4751 #endif
4752 #if CYTHON_USE_MODULE_STATE
4753 #endif
4754 #if CYTHON_USE_MODULE_STATE
4755 #endif
4756 PyTypeObject *__pyx_ptype_7cpython_7complex_complex;
4757 #if CYTHON_USE_MODULE_STATE
4758 #endif
4759 #if CYTHON_USE_MODULE_STATE
4760 #endif
4761 #if CYTHON_USE_MODULE_STATE
4762 #endif
4763 #if CYTHON_USE_MODULE_STATE
4764 #endif
4765 #if CYTHON_USE_MODULE_STATE
4766 #endif
4767 #if CYTHON_USE_MODULE_STATE
4768 #endif
4769 #if CYTHON_USE_MODULE_STATE
4770 #endif
4771 #if CYTHON_USE_MODULE_STATE
4772 #endif
4773 #if CYTHON_USE_MODULE_STATE
4774 #endif
4775 #if CYTHON_USE_MODULE_STATE
4776 #endif
4777 #if CYTHON_USE_MODULE_STATE
4778 #endif
4779 #if CYTHON_USE_MODULE_STATE
4780 #endif
4781 #if CYTHON_USE_MODULE_STATE
4782 #endif
4783 #if CYTHON_USE_MODULE_STATE
4784 #endif
4785 #if CYTHON_USE_MODULE_STATE
4786 #endif
4787 #if CYTHON_USE_MODULE_STATE
4788 #endif
4789 #if CYTHON_USE_MODULE_STATE
4790 #endif
4791 #if CYTHON_USE_MODULE_STATE
4792 #endif
4793 #if CYTHON_USE_MODULE_STATE
4794 #endif
4795 #if CYTHON_USE_MODULE_STATE
4796 #endif
4797 #if CYTHON_USE_MODULE_STATE
4798 #endif
4799 #if CYTHON_USE_MODULE_STATE
4800 #endif
4801 PyTypeObject *__pyx_ptype_7cpython_5array_array;
4802 #if CYTHON_USE_MODULE_STATE
4803 #endif
4804 #if CYTHON_USE_MODULE_STATE
4805 PyObject *__pyx_type_5pysam_7libcvcf_VCFRecord;
4806 PyObject *__pyx_type_5pysam_7libcvcf_asVCFRecord;
4807 PyObject *__pyx_type_5pysam_7libcvcf___pyx_scope_struct___parse;
4808 #endif
4809 PyTypeObject *__pyx_ptype_5pysam_7libcvcf_VCFRecord;
4810 PyTypeObject *__pyx_ptype_5pysam_7libcvcf_asVCFRecord;
4811 PyTypeObject *__pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse;
4812 PyObject *__pyx_kp_u_;
4813 PyObject *__pyx_kp_b_0;
4814 PyObject *__pyx_kp_u_0;
4815 PyObject *__pyx_n_u_A;
4816 PyObject *__pyx_n_u_ACGTN;
4817 PyObject *__pyx_kp_u_ACGTN_2;
4818 PyObject *__pyx_n_u_ALT;
4819 PyObject *__pyx_n_s_AssertionError;
4820 PyObject *__pyx_n_s_BADLY_FORMATTED_FORMAT_STRING;
4821 PyObject *__pyx_kp_u_BADLY_FORMATTED_FORMAT_STRING_Fo;
4822 PyObject *__pyx_n_s_BADLY_FORMATTED_HEADING;
4823 PyObject *__pyx_kp_u_BADLY_FORMATTED_HEADING_Did_not;
4824 PyObject *__pyx_kp_u_BAD_CHR_TAG_Error_calculating_ch;
4825 PyObject *__pyx_n_s_BAD_GENOTYPE;
4826 PyObject *__pyx_kp_u_BAD_GENOTYPE_Cannot_parse_genoty;
4827 PyObject *__pyx_n_s_BAD_NUMBER_OF_COLUMNS;
4828 PyObject *__pyx_kp_u_BAD_NUMBER_OF_COLUMNS_Wrong_numb;
4829 PyObject *__pyx_n_s_BAD_NUMBER_OF_PARAMETERS;
4830 PyObject *__pyx_kp_u_BAD_NUMBER_OF_PARAMETERS_Found_u;
4831 PyObject *__pyx_n_s_BAD_NUMBER_OF_VALUES;
4832 PyObject *__pyx_kp_u_BAD_NUMBER_OF_VALUES_Found_too_m;
4833 PyObject *__pyx_n_u_CHROM;
4834 PyObject *__pyx_kp_u_Can_only_handle_v3_3_and_v4_0_VC;
4835 PyObject *__pyx_n_u_Character;
4836 PyObject *__pyx_kp_u_Conditional_genotype_quality;
4837 PyObject *__pyx_n_u_D;
4838 PyObject *__pyx_n_u_DP;
4839 PyObject *__pyx_kp_u_Description;
4840 PyObject *__pyx_n_u_Description_2;
4841 PyObject *__pyx_kp_u_Don_t_understand_region_string_s;
4842 PyObject *__pyx_n_u_EC;
4843 PyObject *__pyx_n_s_ERROR_FLAG_HAS_VALUE;
4844 PyObject *__pyx_kp_u_ERROR_FLAG_HAS_VALUE_Flag_fields;
4845 PyObject *__pyx_n_s_ERROR_FORMAT_NOT_CHAR;
4846 PyObject *__pyx_kp_u_ERROR_FORMAT_NOT_CHAR_Eexpected;
4847 PyObject *__pyx_n_s_ERROR_FORMAT_NOT_INTEGER;
4848 PyObject *__pyx_kp_u_ERROR_FORMAT_NOT_INTEGER_Expecte;
4849 PyObject *__pyx_n_s_ERROR_FORMAT_NOT_NUMERICAL;
4850 PyObject *__pyx_kp_u_ERROR_FORMAT_NOT_NUMERICAL_Expec;
4851 PyObject *__pyx_n_s_ERROR_INFO_STRING;
4852 PyObject *__pyx_kp_u_ERROR_INFO_STRING_Error_while_pa;
4853 PyObject *__pyx_n_s_ERROR_TRAILING_DATA;
4854 PyObject *__pyx_kp_u_ERROR_TRAILING_DATA_Numerical_fi;
4855 PyObject *__pyx_n_s_ERROR_UNKNOWN_KEY;
4856 PyObject *__pyx_kp_u_ERROR_UNKNOWN_KEY_Unknown_key_s;
4857 PyObject *__pyx_n_u_Error;
4858 PyObject *__pyx_kp_u_Expected_alternate_allel_counts;
4859 PyObject *__pyx_n_u_FILTER;
4860 PyObject *__pyx_n_s_FILTER_NOT_DEFINED;
4861 PyObject *__pyx_kp_u_FILTER_NOT_DEFINED_Identifier_s;
4862 PyObject *__pyx_n_s_FORMAT;
4863 PyObject *__pyx_n_u_FORMAT;
4864 PyObject *__pyx_n_s_FORMAT_MISSING_QUOTES;
4865 PyObject *__pyx_kp_u_FORMAT_MISSING_QUOTES_Descriptio;
4866 PyObject *__pyx_n_s_FORMAT_NOT_DEFINED;
4867 PyObject *__pyx_kp_u_FORMAT_NOT_DEFINED_Identifier_s;
4868 PyObject *__pyx_n_u_FT;
4869 PyObject *__pyx_n_u_Flag;
4870 PyObject *__pyx_n_u_Float;
4871 PyObject *__pyx_n_u_G;
4872 PyObject *__pyx_n_u_GL;
4873 PyObject *__pyx_n_u_GLE;
4874 PyObject *__pyx_n_u_GP;
4875 PyObject *__pyx_n_u_GQ;
4876 PyObject *__pyx_n_u_GT;
4877 PyObject *__pyx_n_s_GTdata;
4878 PyObject *__pyx_n_s_GTstring;
4879 PyObject *__pyx_n_u_Genotype;
4880 PyObject *__pyx_kp_u_Genotype_Quality;
4881 PyObject *__pyx_kp_u_Genotype_likelihoods;
4882 PyObject *__pyx_kp_u_Genotype_posterior_probabilities;
4883 PyObject *__pyx_n_s_HEADING_NOT_SEPARATED_BY_TABS;
4884 PyObject *__pyx_kp_u_HEADING_NOT_SEPARATED_BY_TABS_He;
4885 PyObject *__pyx_n_u_HQ;
4886 PyObject *__pyx_kp_u_Haplotype_Quality;
4887 PyObject *__pyx_n_u_I;
4888 PyObject *__pyx_kp_u_ID;
4889 PyObject *__pyx_n_u_ID_2;
4890 PyObject *__pyx_n_u_INFO;
4891 PyObject *__pyx_kp_s_Incompatible_checksums_0x_x_vs_0;
4892 PyObject *__pyx_n_u_Integer;
4893 PyObject *__pyx_kp_u_Invalid_error_string_s;
4894 PyObject *__pyx_n_s_KeyError;
4895 PyObject *__pyx_n_s_MISSING_INDEL_ALLELE_REF_BASE;
4896 PyObject *__pyx_kp_u_MISSING_INDEL_ALLELE_REF_BASE_In;
4897 PyObject *__pyx_n_s_MISSING_REF;
4898 PyObject *__pyx_kp_u_MISSING_REF_Reference_allele_mis;
4899 PyObject *__pyx_n_u_MQ;
4900 PyObject *__pyx_n_s_MemoryError;
4901 PyObject *__pyx_n_u_N;
4902 PyObject *__pyx_n_s_NT_ALLELES;
4903 PyObject *__pyx_n_s_NT_GENOTYPES;
4904 PyObject *__pyx_n_s_NT_NR_ALLELES;
4905 PyObject *__pyx_n_s_NT_NUMBER;
4906 PyObject *__pyx_n_s_NT_PHASED_GENOTYPES;
4907 PyObject *__pyx_n_s_NT_UNKNOWN;
4908 PyObject *__pyx_n_s_NotImplementedError;
4909 PyObject *__pyx_kp_u_Number;
4910 PyObject *__pyx_n_u_Number_2;
4911 PyObject *__pyx_n_b_PASS;
4912 PyObject *__pyx_n_u_PASS;
4913 PyObject *__pyx_n_u_PL;
4914 PyObject *__pyx_n_u_POS;
4915 PyObject *__pyx_n_s_POS_NOT_NUMERICAL;
4916 PyObject *__pyx_kp_u_POS_NOT_NUMERICAL_Position_colum;
4917 PyObject *__pyx_n_s_POS_NOT_POSITIVE;
4918 PyObject *__pyx_kp_u_POS_NOT_POSITIVE_Position_field;
4919 PyObject *__pyx_n_u_PQ;
4920 PyObject *__pyx_n_u_PS;
4921 PyObject *__pyx_kp_u_Phase_set;
4922 PyObject *__pyx_kp_u_Phasing_quality;
4923 PyObject *__pyx_kp_u_Phred_scaled_genotype_likelihood;
4924 PyObject *__pyx_n_s_PickleError;
4925 PyObject *__pyx_n_u_QUAL;
4926 PyObject *__pyx_n_s_QUAL_NOT_NUMERICAL;
4927 PyObject *__pyx_kp_u_QUAL_NOT_NUMERICAL_Quality_field;
4928 PyObject *__pyx_n_u_REF;
4929 PyObject *__pyx_kp_u_RMS_mapping_quality;
4930 PyObject *__pyx_kp_u_Read_depth_at_this_position_for;
4931 PyObject *__pyx_kp_u_Required_key_s_not_found_in_data;
4932 PyObject *__pyx_kp_u_Sample_Genotype_Filter;
4933 PyObject *__pyx_n_s_StopIteration;
4934 PyObject *__pyx_n_u_String;
4935 PyObject *__pyx_n_s_Tabixfile;
4936 PyObject *__pyx_kp_u_Type;
4937 PyObject *__pyx_n_s_TypeError;
4938 PyObject *__pyx_n_u_Type_2;
4939 PyObject *__pyx_n_s_UNKNOWN_CHAR_IN_REF;
4940 PyObject *__pyx_kp_u_UNKNOWN_CHAR_IN_REF_Unknown_char;
4941 PyObject *__pyx_n_s_UNKNOWN_FORMAT_STRING;
4942 PyObject *__pyx_kp_u_UNKNOWN_FORMAT_STRING_Unknown_fi;
4943 PyObject *__pyx_kp_u_Undefined_tag;
4944 PyObject *__pyx_kp_u_Unknown_number_type_encountered;
4945 PyObject *__pyx_n_s_V33_BAD_ALLELE;
4946 PyObject *__pyx_kp_u_V33_BAD_ALLELE_Cannot_interpret;
4947 PyObject *__pyx_n_s_V33_BAD_REF;
4948 PyObject *__pyx_kp_u_V33_BAD_REF_Reference_should_be;
4949 PyObject *__pyx_n_s_V33_UNMATCHED_DELETION;
4950 PyObject *__pyx_kp_u_V33_UNMATCHED_DELETION_Deleted_s;
4951 PyObject *__pyx_n_s_V40_BAD_ALLELE;
4952 PyObject *__pyx_kp_u_V40_BAD_ALLELE_Bad_allele_found;
4953 PyObject *__pyx_n_s_V40_FORMAT_MUST_HAVE_NAMED_FIELD;
4954 PyObject *__pyx_kp_u_V40_FORMAT_MUST_HAVE_NAMED_FIELD_2;
4955 PyObject *__pyx_n_s_V40_MISSING_ANGLE_BRACKETS;
4956 PyObject *__pyx_kp_u_V40_MISSING_ANGLE_BRACKETS_Forma;
4957 PyObject *__pyx_n_s_VCF;
4958 PyObject *__pyx_n_u_VCF;
4959 PyObject *__pyx_n_s_VCFRecord;
4960 PyObject *__pyx_n_u_VCFRecord;
4961 PyObject *__pyx_n_s_VCFRecord___reduce_cython;
4962 PyObject *__pyx_n_s_VCFRecord___setstate_cython;
4963 PyObject *__pyx_n_s_VCFRecord_error;
4964 PyObject *__pyx_n_s_VCF___del;
4965 PyObject *__pyx_n_s_VCF___init;
4966 PyObject *__pyx_n_s_VCF__add_definition;
4967 PyObject *__pyx_n_s_VCF__parse;
4968 PyObject *__pyx_n_s_VCF__parse_header;
4969 PyObject *__pyx_n_s_VCF_close;
4970 PyObject *__pyx_n_s_VCF_compare_calls;
4971 PyObject *__pyx_n_s_VCF_connect;
4972 PyObject *__pyx_n_s_VCF_convertGT;
4973 PyObject *__pyx_n_s_VCF_convertGTback;
4974 PyObject *__pyx_n_s_VCF_enter_default_format;
4975 PyObject *__pyx_n_s_VCF_error;
4976 PyObject *__pyx_n_s_VCF_fetch;
4977 PyObject *__pyx_n_s_VCF_format_format;
4978 PyObject *__pyx_n_s_VCF_format_formatdata;
4979 PyObject *__pyx_n_s_VCF_get_expected;
4980 PyObject *__pyx_n_s_VCF_getfilter;
4981 PyObject *__pyx_n_s_VCF_getformat;
4982 PyObject *__pyx_n_s_VCF_getheader;
4983 PyObject *__pyx_n_s_VCF_getinfo;
4984 PyObject *__pyx_n_s_VCF_getsamples;
4985 PyObject *__pyx_n_s_VCF_ignoreerror;
4986 PyObject *__pyx_n_s_VCF_inregion;
4987 PyObject *__pyx_n_s_VCF_parse;
4988 PyObject *__pyx_n_s_VCF_parse_data;
4989 PyObject *__pyx_n_s_VCF_parse_format;
4990 PyObject *__pyx_n_s_VCF_parse_formatdata;
4991 PyObject *__pyx_n_s_VCF_parse_header;
4992 PyObject *__pyx_n_s_VCF_parse_heading;
4993 PyObject *__pyx_kp_u_VCF_says;
4994 PyObject *__pyx_n_s_VCF_setfilter;
4995 PyObject *__pyx_n_s_VCF_setformat;
4996 PyObject *__pyx_n_s_VCF_setheader;
4997 PyObject *__pyx_n_s_VCF_setinfo;
4998 PyObject *__pyx_n_s_VCF_setreference;
4999 PyObject *__pyx_n_s_VCF_setregions;
5000 PyObject *__pyx_n_s_VCF_setsamples;
5001 PyObject *__pyx_n_s_VCF_setversion;
5002 PyObject *__pyx_n_s_VCF_validate;
5003 PyObject *__pyx_n_s_VCF_warnerror;
5004 PyObject *__pyx_n_s_VCF_write;
5005 PyObject *__pyx_n_s_VCF_write_data;
5006 PyObject *__pyx_n_s_VCF_write_header;
5007 PyObject *__pyx_n_s_VCF_write_heading;
5008 PyObject *__pyx_n_s_VCF_writeheader;
5009 PyObject *__pyx_kp_u_VCFv3_3;
5010 PyObject *__pyx_kp_u_VCFv4_0;
5011 PyObject *__pyx_kp_u_VCFv4_1;
5012 PyObject *__pyx_kp_u_VCFv4_2;
5013 PyObject *__pyx_n_s_ValueError;
5014 PyObject *__pyx_n_s_WRONG_REF;
5015 PyObject *__pyx_kp_u_WRONG_REF_Wrong_reference_s;
5016 PyObject *__pyx_n_u_Warning;
5017 PyObject *__pyx_n_s_ZERO_FOR_NON_FLAG_FIELD;
5018 PyObject *__pyx_kp_u_ZERO_FOR_NON_FLAG_FIELD_number_s;
5019 PyObject *__pyx_n_s_ZERO_LENGTH_ALLELE;
5020 PyObject *__pyx_kp_u_ZERO_LENGTH_ALLELE_Found_zero_le;
5021 PyObject *__pyx_kp_u__10;
5022 PyObject *__pyx_kp_u__11;
5023 PyObject *__pyx_kp_u__12;
5024 PyObject *__pyx_kp_u__13;
5025 PyObject *__pyx_n_s__139;
5026 PyObject *__pyx_kp_u__14;
5027 PyObject *__pyx_kp_u__15;
5028 PyObject *__pyx_kp_u__16;
5029 PyObject *__pyx_kp_u__19;
5030 PyObject *__pyx_kp_u__2;
5031 PyObject *__pyx_kp_u__23;
5032 PyObject *__pyx_kp_u__24;
5033 PyObject *__pyx_kp_u__25;
5034 PyObject *__pyx_kp_u__27;
5035 PyObject *__pyx_kp_u__3;
5036 PyObject *__pyx_n_s__33;
5037 PyObject *__pyx_kp_u__34;
5038 PyObject *__pyx_kp_u__4;
5039 PyObject *__pyx_kp_b__5;
5040 PyObject *__pyx_kp_u__5;
5041 PyObject *__pyx_kp_u__6;
5042 PyObject *__pyx_kp_u__7;
5043 PyObject *__pyx_kp_u__8;
5044 PyObject *__pyx_n_s_a;
5045 PyObject *__pyx_n_s_add;
5046 PyObject *__pyx_n_s_add_definition;
5047 PyObject *__pyx_n_s_addn;
5048 PyObject *__pyx_n_s_addns;
5049 PyObject *__pyx_n_s_all;
5050 PyObject *__pyx_n_s_allele;
5051 PyObject *__pyx_n_s_alleleRegEx;
5052 PyObject *__pyx_kp_u_alleles;
5053 PyObject *__pyx_n_s_alt;
5054 PyObject *__pyx_n_u_alt;
5055 PyObject *__pyx_n_s_alt1;
5056 PyObject *__pyx_n_s_alt2;
5057 PyObject *__pyx_n_s_append;
5058 PyObject *__pyx_n_s_args;
5059 PyObject *__pyx_n_s_asVCFRecord;
5060 PyObject *__pyx_n_s_asVCFRecord___reduce_cython;
5061 PyObject *__pyx_n_s_asVCFRecord___setstate_cython;
5062 PyObject *__pyx_n_u_ascii;
5063 PyObject *__pyx_n_s_asyncio_coroutines;
5064 PyObject *__pyx_n_s_bisect;
5065 PyObject *__pyx_n_s_blurp;
5066 PyObject *__pyx_n_s_c;
5067 PyObject *__pyx_n_s_chrom;
5068 PyObject *__pyx_n_u_chrom;
5069 PyObject *__pyx_n_s_class_getitem;
5070 PyObject *__pyx_n_s_cline_in_traceback;
5071 PyObject *__pyx_n_s_close;
5072 PyObject *__pyx_n_s_collections;
5073 PyObject *__pyx_n_s_cols;
5074 PyObject *__pyx_n_s_compare_calls;
5075 PyObject *__pyx_n_s_compile;
5076 PyObject *__pyx_n_s_connect;
5077 PyObject *__pyx_n_s_convertGT;
5078 PyObject *__pyx_n_s_convertGTback;
5079 PyObject *__pyx_n_s_copy;
5080 PyObject *__pyx_n_s_copy_2;
5081 PyObject *__pyx_n_s_d;
5082 PyObject *__pyx_n_s_data;
5083 PyObject *__pyx_n_s_datagenerator;
5084 PyObject *__pyx_n_s_deepcopy;
5085 PyObject *__pyx_n_s_defaultdict;
5086 PyObject *__pyx_n_s_del;
5087 PyObject *__pyx_kp_u_deletion_is;
5088 PyObject *__pyx_n_u_descr;
5089 PyObject *__pyx_n_s_description;
5090 PyObject *__pyx_n_s_dict;
5091 PyObject *__pyx_n_s_dict_2;
5092 PyObject *__pyx_n_s_dict_3;
5093 PyObject *__pyx_kp_u_disable;
5094 PyObject *__pyx_n_s_doc;
5095 PyObject *__pyx_n_s_elts;
5096 PyObject *__pyx_kp_u_enable;
5097 PyObject *__pyx_n_s_encoding;
5098 PyObject *__pyx_n_s_end;
5099 PyObject *__pyx_n_s_endswith;
5100 PyObject *__pyx_n_s_enter_default_format;
5101 PyObject *__pyx_n_s_enumerate;
5102 PyObject *__pyx_n_s_err;
5103 PyObject *__pyx_n_s_error;
5104 PyObject *__pyx_n_s_errorlabel;
5105 PyObject *__pyx_n_s_errors;
5106 PyObject *__pyx_n_s_errorstring;
5107 PyObject *__pyx_n_s_errwarn;
5108 PyObject *__pyx_kp_u_expected;
5109 PyObject *__pyx_kp_u_expected_2;
5110 PyObject *__pyx_kp_u_expected_3;
5111 PyObject *__pyx_n_s_expected_4;
5112 PyObject *__pyx_n_s_f;
5113 PyObject *__pyx_n_s_fa;
5114 PyObject *__pyx_n_s_faref;
5115 PyObject *__pyx_n_s_faref_leftflank;
5116 PyObject *__pyx_n_s_fetch;
5117 PyObject *__pyx_n_u_fileformat;
5118 PyObject *__pyx_kp_u_fileformat_VCFv;
5119 PyObject *__pyx_n_s_filename;
5120 PyObject *__pyx_n_s_filter;
5121 PyObject *__pyx_n_s_filter_2;
5122 PyObject *__pyx_n_u_filter_2;
5123 PyObject *__pyx_n_s_find;
5124 PyObject *__pyx_n_s_first;
5125 PyObject *__pyx_n_s_fmt;
5126 PyObject *__pyx_kp_u_for;
5127 PyObject *__pyx_n_s_format;
5128 PyObject *__pyx_n_u_format;
5129 PyObject *__pyx_n_s_format_2;
5130 PyObject *__pyx_n_s_format_format;
5131 PyObject *__pyx_n_s_format_formatdata;
5132 PyObject *__pyx_n_s_formatdict;
5133 PyObject *__pyx_kp_u_found;
5134 PyObject *__pyx_kp_u_gc;
5135 PyObject *__pyx_kp_u_genotypes;
5136 PyObject *__pyx_n_s_get;
5137 PyObject *__pyx_n_s_get_expected;
5138 PyObject *__pyx_n_s_get_sequence;
5139 PyObject *__pyx_n_s_getfilter;
5140 PyObject *__pyx_n_s_getformat;
5141 PyObject *__pyx_n_s_getheader;
5142 PyObject *__pyx_n_s_getinfo;
5143 PyObject *__pyx_n_s_getsamples;
5144 PyObject *__pyx_n_s_getstate;
5145 PyObject *__pyx_kp_u_got;
5146 PyObject *__pyx_n_s_gts;
5147 PyObject *__pyx_n_s_gtsRegEx;
5148 PyObject *__pyx_n_s_have_deletions;
5149 PyObject *__pyx_n_s_header;
5150 PyObject *__pyx_n_s_header_2;
5151 PyObject *__pyx_n_s_headings;
5152 PyObject *__pyx_n_s_i;
5153 PyObject *__pyx_kp_u_id;
5154 PyObject *__pyx_n_s_id_2;
5155 PyObject *__pyx_n_u_id_2;
5156 PyObject *__pyx_kp_u_id_numbertype_number_type_descri;
5157 PyObject *__pyx_n_s_idx;
5158 PyObject *__pyx_n_s_ielts;
5159 PyObject *__pyx_n_s_ignored_errors;
5160 PyObject *__pyx_n_s_ignoreerror;
5161 PyObject *__pyx_n_s_import;
5162 PyObject *__pyx_kp_u_in_line;
5163 PyObject *__pyx_n_s_info;
5164 PyObject *__pyx_n_s_info_2;
5165 PyObject *__pyx_n_u_info_2;
5166 PyObject *__pyx_n_s_init;
5167 PyObject *__pyx_n_s_init_subclass;
5168 PyObject *__pyx_n_s_initializing;
5169 PyObject *__pyx_n_s_inregion;
5170 PyObject *__pyx_n_s_is_coroutine;
5171 PyObject *__pyx_kp_u_isenabled;
5172 PyObject *__pyx_n_s_itemgetter;
5173 PyObject *__pyx_n_s_itervalues;
5174 PyObject *__pyx_n_s_join;
5175 PyObject *__pyx_n_s_k;
5176 PyObject *__pyx_n_s_key;
5177 PyObject *__pyx_n_s_keys;
5178 PyObject *__pyx_n_s_l;
5179 PyObject *__pyx_n_s_label;
5180 PyObject *__pyx_n_s_last;
5181 PyObject *__pyx_n_s_last_line;
5182 PyObject *__pyx_n_s_left;
5183 PyObject *__pyx_n_s_leftalign;
5184 PyObject *__pyx_n_s_leftalign_2;
5185 PyObject *__pyx_n_s_line;
5186 PyObject *__pyx_n_s_line_2;
5187 PyObject *__pyx_n_s_lineno;
5188 PyObject *__pyx_n_s_lineparse;
5189 PyObject *__pyx_n_s_lines;
5190 PyObject *__pyx_n_s_lines_2;
5191 PyObject *__pyx_n_s_longest;
5192 PyObject *__pyx_n_s_main;
5193 PyObject *__pyx_n_s_map;
5194 PyObject *__pyx_n_s_match;
5195 PyObject *__pyx_n_s_metaclass;
5196 PyObject *__pyx_n_s_min;
5197 PyObject *__pyx_n_u_missing;
5198 PyObject *__pyx_n_s_missingvalue;
5199 PyObject *__pyx_n_s_module;
5200 PyObject *__pyx_n_s_movable;
5201 PyObject *__pyx_n_s_mro_entries;
5202 PyObject *__pyx_n_s_n;
5203 PyObject *__pyx_n_s_na;
5204 PyObject *__pyx_n_s_name;
5205 PyObject *__pyx_n_s_namedtuple;
5206 PyObject *__pyx_kp_u_needs_to_be_checked;
5207 PyObject *__pyx_n_s_new;
5208 PyObject *__pyx_n_s_newalts;
5209 PyObject *__pyx_n_s_nmb;
5210 PyObject *__pyx_kp_s_no_default___reduce___due_to_non;
5211 PyObject *__pyx_kp_u_nonref_alleles;
5212 PyObject *__pyx_n_s_number;
5213 PyObject *__pyx_n_u_number;
5214 PyObject *__pyx_n_s_numbertype;
5215 PyObject *__pyx_n_s_object;
5216 PyObject *__pyx_n_s_operator;
5217 PyObject *__pyx_n_s_opt;
5218 PyObject *__pyx_kp_u_output;
5219 PyObject *__pyx_n_s_output_2;
5220 PyObject *__pyx_kp_u_parameters_got;
5221 PyObject *__pyx_n_s_parse;
5222 PyObject *__pyx_n_s_parse_2;
5223 PyObject *__pyx_n_s_parse_data;
5224 PyObject *__pyx_n_s_parse_format;
5225 PyObject *__pyx_n_s_parse_formatdata;
5226 PyObject *__pyx_n_s_parse_header;
5227 PyObject *__pyx_n_s_parse_header_2;
5228 PyObject *__pyx_n_s_parse_heading;
5229 PyObject *__pyx_n_s_parse_regions;
5230 PyObject *__pyx_n_s_parser;
5231 PyObject *__pyx_kp_u_phased_genotypes;
5232 PyObject *__pyx_n_s_pickle;
5233 PyObject *__pyx_n_s_pos;
5234 PyObject *__pyx_n_u_pos;
5235 PyObject *__pyx_n_s_pos1;
5236 PyObject *__pyx_n_s_pos2;
5237 PyObject *__pyx_n_s_prepare;
5238 PyObject *__pyx_n_s_pysam;
5239 PyObject *__pyx_n_s_pysam_libcvcf;
5240 PyObject *__pyx_kp_s_pysam_libcvcf_pyx;
5241 PyObject *__pyx_n_s_pyx_PickleError;
5242 PyObject *__pyx_n_s_pyx_checksum;
5243 PyObject *__pyx_n_s_pyx_result;
5244 PyObject *__pyx_n_s_pyx_state;
5245 PyObject *__pyx_n_s_pyx_type;
5246 PyObject *__pyx_n_s_pyx_unpickle_asVCFRecord;
5247 PyObject *__pyx_n_s_pyx_vtable;
5248 PyObject *__pyx_n_s_qual;
5249 PyObject *__pyx_n_u_qual;
5250 PyObject *__pyx_n_s_qualname;
5251 PyObject *__pyx_n_s_r;
5252 PyObject *__pyx_n_s_range;
5253 PyObject *__pyx_n_s_re;
5254 PyObject *__pyx_n_s_record;
5255 PyObject *__pyx_n_s_reduce;
5256 PyObject *__pyx_n_s_reduce_cython;
5257 PyObject *__pyx_n_s_reduce_ex;
5258 PyObject *__pyx_n_s_ref;
5259 PyObject *__pyx_n_u_ref;
5260 PyObject *__pyx_n_s_ref1;
5261 PyObject *__pyx_n_s_ref2;
5262 PyObject *__pyx_n_s_reference;
5263 PyObject *__pyx_n_s_reference_2;
5264 PyObject *__pyx_kp_u_reference_is;
5265 PyObject *__pyx_kp_u_reference_is_2;
5266 PyObject *__pyx_n_s_region;
5267 PyObject *__pyx_n_s_regions;
5268 PyObject *__pyx_n_s_regions_2;
5269 PyObject *__pyx_n_s_replace;
5270 PyObject *__pyx_n_s_required;
5271 PyObject *__pyx_n_s_required_2;
5272 PyObject *__pyx_n_s_rest;
5273 PyObject *__pyx_n_s_result;
5274 PyObject *__pyx_n_s_s;
5275 PyObject *__pyx_n_s_sample;
5276 PyObject *__pyx_n_s_sample2column;
5277 PyObject *__pyx_n_s_samples;
5278 PyObject *__pyx_kp_u_samples_2;
5279 PyObject *__pyx_n_s_samples_3;
5280 PyObject *__pyx_n_s_sdata;
5281 PyObject *__pyx_n_s_self;
5282 PyObject *__pyx_n_s_send;
5283 PyObject *__pyx_n_s_separator;
5284 PyObject *__pyx_n_s_sequence;
5285 PyObject *__pyx_n_s_set_name;
5286 PyObject *__pyx_n_s_setfilter;
5287 PyObject *__pyx_n_s_setformat;
5288 PyObject *__pyx_n_s_setheader;
5289 PyObject *__pyx_n_s_setinfo;
5290 PyObject *__pyx_n_s_setreference;
5291 PyObject *__pyx_n_s_setregions;
5292 PyObject *__pyx_n_s_setsamples;
5293 PyObject *__pyx_n_s_setstate;
5294 PyObject *__pyx_n_s_setstate_cython;
5295 PyObject *__pyx_n_s_setversion;
5296 PyObject *__pyx_n_s_shortest;
5297 PyObject *__pyx_n_s_spec;
5298 PyObject *__pyx_n_s_split;
5299 PyObject *__pyx_n_s_start;
5300 PyObject *__pyx_n_s_startswith;
5301 PyObject *__pyx_n_s_state;
5302 PyObject *__pyx_kp_u_sth_entry_not_found;
5303 PyObject *__pyx_n_s_stream;
5304 PyObject *__pyx_n_s_string;
5305 PyObject *__pyx_kp_s_stringsource;
5306 PyObject *__pyx_n_s_strip;
5307 PyObject *__pyx_n_s_super;
5308 PyObject *__pyx_n_s_sys;
5309 PyObject *__pyx_n_s_t;
5310 PyObject *__pyx_n_s_tabixfile;
5311 PyObject *__pyx_n_s_test;
5312 PyObject *__pyx_n_s_throw;
5313 PyObject *__pyx_n_s_type;
5314 PyObject *__pyx_n_u_type;
5315 PyObject *__pyx_n_s_update;
5316 PyObject *__pyx_n_s_upper;
5317 PyObject *__pyx_n_s_use_setstate;
5318 PyObject *__pyx_n_s_v;
5319 PyObject *__pyx_n_s_validate;
5320 PyObject *__pyx_n_s_value;
5321 PyObject *__pyx_n_s_values;
5322 PyObject *__pyx_kp_u_values_in_element;
5323 PyObject *__pyx_n_s_var;
5324 PyObject *__pyx_n_s_vcf;
5325 PyObject *__pyx_n_s_vcffile;
5326 PyObject *__pyx_n_s_version;
5327 PyObject *__pyx_n_s_version_2;
5328 PyObject *__pyx_n_s_warn_errors;
5329 PyObject *__pyx_n_s_warnerror;
5330 PyObject *__pyx_n_s_write;
5331 PyObject *__pyx_n_s_write_data;
5332 PyObject *__pyx_n_s_write_header;
5333 PyObject *__pyx_n_s_write_heading;
5334 PyObject *__pyx_n_s_writeheader;
5335 PyObject *__pyx_n_s_x;
5336 PyObject *__pyx_n_s_y;
5337 PyObject *__pyx_n_s_zip;
5338 PyObject *__pyx_float_0_0;
5339 PyObject *__pyx_int_0;
5340 PyObject *__pyx_int_1;
5341 PyObject *__pyx_int_2;
5342 PyObject *__pyx_int_3;
5343 PyObject *__pyx_int_4;
5344 PyObject *__pyx_int_5;
5345 PyObject *__pyx_int_6;
5346 PyObject *__pyx_int_7;
5347 PyObject *__pyx_int_8;
5348 PyObject *__pyx_int_9;
5349 PyObject *__pyx_int_10;
5350 PyObject *__pyx_int_11;
5351 PyObject *__pyx_int_12;
5352 PyObject *__pyx_int_13;
5353 PyObject *__pyx_int_14;
5354 PyObject *__pyx_int_15;
5355 PyObject *__pyx_int_16;
5356 PyObject *__pyx_int_17;
5357 PyObject *__pyx_int_18;
5358 PyObject *__pyx_int_19;
5359 PyObject *__pyx_int_20;
5360 PyObject *__pyx_int_21;
5361 PyObject *__pyx_int_22;
5362 PyObject *__pyx_int_23;
5363 PyObject *__pyx_int_24;
5364 PyObject *__pyx_int_25;
5365 PyObject *__pyx_int_26;
5366 PyObject *__pyx_int_27;
5367 PyObject *__pyx_int_28;
5368 PyObject *__pyx_int_29;
5369 PyObject *__pyx_int_30;
5370 PyObject *__pyx_int_31;
5371 PyObject *__pyx_int_32;
5372 PyObject *__pyx_int_33;
5373 PyObject *__pyx_int_40;
5374 PyObject *__pyx_int_100;
5375 PyObject *__pyx_int_29527880;
5376 PyObject *__pyx_int_214161357;
5377 PyObject *__pyx_int_239654613;
5378 PyObject *__pyx_int_3000000000;
5379 PyObject *__pyx_int_neg_1;
5380 PyObject *__pyx_slice__9;
5381 PyObject *__pyx_slice__17;
5382 PyObject *__pyx_slice__18;
5383 PyObject *__pyx_slice__20;
5384 PyObject *__pyx_slice__26;
5385 PyObject *__pyx_slice__28;
5386 PyObject *__pyx_tuple__21;
5387 PyObject *__pyx_tuple__22;
5388 PyObject *__pyx_tuple__30;
5389 PyObject *__pyx_tuple__31;
5390 PyObject *__pyx_tuple__32;
5391 PyObject *__pyx_tuple__35;
5392 PyObject *__pyx_tuple__36;
5393 PyObject *__pyx_tuple__37;
5394 PyObject *__pyx_tuple__39;
5395 PyObject *__pyx_tuple__41;
5396 PyObject *__pyx_tuple__42;
5397 PyObject *__pyx_tuple__44;
5398 PyObject *__pyx_tuple__45;
5399 PyObject *__pyx_tuple__47;
5400 PyObject *__pyx_tuple__49;
5401 PyObject *__pyx_tuple__52;
5402 PyObject *__pyx_tuple__53;
5403 PyObject *__pyx_tuple__54;
5404 PyObject *__pyx_tuple__56;
5405 PyObject *__pyx_tuple__57;
5406 PyObject *__pyx_tuple__59;
5407 PyObject *__pyx_tuple__61;
5408 PyObject *__pyx_tuple__62;
5409 PyObject *__pyx_tuple__64;
5410 PyObject *__pyx_tuple__66;
5411 PyObject *__pyx_tuple__68;
5412 PyObject *__pyx_tuple__70;
5413 PyObject *__pyx_tuple__71;
5414 PyObject *__pyx_tuple__73;
5415 PyObject *__pyx_tuple__75;
5416 PyObject *__pyx_tuple__77;
5417 PyObject *__pyx_tuple__79;
5418 PyObject *__pyx_tuple__81;
5419 PyObject *__pyx_tuple__83;
5420 PyObject *__pyx_tuple__85;
5421 PyObject *__pyx_tuple__87;
5422 PyObject *__pyx_tuple__89;
5423 PyObject *__pyx_tuple__91;
5424 PyObject *__pyx_tuple__93;
5425 PyObject *__pyx_tuple__95;
5426 PyObject *__pyx_tuple__97;
5427 PyObject *__pyx_tuple__100;
5428 PyObject *__pyx_tuple__103;
5429 PyObject *__pyx_tuple__106;
5430 PyObject *__pyx_tuple__109;
5431 PyObject *__pyx_tuple__111;
5432 PyObject *__pyx_tuple__113;
5433 PyObject *__pyx_tuple__115;
5434 PyObject *__pyx_tuple__117;
5435 PyObject *__pyx_tuple__120;
5436 PyObject *__pyx_tuple__122;
5437 PyObject *__pyx_tuple__125;
5438 PyObject *__pyx_tuple__127;
5439 PyObject *__pyx_tuple__129;
5440 PyObject *__pyx_tuple__132;
5441 PyObject *__pyx_tuple__134;
5442 PyObject *__pyx_tuple__135;
5443 PyObject *__pyx_tuple__137;
5444 PyObject *__pyx_codeobj__29;
5445 PyObject *__pyx_codeobj__38;
5446 PyObject *__pyx_codeobj__40;
5447 PyObject *__pyx_codeobj__43;
5448 PyObject *__pyx_codeobj__46;
5449 PyObject *__pyx_codeobj__48;
5450 PyObject *__pyx_codeobj__50;
5451 PyObject *__pyx_codeobj__51;
5452 PyObject *__pyx_codeobj__55;
5453 PyObject *__pyx_codeobj__58;
5454 PyObject *__pyx_codeobj__60;
5455 PyObject *__pyx_codeobj__63;
5456 PyObject *__pyx_codeobj__65;
5457 PyObject *__pyx_codeobj__67;
5458 PyObject *__pyx_codeobj__69;
5459 PyObject *__pyx_codeobj__72;
5460 PyObject *__pyx_codeobj__74;
5461 PyObject *__pyx_codeobj__76;
5462 PyObject *__pyx_codeobj__78;
5463 PyObject *__pyx_codeobj__80;
5464 PyObject *__pyx_codeobj__82;
5465 PyObject *__pyx_codeobj__84;
5466 PyObject *__pyx_codeobj__86;
5467 PyObject *__pyx_codeobj__88;
5468 PyObject *__pyx_codeobj__90;
5469 PyObject *__pyx_codeobj__92;
5470 PyObject *__pyx_codeobj__94;
5471 PyObject *__pyx_codeobj__96;
5472 PyObject *__pyx_codeobj__98;
5473 PyObject *__pyx_codeobj__99;
5474 PyObject *__pyx_codeobj__101;
5475 PyObject *__pyx_codeobj__102;
5476 PyObject *__pyx_codeobj__104;
5477 PyObject *__pyx_codeobj__105;
5478 PyObject *__pyx_codeobj__107;
5479 PyObject *__pyx_codeobj__108;
5480 PyObject *__pyx_codeobj__110;
5481 PyObject *__pyx_codeobj__112;
5482 PyObject *__pyx_codeobj__114;
5483 PyObject *__pyx_codeobj__116;
5484 PyObject *__pyx_codeobj__118;
5485 PyObject *__pyx_codeobj__119;
5486 PyObject *__pyx_codeobj__121;
5487 PyObject *__pyx_codeobj__123;
5488 PyObject *__pyx_codeobj__124;
5489 PyObject *__pyx_codeobj__126;
5490 PyObject *__pyx_codeobj__128;
5491 PyObject *__pyx_codeobj__130;
5492 PyObject *__pyx_codeobj__131;
5493 PyObject *__pyx_codeobj__133;
5494 PyObject *__pyx_codeobj__136;
5495 PyObject *__pyx_codeobj__138;
5496 } __pyx_mstate;
5497
5498 #if CYTHON_USE_MODULE_STATE
5499 #ifdef __cplusplus
5500 namespace {
5501 extern struct PyModuleDef __pyx_moduledef;
5502 } /* anonymous namespace */
5503 #else
5504 static struct PyModuleDef __pyx_moduledef;
5505 #endif
5506
5507 #define __pyx_mstate(o) ((__pyx_mstate *)__Pyx_PyModule_GetState(o))
5508
5509 #define __pyx_mstate_global (__pyx_mstate(PyState_FindModule(&__pyx_moduledef)))
5510
5511 #define __pyx_m (PyState_FindModule(&__pyx_moduledef))
5512 #else
5513 static __pyx_mstate __pyx_mstate_global_static =
5514 #ifdef __cplusplus
5515 {};
5516 #else
5517 {0};
5518 #endif
5519 static __pyx_mstate *__pyx_mstate_global = &__pyx_mstate_global_static;
5520 #endif
5521 /* #### Code section: module_state_clear ### */
5522 #if CYTHON_USE_MODULE_STATE
5523 static int __pyx_m_clear(PyObject *m) {
5524 __pyx_mstate *clear_module_state = __pyx_mstate(m);
5525 if (!clear_module_state) return 0;
5526 Py_CLEAR(clear_module_state->__pyx_d);
5527 Py_CLEAR(clear_module_state->__pyx_b);
5528 Py_CLEAR(clear_module_state->__pyx_cython_runtime);
5529 Py_CLEAR(clear_module_state->__pyx_empty_tuple);
5530 Py_CLEAR(clear_module_state->__pyx_empty_bytes);
5531 Py_CLEAR(clear_module_state->__pyx_empty_unicode);
5532 #ifdef __Pyx_CyFunction_USED
5533 Py_CLEAR(clear_module_state->__pyx_CyFunctionType);
5534 #endif
5535 #ifdef __Pyx_FusedFunction_USED
5536 Py_CLEAR(clear_module_state->__pyx_FusedFunctionType);
5537 #endif
5538 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_10libchtslib_HTSFile);
5539 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_tabix_file_iterator);
5540 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_TabixFile);
5541 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_Parser);
5542 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asTuple);
5543 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asGTF);
5544 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asGFF3);
5545 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asBed);
5546 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asVCF);
5547 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_TabixIterator);
5548 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed);
5549 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_GZIterator);
5550 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_GZIteratorHead);
5551 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_GZIteratorParsed);
5552 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_Tabixfile);
5553 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_TupleProxy);
5554 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator);
5555 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy);
5556 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_GTFProxy);
5557 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy);
5558 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_BedProxy);
5559 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_VCFProxy);
5560 Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_4type_type);
5561 Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_4bool_bool);
5562 Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_7complex_complex);
5563 Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_5array_array);
5564 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_7libcvcf_VCFRecord);
5565 Py_CLEAR(clear_module_state->__pyx_type_5pysam_7libcvcf_VCFRecord);
5566 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_7libcvcf_asVCFRecord);
5567 Py_CLEAR(clear_module_state->__pyx_type_5pysam_7libcvcf_asVCFRecord);
5568 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse);
5569 Py_CLEAR(clear_module_state->__pyx_type_5pysam_7libcvcf___pyx_scope_struct___parse);
5570 Py_CLEAR(clear_module_state->__pyx_kp_u_);
5571 Py_CLEAR(clear_module_state->__pyx_kp_b_0);
5572 Py_CLEAR(clear_module_state->__pyx_kp_u_0);
5573 Py_CLEAR(clear_module_state->__pyx_n_u_A);
5574 Py_CLEAR(clear_module_state->__pyx_n_u_ACGTN);
5575 Py_CLEAR(clear_module_state->__pyx_kp_u_ACGTN_2);
5576 Py_CLEAR(clear_module_state->__pyx_n_u_ALT);
5577 Py_CLEAR(clear_module_state->__pyx_n_s_AssertionError);
5578 Py_CLEAR(clear_module_state->__pyx_n_s_BADLY_FORMATTED_FORMAT_STRING);
5579 Py_CLEAR(clear_module_state->__pyx_kp_u_BADLY_FORMATTED_FORMAT_STRING_Fo);
5580 Py_CLEAR(clear_module_state->__pyx_n_s_BADLY_FORMATTED_HEADING);
5581 Py_CLEAR(clear_module_state->__pyx_kp_u_BADLY_FORMATTED_HEADING_Did_not);
5582 Py_CLEAR(clear_module_state->__pyx_kp_u_BAD_CHR_TAG_Error_calculating_ch);
5583 Py_CLEAR(clear_module_state->__pyx_n_s_BAD_GENOTYPE);
5584 Py_CLEAR(clear_module_state->__pyx_kp_u_BAD_GENOTYPE_Cannot_parse_genoty);
5585 Py_CLEAR(clear_module_state->__pyx_n_s_BAD_NUMBER_OF_COLUMNS);
5586 Py_CLEAR(clear_module_state->__pyx_kp_u_BAD_NUMBER_OF_COLUMNS_Wrong_numb);
5587 Py_CLEAR(clear_module_state->__pyx_n_s_BAD_NUMBER_OF_PARAMETERS);
5588 Py_CLEAR(clear_module_state->__pyx_kp_u_BAD_NUMBER_OF_PARAMETERS_Found_u);
5589 Py_CLEAR(clear_module_state->__pyx_n_s_BAD_NUMBER_OF_VALUES);
5590 Py_CLEAR(clear_module_state->__pyx_kp_u_BAD_NUMBER_OF_VALUES_Found_too_m);
5591 Py_CLEAR(clear_module_state->__pyx_n_u_CHROM);
5592 Py_CLEAR(clear_module_state->__pyx_kp_u_Can_only_handle_v3_3_and_v4_0_VC);
5593 Py_CLEAR(clear_module_state->__pyx_n_u_Character);
5594 Py_CLEAR(clear_module_state->__pyx_kp_u_Conditional_genotype_quality);
5595 Py_CLEAR(clear_module_state->__pyx_n_u_D);
5596 Py_CLEAR(clear_module_state->__pyx_n_u_DP);
5597 Py_CLEAR(clear_module_state->__pyx_kp_u_Description);
5598 Py_CLEAR(clear_module_state->__pyx_n_u_Description_2);
5599 Py_CLEAR(clear_module_state->__pyx_kp_u_Don_t_understand_region_string_s);
5600 Py_CLEAR(clear_module_state->__pyx_n_u_EC);
5601 Py_CLEAR(clear_module_state->__pyx_n_s_ERROR_FLAG_HAS_VALUE);
5602 Py_CLEAR(clear_module_state->__pyx_kp_u_ERROR_FLAG_HAS_VALUE_Flag_fields);
5603 Py_CLEAR(clear_module_state->__pyx_n_s_ERROR_FORMAT_NOT_CHAR);
5604 Py_CLEAR(clear_module_state->__pyx_kp_u_ERROR_FORMAT_NOT_CHAR_Eexpected);
5605 Py_CLEAR(clear_module_state->__pyx_n_s_ERROR_FORMAT_NOT_INTEGER);
5606 Py_CLEAR(clear_module_state->__pyx_kp_u_ERROR_FORMAT_NOT_INTEGER_Expecte);
5607 Py_CLEAR(clear_module_state->__pyx_n_s_ERROR_FORMAT_NOT_NUMERICAL);
5608 Py_CLEAR(clear_module_state->__pyx_kp_u_ERROR_FORMAT_NOT_NUMERICAL_Expec);
5609 Py_CLEAR(clear_module_state->__pyx_n_s_ERROR_INFO_STRING);
5610 Py_CLEAR(clear_module_state->__pyx_kp_u_ERROR_INFO_STRING_Error_while_pa);
5611 Py_CLEAR(clear_module_state->__pyx_n_s_ERROR_TRAILING_DATA);
5612 Py_CLEAR(clear_module_state->__pyx_kp_u_ERROR_TRAILING_DATA_Numerical_fi);
5613 Py_CLEAR(clear_module_state->__pyx_n_s_ERROR_UNKNOWN_KEY);
5614 Py_CLEAR(clear_module_state->__pyx_kp_u_ERROR_UNKNOWN_KEY_Unknown_key_s);
5615 Py_CLEAR(clear_module_state->__pyx_n_u_Error);
5616 Py_CLEAR(clear_module_state->__pyx_kp_u_Expected_alternate_allel_counts);
5617 Py_CLEAR(clear_module_state->__pyx_n_u_FILTER);
5618 Py_CLEAR(clear_module_state->__pyx_n_s_FILTER_NOT_DEFINED);
5619 Py_CLEAR(clear_module_state->__pyx_kp_u_FILTER_NOT_DEFINED_Identifier_s);
5620 Py_CLEAR(clear_module_state->__pyx_n_s_FORMAT);
5621 Py_CLEAR(clear_module_state->__pyx_n_u_FORMAT);
5622 Py_CLEAR(clear_module_state->__pyx_n_s_FORMAT_MISSING_QUOTES);
5623 Py_CLEAR(clear_module_state->__pyx_kp_u_FORMAT_MISSING_QUOTES_Descriptio);
5624 Py_CLEAR(clear_module_state->__pyx_n_s_FORMAT_NOT_DEFINED);
5625 Py_CLEAR(clear_module_state->__pyx_kp_u_FORMAT_NOT_DEFINED_Identifier_s);
5626 Py_CLEAR(clear_module_state->__pyx_n_u_FT);
5627 Py_CLEAR(clear_module_state->__pyx_n_u_Flag);
5628 Py_CLEAR(clear_module_state->__pyx_n_u_Float);
5629 Py_CLEAR(clear_module_state->__pyx_n_u_G);
5630 Py_CLEAR(clear_module_state->__pyx_n_u_GL);
5631 Py_CLEAR(clear_module_state->__pyx_n_u_GLE);
5632 Py_CLEAR(clear_module_state->__pyx_n_u_GP);
5633 Py_CLEAR(clear_module_state->__pyx_n_u_GQ);
5634 Py_CLEAR(clear_module_state->__pyx_n_u_GT);
5635 Py_CLEAR(clear_module_state->__pyx_n_s_GTdata);
5636 Py_CLEAR(clear_module_state->__pyx_n_s_GTstring);
5637 Py_CLEAR(clear_module_state->__pyx_n_u_Genotype);
5638 Py_CLEAR(clear_module_state->__pyx_kp_u_Genotype_Quality);
5639 Py_CLEAR(clear_module_state->__pyx_kp_u_Genotype_likelihoods);
5640 Py_CLEAR(clear_module_state->__pyx_kp_u_Genotype_posterior_probabilities);
5641 Py_CLEAR(clear_module_state->__pyx_n_s_HEADING_NOT_SEPARATED_BY_TABS);
5642 Py_CLEAR(clear_module_state->__pyx_kp_u_HEADING_NOT_SEPARATED_BY_TABS_He);
5643 Py_CLEAR(clear_module_state->__pyx_n_u_HQ);
5644 Py_CLEAR(clear_module_state->__pyx_kp_u_Haplotype_Quality);
5645 Py_CLEAR(clear_module_state->__pyx_n_u_I);
5646 Py_CLEAR(clear_module_state->__pyx_kp_u_ID);
5647 Py_CLEAR(clear_module_state->__pyx_n_u_ID_2);
5648 Py_CLEAR(clear_module_state->__pyx_n_u_INFO);
5649 Py_CLEAR(clear_module_state->__pyx_kp_s_Incompatible_checksums_0x_x_vs_0);
5650 Py_CLEAR(clear_module_state->__pyx_n_u_Integer);
5651 Py_CLEAR(clear_module_state->__pyx_kp_u_Invalid_error_string_s);
5652 Py_CLEAR(clear_module_state->__pyx_n_s_KeyError);
5653 Py_CLEAR(clear_module_state->__pyx_n_s_MISSING_INDEL_ALLELE_REF_BASE);
5654 Py_CLEAR(clear_module_state->__pyx_kp_u_MISSING_INDEL_ALLELE_REF_BASE_In);
5655 Py_CLEAR(clear_module_state->__pyx_n_s_MISSING_REF);
5656 Py_CLEAR(clear_module_state->__pyx_kp_u_MISSING_REF_Reference_allele_mis);
5657 Py_CLEAR(clear_module_state->__pyx_n_u_MQ);
5658 Py_CLEAR(clear_module_state->__pyx_n_s_MemoryError);
5659 Py_CLEAR(clear_module_state->__pyx_n_u_N);
5660 Py_CLEAR(clear_module_state->__pyx_n_s_NT_ALLELES);
5661 Py_CLEAR(clear_module_state->__pyx_n_s_NT_GENOTYPES);
5662 Py_CLEAR(clear_module_state->__pyx_n_s_NT_NR_ALLELES);
5663 Py_CLEAR(clear_module_state->__pyx_n_s_NT_NUMBER);
5664 Py_CLEAR(clear_module_state->__pyx_n_s_NT_PHASED_GENOTYPES);
5665 Py_CLEAR(clear_module_state->__pyx_n_s_NT_UNKNOWN);
5666 Py_CLEAR(clear_module_state->__pyx_n_s_NotImplementedError);
5667 Py_CLEAR(clear_module_state->__pyx_kp_u_Number);
5668 Py_CLEAR(clear_module_state->__pyx_n_u_Number_2);
5669 Py_CLEAR(clear_module_state->__pyx_n_b_PASS);
5670 Py_CLEAR(clear_module_state->__pyx_n_u_PASS);
5671 Py_CLEAR(clear_module_state->__pyx_n_u_PL);
5672 Py_CLEAR(clear_module_state->__pyx_n_u_POS);
5673 Py_CLEAR(clear_module_state->__pyx_n_s_POS_NOT_NUMERICAL);
5674 Py_CLEAR(clear_module_state->__pyx_kp_u_POS_NOT_NUMERICAL_Position_colum);
5675 Py_CLEAR(clear_module_state->__pyx_n_s_POS_NOT_POSITIVE);
5676 Py_CLEAR(clear_module_state->__pyx_kp_u_POS_NOT_POSITIVE_Position_field);
5677 Py_CLEAR(clear_module_state->__pyx_n_u_PQ);
5678 Py_CLEAR(clear_module_state->__pyx_n_u_PS);
5679 Py_CLEAR(clear_module_state->__pyx_kp_u_Phase_set);
5680 Py_CLEAR(clear_module_state->__pyx_kp_u_Phasing_quality);
5681 Py_CLEAR(clear_module_state->__pyx_kp_u_Phred_scaled_genotype_likelihood);
5682 Py_CLEAR(clear_module_state->__pyx_n_s_PickleError);
5683 Py_CLEAR(clear_module_state->__pyx_n_u_QUAL);
5684 Py_CLEAR(clear_module_state->__pyx_n_s_QUAL_NOT_NUMERICAL);
5685 Py_CLEAR(clear_module_state->__pyx_kp_u_QUAL_NOT_NUMERICAL_Quality_field);
5686 Py_CLEAR(clear_module_state->__pyx_n_u_REF);
5687 Py_CLEAR(clear_module_state->__pyx_kp_u_RMS_mapping_quality);
5688 Py_CLEAR(clear_module_state->__pyx_kp_u_Read_depth_at_this_position_for);
5689 Py_CLEAR(clear_module_state->__pyx_kp_u_Required_key_s_not_found_in_data);
5690 Py_CLEAR(clear_module_state->__pyx_kp_u_Sample_Genotype_Filter);
5691 Py_CLEAR(clear_module_state->__pyx_n_s_StopIteration);
5692 Py_CLEAR(clear_module_state->__pyx_n_u_String);
5693 Py_CLEAR(clear_module_state->__pyx_n_s_Tabixfile);
5694 Py_CLEAR(clear_module_state->__pyx_kp_u_Type);
5695 Py_CLEAR(clear_module_state->__pyx_n_s_TypeError);
5696 Py_CLEAR(clear_module_state->__pyx_n_u_Type_2);
5697 Py_CLEAR(clear_module_state->__pyx_n_s_UNKNOWN_CHAR_IN_REF);
5698 Py_CLEAR(clear_module_state->__pyx_kp_u_UNKNOWN_CHAR_IN_REF_Unknown_char);
5699 Py_CLEAR(clear_module_state->__pyx_n_s_UNKNOWN_FORMAT_STRING);
5700 Py_CLEAR(clear_module_state->__pyx_kp_u_UNKNOWN_FORMAT_STRING_Unknown_fi);
5701 Py_CLEAR(clear_module_state->__pyx_kp_u_Undefined_tag);
5702 Py_CLEAR(clear_module_state->__pyx_kp_u_Unknown_number_type_encountered);
5703 Py_CLEAR(clear_module_state->__pyx_n_s_V33_BAD_ALLELE);
5704 Py_CLEAR(clear_module_state->__pyx_kp_u_V33_BAD_ALLELE_Cannot_interpret);
5705 Py_CLEAR(clear_module_state->__pyx_n_s_V33_BAD_REF);
5706 Py_CLEAR(clear_module_state->__pyx_kp_u_V33_BAD_REF_Reference_should_be);
5707 Py_CLEAR(clear_module_state->__pyx_n_s_V33_UNMATCHED_DELETION);
5708 Py_CLEAR(clear_module_state->__pyx_kp_u_V33_UNMATCHED_DELETION_Deleted_s);
5709 Py_CLEAR(clear_module_state->__pyx_n_s_V40_BAD_ALLELE);
5710 Py_CLEAR(clear_module_state->__pyx_kp_u_V40_BAD_ALLELE_Bad_allele_found);
5711 Py_CLEAR(clear_module_state->__pyx_n_s_V40_FORMAT_MUST_HAVE_NAMED_FIELD);
5712 Py_CLEAR(clear_module_state->__pyx_kp_u_V40_FORMAT_MUST_HAVE_NAMED_FIELD_2);
5713 Py_CLEAR(clear_module_state->__pyx_n_s_V40_MISSING_ANGLE_BRACKETS);
5714 Py_CLEAR(clear_module_state->__pyx_kp_u_V40_MISSING_ANGLE_BRACKETS_Forma);
5715 Py_CLEAR(clear_module_state->__pyx_n_s_VCF);
5716 Py_CLEAR(clear_module_state->__pyx_n_u_VCF);
5717 Py_CLEAR(clear_module_state->__pyx_n_s_VCFRecord);
5718 Py_CLEAR(clear_module_state->__pyx_n_u_VCFRecord);
5719 Py_CLEAR(clear_module_state->__pyx_n_s_VCFRecord___reduce_cython);
5720 Py_CLEAR(clear_module_state->__pyx_n_s_VCFRecord___setstate_cython);
5721 Py_CLEAR(clear_module_state->__pyx_n_s_VCFRecord_error);
5722 Py_CLEAR(clear_module_state->__pyx_n_s_VCF___del);
5723 Py_CLEAR(clear_module_state->__pyx_n_s_VCF___init);
5724 Py_CLEAR(clear_module_state->__pyx_n_s_VCF__add_definition);
5725 Py_CLEAR(clear_module_state->__pyx_n_s_VCF__parse);
5726 Py_CLEAR(clear_module_state->__pyx_n_s_VCF__parse_header);
5727 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_close);
5728 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_compare_calls);
5729 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_connect);
5730 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_convertGT);
5731 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_convertGTback);
5732 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_enter_default_format);
5733 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_error);
5734 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_fetch);
5735 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_format_format);
5736 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_format_formatdata);
5737 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_get_expected);
5738 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_getfilter);
5739 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_getformat);
5740 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_getheader);
5741 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_getinfo);
5742 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_getsamples);
5743 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_ignoreerror);
5744 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_inregion);
5745 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_parse);
5746 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_parse_data);
5747 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_parse_format);
5748 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_parse_formatdata);
5749 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_parse_header);
5750 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_parse_heading);
5751 Py_CLEAR(clear_module_state->__pyx_kp_u_VCF_says);
5752 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_setfilter);
5753 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_setformat);
5754 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_setheader);
5755 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_setinfo);
5756 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_setreference);
5757 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_setregions);
5758 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_setsamples);
5759 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_setversion);
5760 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_validate);
5761 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_warnerror);
5762 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_write);
5763 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_write_data);
5764 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_write_header);
5765 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_write_heading);
5766 Py_CLEAR(clear_module_state->__pyx_n_s_VCF_writeheader);
5767 Py_CLEAR(clear_module_state->__pyx_kp_u_VCFv3_3);
5768 Py_CLEAR(clear_module_state->__pyx_kp_u_VCFv4_0);
5769 Py_CLEAR(clear_module_state->__pyx_kp_u_VCFv4_1);
5770 Py_CLEAR(clear_module_state->__pyx_kp_u_VCFv4_2);
5771 Py_CLEAR(clear_module_state->__pyx_n_s_ValueError);
5772 Py_CLEAR(clear_module_state->__pyx_n_s_WRONG_REF);
5773 Py_CLEAR(clear_module_state->__pyx_kp_u_WRONG_REF_Wrong_reference_s);
5774 Py_CLEAR(clear_module_state->__pyx_n_u_Warning);
5775 Py_CLEAR(clear_module_state->__pyx_n_s_ZERO_FOR_NON_FLAG_FIELD);
5776 Py_CLEAR(clear_module_state->__pyx_kp_u_ZERO_FOR_NON_FLAG_FIELD_number_s);
5777 Py_CLEAR(clear_module_state->__pyx_n_s_ZERO_LENGTH_ALLELE);
5778 Py_CLEAR(clear_module_state->__pyx_kp_u_ZERO_LENGTH_ALLELE_Found_zero_le);
5779 Py_CLEAR(clear_module_state->__pyx_kp_u__10);
5780 Py_CLEAR(clear_module_state->__pyx_kp_u__11);
5781 Py_CLEAR(clear_module_state->__pyx_kp_u__12);
5782 Py_CLEAR(clear_module_state->__pyx_kp_u__13);
5783 Py_CLEAR(clear_module_state->__pyx_n_s__139);
5784 Py_CLEAR(clear_module_state->__pyx_kp_u__14);
5785 Py_CLEAR(clear_module_state->__pyx_kp_u__15);
5786 Py_CLEAR(clear_module_state->__pyx_kp_u__16);
5787 Py_CLEAR(clear_module_state->__pyx_kp_u__19);
5788 Py_CLEAR(clear_module_state->__pyx_kp_u__2);
5789 Py_CLEAR(clear_module_state->__pyx_kp_u__23);
5790 Py_CLEAR(clear_module_state->__pyx_kp_u__24);
5791 Py_CLEAR(clear_module_state->__pyx_kp_u__25);
5792 Py_CLEAR(clear_module_state->__pyx_kp_u__27);
5793 Py_CLEAR(clear_module_state->__pyx_kp_u__3);
5794 Py_CLEAR(clear_module_state->__pyx_n_s__33);
5795 Py_CLEAR(clear_module_state->__pyx_kp_u__34);
5796 Py_CLEAR(clear_module_state->__pyx_kp_u__4);
5797 Py_CLEAR(clear_module_state->__pyx_kp_b__5);
5798 Py_CLEAR(clear_module_state->__pyx_kp_u__5);
5799 Py_CLEAR(clear_module_state->__pyx_kp_u__6);
5800 Py_CLEAR(clear_module_state->__pyx_kp_u__7);
5801 Py_CLEAR(clear_module_state->__pyx_kp_u__8);
5802 Py_CLEAR(clear_module_state->__pyx_n_s_a);
5803 Py_CLEAR(clear_module_state->__pyx_n_s_add);
5804 Py_CLEAR(clear_module_state->__pyx_n_s_add_definition);
5805 Py_CLEAR(clear_module_state->__pyx_n_s_addn);
5806 Py_CLEAR(clear_module_state->__pyx_n_s_addns);
5807 Py_CLEAR(clear_module_state->__pyx_n_s_all);
5808 Py_CLEAR(clear_module_state->__pyx_n_s_allele);
5809 Py_CLEAR(clear_module_state->__pyx_n_s_alleleRegEx);
5810 Py_CLEAR(clear_module_state->__pyx_kp_u_alleles);
5811 Py_CLEAR(clear_module_state->__pyx_n_s_alt);
5812 Py_CLEAR(clear_module_state->__pyx_n_u_alt);
5813 Py_CLEAR(clear_module_state->__pyx_n_s_alt1);
5814 Py_CLEAR(clear_module_state->__pyx_n_s_alt2);
5815 Py_CLEAR(clear_module_state->__pyx_n_s_append);
5816 Py_CLEAR(clear_module_state->__pyx_n_s_args);
5817 Py_CLEAR(clear_module_state->__pyx_n_s_asVCFRecord);
5818 Py_CLEAR(clear_module_state->__pyx_n_s_asVCFRecord___reduce_cython);
5819 Py_CLEAR(clear_module_state->__pyx_n_s_asVCFRecord___setstate_cython);
5820 Py_CLEAR(clear_module_state->__pyx_n_u_ascii);
5821 Py_CLEAR(clear_module_state->__pyx_n_s_asyncio_coroutines);
5822 Py_CLEAR(clear_module_state->__pyx_n_s_bisect);
5823 Py_CLEAR(clear_module_state->__pyx_n_s_blurp);
5824 Py_CLEAR(clear_module_state->__pyx_n_s_c);
5825 Py_CLEAR(clear_module_state->__pyx_n_s_chrom);
5826 Py_CLEAR(clear_module_state->__pyx_n_u_chrom);
5827 Py_CLEAR(clear_module_state->__pyx_n_s_class_getitem);
5828 Py_CLEAR(clear_module_state->__pyx_n_s_cline_in_traceback);
5829 Py_CLEAR(clear_module_state->__pyx_n_s_close);
5830 Py_CLEAR(clear_module_state->__pyx_n_s_collections);
5831 Py_CLEAR(clear_module_state->__pyx_n_s_cols);
5832 Py_CLEAR(clear_module_state->__pyx_n_s_compare_calls);
5833 Py_CLEAR(clear_module_state->__pyx_n_s_compile);
5834 Py_CLEAR(clear_module_state->__pyx_n_s_connect);
5835 Py_CLEAR(clear_module_state->__pyx_n_s_convertGT);
5836 Py_CLEAR(clear_module_state->__pyx_n_s_convertGTback);
5837 Py_CLEAR(clear_module_state->__pyx_n_s_copy);
5838 Py_CLEAR(clear_module_state->__pyx_n_s_copy_2);
5839 Py_CLEAR(clear_module_state->__pyx_n_s_d);
5840 Py_CLEAR(clear_module_state->__pyx_n_s_data);
5841 Py_CLEAR(clear_module_state->__pyx_n_s_datagenerator);
5842 Py_CLEAR(clear_module_state->__pyx_n_s_deepcopy);
5843 Py_CLEAR(clear_module_state->__pyx_n_s_defaultdict);
5844 Py_CLEAR(clear_module_state->__pyx_n_s_del);
5845 Py_CLEAR(clear_module_state->__pyx_kp_u_deletion_is);
5846 Py_CLEAR(clear_module_state->__pyx_n_u_descr);
5847 Py_CLEAR(clear_module_state->__pyx_n_s_description);
5848 Py_CLEAR(clear_module_state->__pyx_n_s_dict);
5849 Py_CLEAR(clear_module_state->__pyx_n_s_dict_2);
5850 Py_CLEAR(clear_module_state->__pyx_n_s_dict_3);
5851 Py_CLEAR(clear_module_state->__pyx_kp_u_disable);
5852 Py_CLEAR(clear_module_state->__pyx_n_s_doc);
5853 Py_CLEAR(clear_module_state->__pyx_n_s_elts);
5854 Py_CLEAR(clear_module_state->__pyx_kp_u_enable);
5855 Py_CLEAR(clear_module_state->__pyx_n_s_encoding);
5856 Py_CLEAR(clear_module_state->__pyx_n_s_end);
5857 Py_CLEAR(clear_module_state->__pyx_n_s_endswith);
5858 Py_CLEAR(clear_module_state->__pyx_n_s_enter_default_format);
5859 Py_CLEAR(clear_module_state->__pyx_n_s_enumerate);
5860 Py_CLEAR(clear_module_state->__pyx_n_s_err);
5861 Py_CLEAR(clear_module_state->__pyx_n_s_error);
5862 Py_CLEAR(clear_module_state->__pyx_n_s_errorlabel);
5863 Py_CLEAR(clear_module_state->__pyx_n_s_errors);
5864 Py_CLEAR(clear_module_state->__pyx_n_s_errorstring);
5865 Py_CLEAR(clear_module_state->__pyx_n_s_errwarn);
5866 Py_CLEAR(clear_module_state->__pyx_kp_u_expected);
5867 Py_CLEAR(clear_module_state->__pyx_kp_u_expected_2);
5868 Py_CLEAR(clear_module_state->__pyx_kp_u_expected_3);
5869 Py_CLEAR(clear_module_state->__pyx_n_s_expected_4);
5870 Py_CLEAR(clear_module_state->__pyx_n_s_f);
5871 Py_CLEAR(clear_module_state->__pyx_n_s_fa);
5872 Py_CLEAR(clear_module_state->__pyx_n_s_faref);
5873 Py_CLEAR(clear_module_state->__pyx_n_s_faref_leftflank);
5874 Py_CLEAR(clear_module_state->__pyx_n_s_fetch);
5875 Py_CLEAR(clear_module_state->__pyx_n_u_fileformat);
5876 Py_CLEAR(clear_module_state->__pyx_kp_u_fileformat_VCFv);
5877 Py_CLEAR(clear_module_state->__pyx_n_s_filename);
5878 Py_CLEAR(clear_module_state->__pyx_n_s_filter);
5879 Py_CLEAR(clear_module_state->__pyx_n_s_filter_2);
5880 Py_CLEAR(clear_module_state->__pyx_n_u_filter_2);
5881 Py_CLEAR(clear_module_state->__pyx_n_s_find);
5882 Py_CLEAR(clear_module_state->__pyx_n_s_first);
5883 Py_CLEAR(clear_module_state->__pyx_n_s_fmt);
5884 Py_CLEAR(clear_module_state->__pyx_kp_u_for);
5885 Py_CLEAR(clear_module_state->__pyx_n_s_format);
5886 Py_CLEAR(clear_module_state->__pyx_n_u_format);
5887 Py_CLEAR(clear_module_state->__pyx_n_s_format_2);
5888 Py_CLEAR(clear_module_state->__pyx_n_s_format_format);
5889 Py_CLEAR(clear_module_state->__pyx_n_s_format_formatdata);
5890 Py_CLEAR(clear_module_state->__pyx_n_s_formatdict);
5891 Py_CLEAR(clear_module_state->__pyx_kp_u_found);
5892 Py_CLEAR(clear_module_state->__pyx_kp_u_gc);
5893 Py_CLEAR(clear_module_state->__pyx_kp_u_genotypes);
5894 Py_CLEAR(clear_module_state->__pyx_n_s_get);
5895 Py_CLEAR(clear_module_state->__pyx_n_s_get_expected);
5896 Py_CLEAR(clear_module_state->__pyx_n_s_get_sequence);
5897 Py_CLEAR(clear_module_state->__pyx_n_s_getfilter);
5898 Py_CLEAR(clear_module_state->__pyx_n_s_getformat);
5899 Py_CLEAR(clear_module_state->__pyx_n_s_getheader);
5900 Py_CLEAR(clear_module_state->__pyx_n_s_getinfo);
5901 Py_CLEAR(clear_module_state->__pyx_n_s_getsamples);
5902 Py_CLEAR(clear_module_state->__pyx_n_s_getstate);
5903 Py_CLEAR(clear_module_state->__pyx_kp_u_got);
5904 Py_CLEAR(clear_module_state->__pyx_n_s_gts);
5905 Py_CLEAR(clear_module_state->__pyx_n_s_gtsRegEx);
5906 Py_CLEAR(clear_module_state->__pyx_n_s_have_deletions);
5907 Py_CLEAR(clear_module_state->__pyx_n_s_header);
5908 Py_CLEAR(clear_module_state->__pyx_n_s_header_2);
5909 Py_CLEAR(clear_module_state->__pyx_n_s_headings);
5910 Py_CLEAR(clear_module_state->__pyx_n_s_i);
5911 Py_CLEAR(clear_module_state->__pyx_kp_u_id);
5912 Py_CLEAR(clear_module_state->__pyx_n_s_id_2);
5913 Py_CLEAR(clear_module_state->__pyx_n_u_id_2);
5914 Py_CLEAR(clear_module_state->__pyx_kp_u_id_numbertype_number_type_descri);
5915 Py_CLEAR(clear_module_state->__pyx_n_s_idx);
5916 Py_CLEAR(clear_module_state->__pyx_n_s_ielts);
5917 Py_CLEAR(clear_module_state->__pyx_n_s_ignored_errors);
5918 Py_CLEAR(clear_module_state->__pyx_n_s_ignoreerror);
5919 Py_CLEAR(clear_module_state->__pyx_n_s_import);
5920 Py_CLEAR(clear_module_state->__pyx_kp_u_in_line);
5921 Py_CLEAR(clear_module_state->__pyx_n_s_info);
5922 Py_CLEAR(clear_module_state->__pyx_n_s_info_2);
5923 Py_CLEAR(clear_module_state->__pyx_n_u_info_2);
5924 Py_CLEAR(clear_module_state->__pyx_n_s_init);
5925 Py_CLEAR(clear_module_state->__pyx_n_s_init_subclass);
5926 Py_CLEAR(clear_module_state->__pyx_n_s_initializing);
5927 Py_CLEAR(clear_module_state->__pyx_n_s_inregion);
5928 Py_CLEAR(clear_module_state->__pyx_n_s_is_coroutine);
5929 Py_CLEAR(clear_module_state->__pyx_kp_u_isenabled);
5930 Py_CLEAR(clear_module_state->__pyx_n_s_itemgetter);
5931 Py_CLEAR(clear_module_state->__pyx_n_s_itervalues);
5932 Py_CLEAR(clear_module_state->__pyx_n_s_join);
5933 Py_CLEAR(clear_module_state->__pyx_n_s_k);
5934 Py_CLEAR(clear_module_state->__pyx_n_s_key);
5935 Py_CLEAR(clear_module_state->__pyx_n_s_keys);
5936 Py_CLEAR(clear_module_state->__pyx_n_s_l);
5937 Py_CLEAR(clear_module_state->__pyx_n_s_label);
5938 Py_CLEAR(clear_module_state->__pyx_n_s_last);
5939 Py_CLEAR(clear_module_state->__pyx_n_s_last_line);
5940 Py_CLEAR(clear_module_state->__pyx_n_s_left);
5941 Py_CLEAR(clear_module_state->__pyx_n_s_leftalign);
5942 Py_CLEAR(clear_module_state->__pyx_n_s_leftalign_2);
5943 Py_CLEAR(clear_module_state->__pyx_n_s_line);
5944 Py_CLEAR(clear_module_state->__pyx_n_s_line_2);
5945 Py_CLEAR(clear_module_state->__pyx_n_s_lineno);
5946 Py_CLEAR(clear_module_state->__pyx_n_s_lineparse);
5947 Py_CLEAR(clear_module_state->__pyx_n_s_lines);
5948 Py_CLEAR(clear_module_state->__pyx_n_s_lines_2);
5949 Py_CLEAR(clear_module_state->__pyx_n_s_longest);
5950 Py_CLEAR(clear_module_state->__pyx_n_s_main);
5951 Py_CLEAR(clear_module_state->__pyx_n_s_map);
5952 Py_CLEAR(clear_module_state->__pyx_n_s_match);
5953 Py_CLEAR(clear_module_state->__pyx_n_s_metaclass);
5954 Py_CLEAR(clear_module_state->__pyx_n_s_min);
5955 Py_CLEAR(clear_module_state->__pyx_n_u_missing);
5956 Py_CLEAR(clear_module_state->__pyx_n_s_missingvalue);
5957 Py_CLEAR(clear_module_state->__pyx_n_s_module);
5958 Py_CLEAR(clear_module_state->__pyx_n_s_movable);
5959 Py_CLEAR(clear_module_state->__pyx_n_s_mro_entries);
5960 Py_CLEAR(clear_module_state->__pyx_n_s_n);
5961 Py_CLEAR(clear_module_state->__pyx_n_s_na);
5962 Py_CLEAR(clear_module_state->__pyx_n_s_name);
5963 Py_CLEAR(clear_module_state->__pyx_n_s_namedtuple);
5964 Py_CLEAR(clear_module_state->__pyx_kp_u_needs_to_be_checked);
5965 Py_CLEAR(clear_module_state->__pyx_n_s_new);
5966 Py_CLEAR(clear_module_state->__pyx_n_s_newalts);
5967 Py_CLEAR(clear_module_state->__pyx_n_s_nmb);
5968 Py_CLEAR(clear_module_state->__pyx_kp_s_no_default___reduce___due_to_non);
5969 Py_CLEAR(clear_module_state->__pyx_kp_u_nonref_alleles);
5970 Py_CLEAR(clear_module_state->__pyx_n_s_number);
5971 Py_CLEAR(clear_module_state->__pyx_n_u_number);
5972 Py_CLEAR(clear_module_state->__pyx_n_s_numbertype);
5973 Py_CLEAR(clear_module_state->__pyx_n_s_object);
5974 Py_CLEAR(clear_module_state->__pyx_n_s_operator);
5975 Py_CLEAR(clear_module_state->__pyx_n_s_opt);
5976 Py_CLEAR(clear_module_state->__pyx_kp_u_output);
5977 Py_CLEAR(clear_module_state->__pyx_n_s_output_2);
5978 Py_CLEAR(clear_module_state->__pyx_kp_u_parameters_got);
5979 Py_CLEAR(clear_module_state->__pyx_n_s_parse);
5980 Py_CLEAR(clear_module_state->__pyx_n_s_parse_2);
5981 Py_CLEAR(clear_module_state->__pyx_n_s_parse_data);
5982 Py_CLEAR(clear_module_state->__pyx_n_s_parse_format);
5983 Py_CLEAR(clear_module_state->__pyx_n_s_parse_formatdata);
5984 Py_CLEAR(clear_module_state->__pyx_n_s_parse_header);
5985 Py_CLEAR(clear_module_state->__pyx_n_s_parse_header_2);
5986 Py_CLEAR(clear_module_state->__pyx_n_s_parse_heading);
5987 Py_CLEAR(clear_module_state->__pyx_n_s_parse_regions);
5988 Py_CLEAR(clear_module_state->__pyx_n_s_parser);
5989 Py_CLEAR(clear_module_state->__pyx_kp_u_phased_genotypes);
5990 Py_CLEAR(clear_module_state->__pyx_n_s_pickle);
5991 Py_CLEAR(clear_module_state->__pyx_n_s_pos);
5992 Py_CLEAR(clear_module_state->__pyx_n_u_pos);
5993 Py_CLEAR(clear_module_state->__pyx_n_s_pos1);
5994 Py_CLEAR(clear_module_state->__pyx_n_s_pos2);
5995 Py_CLEAR(clear_module_state->__pyx_n_s_prepare);
5996 Py_CLEAR(clear_module_state->__pyx_n_s_pysam);
5997 Py_CLEAR(clear_module_state->__pyx_n_s_pysam_libcvcf);
5998 Py_CLEAR(clear_module_state->__pyx_kp_s_pysam_libcvcf_pyx);
5999 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_PickleError);
6000 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_checksum);
6001 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_result);
6002 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_state);
6003 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_type);
6004 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_asVCFRecord);
6005 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_vtable);
6006 Py_CLEAR(clear_module_state->__pyx_n_s_qual);
6007 Py_CLEAR(clear_module_state->__pyx_n_u_qual);
6008 Py_CLEAR(clear_module_state->__pyx_n_s_qualname);
6009 Py_CLEAR(clear_module_state->__pyx_n_s_r);
6010 Py_CLEAR(clear_module_state->__pyx_n_s_range);
6011 Py_CLEAR(clear_module_state->__pyx_n_s_re);
6012 Py_CLEAR(clear_module_state->__pyx_n_s_record);
6013 Py_CLEAR(clear_module_state->__pyx_n_s_reduce);
6014 Py_CLEAR(clear_module_state->__pyx_n_s_reduce_cython);
6015 Py_CLEAR(clear_module_state->__pyx_n_s_reduce_ex);
6016 Py_CLEAR(clear_module_state->__pyx_n_s_ref);
6017 Py_CLEAR(clear_module_state->__pyx_n_u_ref);
6018 Py_CLEAR(clear_module_state->__pyx_n_s_ref1);
6019 Py_CLEAR(clear_module_state->__pyx_n_s_ref2);
6020 Py_CLEAR(clear_module_state->__pyx_n_s_reference);
6021 Py_CLEAR(clear_module_state->__pyx_n_s_reference_2);
6022 Py_CLEAR(clear_module_state->__pyx_kp_u_reference_is);
6023 Py_CLEAR(clear_module_state->__pyx_kp_u_reference_is_2);
6024 Py_CLEAR(clear_module_state->__pyx_n_s_region);
6025 Py_CLEAR(clear_module_state->__pyx_n_s_regions);
6026 Py_CLEAR(clear_module_state->__pyx_n_s_regions_2);
6027 Py_CLEAR(clear_module_state->__pyx_n_s_replace);
6028 Py_CLEAR(clear_module_state->__pyx_n_s_required);
6029 Py_CLEAR(clear_module_state->__pyx_n_s_required_2);
6030 Py_CLEAR(clear_module_state->__pyx_n_s_rest);
6031 Py_CLEAR(clear_module_state->__pyx_n_s_result);
6032 Py_CLEAR(clear_module_state->__pyx_n_s_s);
6033 Py_CLEAR(clear_module_state->__pyx_n_s_sample);
6034 Py_CLEAR(clear_module_state->__pyx_n_s_sample2column);
6035 Py_CLEAR(clear_module_state->__pyx_n_s_samples);
6036 Py_CLEAR(clear_module_state->__pyx_kp_u_samples_2);
6037 Py_CLEAR(clear_module_state->__pyx_n_s_samples_3);
6038 Py_CLEAR(clear_module_state->__pyx_n_s_sdata);
6039 Py_CLEAR(clear_module_state->__pyx_n_s_self);
6040 Py_CLEAR(clear_module_state->__pyx_n_s_send);
6041 Py_CLEAR(clear_module_state->__pyx_n_s_separator);
6042 Py_CLEAR(clear_module_state->__pyx_n_s_sequence);
6043 Py_CLEAR(clear_module_state->__pyx_n_s_set_name);
6044 Py_CLEAR(clear_module_state->__pyx_n_s_setfilter);
6045 Py_CLEAR(clear_module_state->__pyx_n_s_setformat);
6046 Py_CLEAR(clear_module_state->__pyx_n_s_setheader);
6047 Py_CLEAR(clear_module_state->__pyx_n_s_setinfo);
6048 Py_CLEAR(clear_module_state->__pyx_n_s_setreference);
6049 Py_CLEAR(clear_module_state->__pyx_n_s_setregions);
6050 Py_CLEAR(clear_module_state->__pyx_n_s_setsamples);
6051 Py_CLEAR(clear_module_state->__pyx_n_s_setstate);
6052 Py_CLEAR(clear_module_state->__pyx_n_s_setstate_cython);
6053 Py_CLEAR(clear_module_state->__pyx_n_s_setversion);
6054 Py_CLEAR(clear_module_state->__pyx_n_s_shortest);
6055 Py_CLEAR(clear_module_state->__pyx_n_s_spec);
6056 Py_CLEAR(clear_module_state->__pyx_n_s_split);
6057 Py_CLEAR(clear_module_state->__pyx_n_s_start);
6058 Py_CLEAR(clear_module_state->__pyx_n_s_startswith);
6059 Py_CLEAR(clear_module_state->__pyx_n_s_state);
6060 Py_CLEAR(clear_module_state->__pyx_kp_u_sth_entry_not_found);
6061 Py_CLEAR(clear_module_state->__pyx_n_s_stream);
6062 Py_CLEAR(clear_module_state->__pyx_n_s_string);
6063 Py_CLEAR(clear_module_state->__pyx_kp_s_stringsource);
6064 Py_CLEAR(clear_module_state->__pyx_n_s_strip);
6065 Py_CLEAR(clear_module_state->__pyx_n_s_super);
6066 Py_CLEAR(clear_module_state->__pyx_n_s_sys);
6067 Py_CLEAR(clear_module_state->__pyx_n_s_t);
6068 Py_CLEAR(clear_module_state->__pyx_n_s_tabixfile);
6069 Py_CLEAR(clear_module_state->__pyx_n_s_test);
6070 Py_CLEAR(clear_module_state->__pyx_n_s_throw);
6071 Py_CLEAR(clear_module_state->__pyx_n_s_type);
6072 Py_CLEAR(clear_module_state->__pyx_n_u_type);
6073 Py_CLEAR(clear_module_state->__pyx_n_s_update);
6074 Py_CLEAR(clear_module_state->__pyx_n_s_upper);
6075 Py_CLEAR(clear_module_state->__pyx_n_s_use_setstate);
6076 Py_CLEAR(clear_module_state->__pyx_n_s_v);
6077 Py_CLEAR(clear_module_state->__pyx_n_s_validate);
6078 Py_CLEAR(clear_module_state->__pyx_n_s_value);
6079 Py_CLEAR(clear_module_state->__pyx_n_s_values);
6080 Py_CLEAR(clear_module_state->__pyx_kp_u_values_in_element);
6081 Py_CLEAR(clear_module_state->__pyx_n_s_var);
6082 Py_CLEAR(clear_module_state->__pyx_n_s_vcf);
6083 Py_CLEAR(clear_module_state->__pyx_n_s_vcffile);
6084 Py_CLEAR(clear_module_state->__pyx_n_s_version);
6085 Py_CLEAR(clear_module_state->__pyx_n_s_version_2);
6086 Py_CLEAR(clear_module_state->__pyx_n_s_warn_errors);
6087 Py_CLEAR(clear_module_state->__pyx_n_s_warnerror);
6088 Py_CLEAR(clear_module_state->__pyx_n_s_write);
6089 Py_CLEAR(clear_module_state->__pyx_n_s_write_data);
6090 Py_CLEAR(clear_module_state->__pyx_n_s_write_header);
6091 Py_CLEAR(clear_module_state->__pyx_n_s_write_heading);
6092 Py_CLEAR(clear_module_state->__pyx_n_s_writeheader);
6093 Py_CLEAR(clear_module_state->__pyx_n_s_x);
6094 Py_CLEAR(clear_module_state->__pyx_n_s_y);
6095 Py_CLEAR(clear_module_state->__pyx_n_s_zip);
6096 Py_CLEAR(clear_module_state->__pyx_float_0_0);
6097 Py_CLEAR(clear_module_state->__pyx_int_0);
6098 Py_CLEAR(clear_module_state->__pyx_int_1);
6099 Py_CLEAR(clear_module_state->__pyx_int_2);
6100 Py_CLEAR(clear_module_state->__pyx_int_3);
6101 Py_CLEAR(clear_module_state->__pyx_int_4);
6102 Py_CLEAR(clear_module_state->__pyx_int_5);
6103 Py_CLEAR(clear_module_state->__pyx_int_6);
6104 Py_CLEAR(clear_module_state->__pyx_int_7);
6105 Py_CLEAR(clear_module_state->__pyx_int_8);
6106 Py_CLEAR(clear_module_state->__pyx_int_9);
6107 Py_CLEAR(clear_module_state->__pyx_int_10);
6108 Py_CLEAR(clear_module_state->__pyx_int_11);
6109 Py_CLEAR(clear_module_state->__pyx_int_12);
6110 Py_CLEAR(clear_module_state->__pyx_int_13);
6111 Py_CLEAR(clear_module_state->__pyx_int_14);
6112 Py_CLEAR(clear_module_state->__pyx_int_15);
6113 Py_CLEAR(clear_module_state->__pyx_int_16);
6114 Py_CLEAR(clear_module_state->__pyx_int_17);
6115 Py_CLEAR(clear_module_state->__pyx_int_18);
6116 Py_CLEAR(clear_module_state->__pyx_int_19);
6117 Py_CLEAR(clear_module_state->__pyx_int_20);
6118 Py_CLEAR(clear_module_state->__pyx_int_21);
6119 Py_CLEAR(clear_module_state->__pyx_int_22);
6120 Py_CLEAR(clear_module_state->__pyx_int_23);
6121 Py_CLEAR(clear_module_state->__pyx_int_24);
6122 Py_CLEAR(clear_module_state->__pyx_int_25);
6123 Py_CLEAR(clear_module_state->__pyx_int_26);
6124 Py_CLEAR(clear_module_state->__pyx_int_27);
6125 Py_CLEAR(clear_module_state->__pyx_int_28);
6126 Py_CLEAR(clear_module_state->__pyx_int_29);
6127 Py_CLEAR(clear_module_state->__pyx_int_30);
6128 Py_CLEAR(clear_module_state->__pyx_int_31);
6129 Py_CLEAR(clear_module_state->__pyx_int_32);
6130 Py_CLEAR(clear_module_state->__pyx_int_33);
6131 Py_CLEAR(clear_module_state->__pyx_int_40);
6132 Py_CLEAR(clear_module_state->__pyx_int_100);
6133 Py_CLEAR(clear_module_state->__pyx_int_29527880);
6134 Py_CLEAR(clear_module_state->__pyx_int_214161357);
6135 Py_CLEAR(clear_module_state->__pyx_int_239654613);
6136 Py_CLEAR(clear_module_state->__pyx_int_3000000000);
6137 Py_CLEAR(clear_module_state->__pyx_int_neg_1);
6138 Py_CLEAR(clear_module_state->__pyx_slice__9);
6139 Py_CLEAR(clear_module_state->__pyx_slice__17);
6140 Py_CLEAR(clear_module_state->__pyx_slice__18);
6141 Py_CLEAR(clear_module_state->__pyx_slice__20);
6142 Py_CLEAR(clear_module_state->__pyx_slice__26);
6143 Py_CLEAR(clear_module_state->__pyx_slice__28);
6144 Py_CLEAR(clear_module_state->__pyx_tuple__21);
6145 Py_CLEAR(clear_module_state->__pyx_tuple__22);
6146 Py_CLEAR(clear_module_state->__pyx_tuple__30);
6147 Py_CLEAR(clear_module_state->__pyx_tuple__31);
6148 Py_CLEAR(clear_module_state->__pyx_tuple__32);
6149 Py_CLEAR(clear_module_state->__pyx_tuple__35);
6150 Py_CLEAR(clear_module_state->__pyx_tuple__36);
6151 Py_CLEAR(clear_module_state->__pyx_tuple__37);
6152 Py_CLEAR(clear_module_state->__pyx_tuple__39);
6153 Py_CLEAR(clear_module_state->__pyx_tuple__41);
6154 Py_CLEAR(clear_module_state->__pyx_tuple__42);
6155 Py_CLEAR(clear_module_state->__pyx_tuple__44);
6156 Py_CLEAR(clear_module_state->__pyx_tuple__45);
6157 Py_CLEAR(clear_module_state->__pyx_tuple__47);
6158 Py_CLEAR(clear_module_state->__pyx_tuple__49);
6159 Py_CLEAR(clear_module_state->__pyx_tuple__52);
6160 Py_CLEAR(clear_module_state->__pyx_tuple__53);
6161 Py_CLEAR(clear_module_state->__pyx_tuple__54);
6162 Py_CLEAR(clear_module_state->__pyx_tuple__56);
6163 Py_CLEAR(clear_module_state->__pyx_tuple__57);
6164 Py_CLEAR(clear_module_state->__pyx_tuple__59);
6165 Py_CLEAR(clear_module_state->__pyx_tuple__61);
6166 Py_CLEAR(clear_module_state->__pyx_tuple__62);
6167 Py_CLEAR(clear_module_state->__pyx_tuple__64);
6168 Py_CLEAR(clear_module_state->__pyx_tuple__66);
6169 Py_CLEAR(clear_module_state->__pyx_tuple__68);
6170 Py_CLEAR(clear_module_state->__pyx_tuple__70);
6171 Py_CLEAR(clear_module_state->__pyx_tuple__71);
6172 Py_CLEAR(clear_module_state->__pyx_tuple__73);
6173 Py_CLEAR(clear_module_state->__pyx_tuple__75);
6174 Py_CLEAR(clear_module_state->__pyx_tuple__77);
6175 Py_CLEAR(clear_module_state->__pyx_tuple__79);
6176 Py_CLEAR(clear_module_state->__pyx_tuple__81);
6177 Py_CLEAR(clear_module_state->__pyx_tuple__83);
6178 Py_CLEAR(clear_module_state->__pyx_tuple__85);
6179 Py_CLEAR(clear_module_state->__pyx_tuple__87);
6180 Py_CLEAR(clear_module_state->__pyx_tuple__89);
6181 Py_CLEAR(clear_module_state->__pyx_tuple__91);
6182 Py_CLEAR(clear_module_state->__pyx_tuple__93);
6183 Py_CLEAR(clear_module_state->__pyx_tuple__95);
6184 Py_CLEAR(clear_module_state->__pyx_tuple__97);
6185 Py_CLEAR(clear_module_state->__pyx_tuple__100);
6186 Py_CLEAR(clear_module_state->__pyx_tuple__103);
6187 Py_CLEAR(clear_module_state->__pyx_tuple__106);
6188 Py_CLEAR(clear_module_state->__pyx_tuple__109);
6189 Py_CLEAR(clear_module_state->__pyx_tuple__111);
6190 Py_CLEAR(clear_module_state->__pyx_tuple__113);
6191 Py_CLEAR(clear_module_state->__pyx_tuple__115);
6192 Py_CLEAR(clear_module_state->__pyx_tuple__117);
6193 Py_CLEAR(clear_module_state->__pyx_tuple__120);
6194 Py_CLEAR(clear_module_state->__pyx_tuple__122);
6195 Py_CLEAR(clear_module_state->__pyx_tuple__125);
6196 Py_CLEAR(clear_module_state->__pyx_tuple__127);
6197 Py_CLEAR(clear_module_state->__pyx_tuple__129);
6198 Py_CLEAR(clear_module_state->__pyx_tuple__132);
6199 Py_CLEAR(clear_module_state->__pyx_tuple__134);
6200 Py_CLEAR(clear_module_state->__pyx_tuple__135);
6201 Py_CLEAR(clear_module_state->__pyx_tuple__137);
6202 Py_CLEAR(clear_module_state->__pyx_codeobj__29);
6203 Py_CLEAR(clear_module_state->__pyx_codeobj__38);
6204 Py_CLEAR(clear_module_state->__pyx_codeobj__40);
6205 Py_CLEAR(clear_module_state->__pyx_codeobj__43);
6206 Py_CLEAR(clear_module_state->__pyx_codeobj__46);
6207 Py_CLEAR(clear_module_state->__pyx_codeobj__48);
6208 Py_CLEAR(clear_module_state->__pyx_codeobj__50);
6209 Py_CLEAR(clear_module_state->__pyx_codeobj__51);
6210 Py_CLEAR(clear_module_state->__pyx_codeobj__55);
6211 Py_CLEAR(clear_module_state->__pyx_codeobj__58);
6212 Py_CLEAR(clear_module_state->__pyx_codeobj__60);
6213 Py_CLEAR(clear_module_state->__pyx_codeobj__63);
6214 Py_CLEAR(clear_module_state->__pyx_codeobj__65);
6215 Py_CLEAR(clear_module_state->__pyx_codeobj__67);
6216 Py_CLEAR(clear_module_state->__pyx_codeobj__69);
6217 Py_CLEAR(clear_module_state->__pyx_codeobj__72);
6218 Py_CLEAR(clear_module_state->__pyx_codeobj__74);
6219 Py_CLEAR(clear_module_state->__pyx_codeobj__76);
6220 Py_CLEAR(clear_module_state->__pyx_codeobj__78);
6221 Py_CLEAR(clear_module_state->__pyx_codeobj__80);
6222 Py_CLEAR(clear_module_state->__pyx_codeobj__82);
6223 Py_CLEAR(clear_module_state->__pyx_codeobj__84);
6224 Py_CLEAR(clear_module_state->__pyx_codeobj__86);
6225 Py_CLEAR(clear_module_state->__pyx_codeobj__88);
6226 Py_CLEAR(clear_module_state->__pyx_codeobj__90);
6227 Py_CLEAR(clear_module_state->__pyx_codeobj__92);
6228 Py_CLEAR(clear_module_state->__pyx_codeobj__94);
6229 Py_CLEAR(clear_module_state->__pyx_codeobj__96);
6230 Py_CLEAR(clear_module_state->__pyx_codeobj__98);
6231 Py_CLEAR(clear_module_state->__pyx_codeobj__99);
6232 Py_CLEAR(clear_module_state->__pyx_codeobj__101);
6233 Py_CLEAR(clear_module_state->__pyx_codeobj__102);
6234 Py_CLEAR(clear_module_state->__pyx_codeobj__104);
6235 Py_CLEAR(clear_module_state->__pyx_codeobj__105);
6236 Py_CLEAR(clear_module_state->__pyx_codeobj__107);
6237 Py_CLEAR(clear_module_state->__pyx_codeobj__108);
6238 Py_CLEAR(clear_module_state->__pyx_codeobj__110);
6239 Py_CLEAR(clear_module_state->__pyx_codeobj__112);
6240 Py_CLEAR(clear_module_state->__pyx_codeobj__114);
6241 Py_CLEAR(clear_module_state->__pyx_codeobj__116);
6242 Py_CLEAR(clear_module_state->__pyx_codeobj__118);
6243 Py_CLEAR(clear_module_state->__pyx_codeobj__119);
6244 Py_CLEAR(clear_module_state->__pyx_codeobj__121);
6245 Py_CLEAR(clear_module_state->__pyx_codeobj__123);
6246 Py_CLEAR(clear_module_state->__pyx_codeobj__124);
6247 Py_CLEAR(clear_module_state->__pyx_codeobj__126);
6248 Py_CLEAR(clear_module_state->__pyx_codeobj__128);
6249 Py_CLEAR(clear_module_state->__pyx_codeobj__130);
6250 Py_CLEAR(clear_module_state->__pyx_codeobj__131);
6251 Py_CLEAR(clear_module_state->__pyx_codeobj__133);
6252 Py_CLEAR(clear_module_state->__pyx_codeobj__136);
6253 Py_CLEAR(clear_module_state->__pyx_codeobj__138);
6254 return 0;
6255 }
6256 #endif
6257 /* #### Code section: module_state_traverse ### */
6258 #if CYTHON_USE_MODULE_STATE
6259 static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) {
6260 __pyx_mstate *traverse_module_state = __pyx_mstate(m);
6261 if (!traverse_module_state) return 0;
6262 Py_VISIT(traverse_module_state->__pyx_d);
6263 Py_VISIT(traverse_module_state->__pyx_b);
6264 Py_VISIT(traverse_module_state->__pyx_cython_runtime);
6265 Py_VISIT(traverse_module_state->__pyx_empty_tuple);
6266 Py_VISIT(traverse_module_state->__pyx_empty_bytes);
6267 Py_VISIT(traverse_module_state->__pyx_empty_unicode);
6268 #ifdef __Pyx_CyFunction_USED
6269 Py_VISIT(traverse_module_state->__pyx_CyFunctionType);
6270 #endif
6271 #ifdef __Pyx_FusedFunction_USED
6272 Py_VISIT(traverse_module_state->__pyx_FusedFunctionType);
6273 #endif
6274 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_10libchtslib_HTSFile);
6275 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_tabix_file_iterator);
6276 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_TabixFile);
6277 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_Parser);
6278 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asTuple);
6279 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asGTF);
6280 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asGFF3);
6281 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asBed);
6282 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asVCF);
6283 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_TabixIterator);
6284 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed);
6285 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_GZIterator);
6286 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_GZIteratorHead);
6287 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_GZIteratorParsed);
6288 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_Tabixfile);
6289 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_TupleProxy);
6290 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator);
6291 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy);
6292 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_GTFProxy);
6293 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy);
6294 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_BedProxy);
6295 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_VCFProxy);
6296 Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_4type_type);
6297 Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_4bool_bool);
6298 Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_7complex_complex);
6299 Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_5array_array);
6300 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_7libcvcf_VCFRecord);
6301 Py_VISIT(traverse_module_state->__pyx_type_5pysam_7libcvcf_VCFRecord);
6302 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_7libcvcf_asVCFRecord);
6303 Py_VISIT(traverse_module_state->__pyx_type_5pysam_7libcvcf_asVCFRecord);
6304 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse);
6305 Py_VISIT(traverse_module_state->__pyx_type_5pysam_7libcvcf___pyx_scope_struct___parse);
6306 Py_VISIT(traverse_module_state->__pyx_kp_u_);
6307 Py_VISIT(traverse_module_state->__pyx_kp_b_0);
6308 Py_VISIT(traverse_module_state->__pyx_kp_u_0);
6309 Py_VISIT(traverse_module_state->__pyx_n_u_A);
6310 Py_VISIT(traverse_module_state->__pyx_n_u_ACGTN);
6311 Py_VISIT(traverse_module_state->__pyx_kp_u_ACGTN_2);
6312 Py_VISIT(traverse_module_state->__pyx_n_u_ALT);
6313 Py_VISIT(traverse_module_state->__pyx_n_s_AssertionError);
6314 Py_VISIT(traverse_module_state->__pyx_n_s_BADLY_FORMATTED_FORMAT_STRING);
6315 Py_VISIT(traverse_module_state->__pyx_kp_u_BADLY_FORMATTED_FORMAT_STRING_Fo);
6316 Py_VISIT(traverse_module_state->__pyx_n_s_BADLY_FORMATTED_HEADING);
6317 Py_VISIT(traverse_module_state->__pyx_kp_u_BADLY_FORMATTED_HEADING_Did_not);
6318 Py_VISIT(traverse_module_state->__pyx_kp_u_BAD_CHR_TAG_Error_calculating_ch);
6319 Py_VISIT(traverse_module_state->__pyx_n_s_BAD_GENOTYPE);
6320 Py_VISIT(traverse_module_state->__pyx_kp_u_BAD_GENOTYPE_Cannot_parse_genoty);
6321 Py_VISIT(traverse_module_state->__pyx_n_s_BAD_NUMBER_OF_COLUMNS);
6322 Py_VISIT(traverse_module_state->__pyx_kp_u_BAD_NUMBER_OF_COLUMNS_Wrong_numb);
6323 Py_VISIT(traverse_module_state->__pyx_n_s_BAD_NUMBER_OF_PARAMETERS);
6324 Py_VISIT(traverse_module_state->__pyx_kp_u_BAD_NUMBER_OF_PARAMETERS_Found_u);
6325 Py_VISIT(traverse_module_state->__pyx_n_s_BAD_NUMBER_OF_VALUES);
6326 Py_VISIT(traverse_module_state->__pyx_kp_u_BAD_NUMBER_OF_VALUES_Found_too_m);
6327 Py_VISIT(traverse_module_state->__pyx_n_u_CHROM);
6328 Py_VISIT(traverse_module_state->__pyx_kp_u_Can_only_handle_v3_3_and_v4_0_VC);
6329 Py_VISIT(traverse_module_state->__pyx_n_u_Character);
6330 Py_VISIT(traverse_module_state->__pyx_kp_u_Conditional_genotype_quality);
6331 Py_VISIT(traverse_module_state->__pyx_n_u_D);
6332 Py_VISIT(traverse_module_state->__pyx_n_u_DP);
6333 Py_VISIT(traverse_module_state->__pyx_kp_u_Description);
6334 Py_VISIT(traverse_module_state->__pyx_n_u_Description_2);
6335 Py_VISIT(traverse_module_state->__pyx_kp_u_Don_t_understand_region_string_s);
6336 Py_VISIT(traverse_module_state->__pyx_n_u_EC);
6337 Py_VISIT(traverse_module_state->__pyx_n_s_ERROR_FLAG_HAS_VALUE);
6338 Py_VISIT(traverse_module_state->__pyx_kp_u_ERROR_FLAG_HAS_VALUE_Flag_fields);
6339 Py_VISIT(traverse_module_state->__pyx_n_s_ERROR_FORMAT_NOT_CHAR);
6340 Py_VISIT(traverse_module_state->__pyx_kp_u_ERROR_FORMAT_NOT_CHAR_Eexpected);
6341 Py_VISIT(traverse_module_state->__pyx_n_s_ERROR_FORMAT_NOT_INTEGER);
6342 Py_VISIT(traverse_module_state->__pyx_kp_u_ERROR_FORMAT_NOT_INTEGER_Expecte);
6343 Py_VISIT(traverse_module_state->__pyx_n_s_ERROR_FORMAT_NOT_NUMERICAL);
6344 Py_VISIT(traverse_module_state->__pyx_kp_u_ERROR_FORMAT_NOT_NUMERICAL_Expec);
6345 Py_VISIT(traverse_module_state->__pyx_n_s_ERROR_INFO_STRING);
6346 Py_VISIT(traverse_module_state->__pyx_kp_u_ERROR_INFO_STRING_Error_while_pa);
6347 Py_VISIT(traverse_module_state->__pyx_n_s_ERROR_TRAILING_DATA);
6348 Py_VISIT(traverse_module_state->__pyx_kp_u_ERROR_TRAILING_DATA_Numerical_fi);
6349 Py_VISIT(traverse_module_state->__pyx_n_s_ERROR_UNKNOWN_KEY);
6350 Py_VISIT(traverse_module_state->__pyx_kp_u_ERROR_UNKNOWN_KEY_Unknown_key_s);
6351 Py_VISIT(traverse_module_state->__pyx_n_u_Error);
6352 Py_VISIT(traverse_module_state->__pyx_kp_u_Expected_alternate_allel_counts);
6353 Py_VISIT(traverse_module_state->__pyx_n_u_FILTER);
6354 Py_VISIT(traverse_module_state->__pyx_n_s_FILTER_NOT_DEFINED);
6355 Py_VISIT(traverse_module_state->__pyx_kp_u_FILTER_NOT_DEFINED_Identifier_s);
6356 Py_VISIT(traverse_module_state->__pyx_n_s_FORMAT);
6357 Py_VISIT(traverse_module_state->__pyx_n_u_FORMAT);
6358 Py_VISIT(traverse_module_state->__pyx_n_s_FORMAT_MISSING_QUOTES);
6359 Py_VISIT(traverse_module_state->__pyx_kp_u_FORMAT_MISSING_QUOTES_Descriptio);
6360 Py_VISIT(traverse_module_state->__pyx_n_s_FORMAT_NOT_DEFINED);
6361 Py_VISIT(traverse_module_state->__pyx_kp_u_FORMAT_NOT_DEFINED_Identifier_s);
6362 Py_VISIT(traverse_module_state->__pyx_n_u_FT);
6363 Py_VISIT(traverse_module_state->__pyx_n_u_Flag);
6364 Py_VISIT(traverse_module_state->__pyx_n_u_Float);
6365 Py_VISIT(traverse_module_state->__pyx_n_u_G);
6366 Py_VISIT(traverse_module_state->__pyx_n_u_GL);
6367 Py_VISIT(traverse_module_state->__pyx_n_u_GLE);
6368 Py_VISIT(traverse_module_state->__pyx_n_u_GP);
6369 Py_VISIT(traverse_module_state->__pyx_n_u_GQ);
6370 Py_VISIT(traverse_module_state->__pyx_n_u_GT);
6371 Py_VISIT(traverse_module_state->__pyx_n_s_GTdata);
6372 Py_VISIT(traverse_module_state->__pyx_n_s_GTstring);
6373 Py_VISIT(traverse_module_state->__pyx_n_u_Genotype);
6374 Py_VISIT(traverse_module_state->__pyx_kp_u_Genotype_Quality);
6375 Py_VISIT(traverse_module_state->__pyx_kp_u_Genotype_likelihoods);
6376 Py_VISIT(traverse_module_state->__pyx_kp_u_Genotype_posterior_probabilities);
6377 Py_VISIT(traverse_module_state->__pyx_n_s_HEADING_NOT_SEPARATED_BY_TABS);
6378 Py_VISIT(traverse_module_state->__pyx_kp_u_HEADING_NOT_SEPARATED_BY_TABS_He);
6379 Py_VISIT(traverse_module_state->__pyx_n_u_HQ);
6380 Py_VISIT(traverse_module_state->__pyx_kp_u_Haplotype_Quality);
6381 Py_VISIT(traverse_module_state->__pyx_n_u_I);
6382 Py_VISIT(traverse_module_state->__pyx_kp_u_ID);
6383 Py_VISIT(traverse_module_state->__pyx_n_u_ID_2);
6384 Py_VISIT(traverse_module_state->__pyx_n_u_INFO);
6385 Py_VISIT(traverse_module_state->__pyx_kp_s_Incompatible_checksums_0x_x_vs_0);
6386 Py_VISIT(traverse_module_state->__pyx_n_u_Integer);
6387 Py_VISIT(traverse_module_state->__pyx_kp_u_Invalid_error_string_s);
6388 Py_VISIT(traverse_module_state->__pyx_n_s_KeyError);
6389 Py_VISIT(traverse_module_state->__pyx_n_s_MISSING_INDEL_ALLELE_REF_BASE);
6390 Py_VISIT(traverse_module_state->__pyx_kp_u_MISSING_INDEL_ALLELE_REF_BASE_In);
6391 Py_VISIT(traverse_module_state->__pyx_n_s_MISSING_REF);
6392 Py_VISIT(traverse_module_state->__pyx_kp_u_MISSING_REF_Reference_allele_mis);
6393 Py_VISIT(traverse_module_state->__pyx_n_u_MQ);
6394 Py_VISIT(traverse_module_state->__pyx_n_s_MemoryError);
6395 Py_VISIT(traverse_module_state->__pyx_n_u_N);
6396 Py_VISIT(traverse_module_state->__pyx_n_s_NT_ALLELES);
6397 Py_VISIT(traverse_module_state->__pyx_n_s_NT_GENOTYPES);
6398 Py_VISIT(traverse_module_state->__pyx_n_s_NT_NR_ALLELES);
6399 Py_VISIT(traverse_module_state->__pyx_n_s_NT_NUMBER);
6400 Py_VISIT(traverse_module_state->__pyx_n_s_NT_PHASED_GENOTYPES);
6401 Py_VISIT(traverse_module_state->__pyx_n_s_NT_UNKNOWN);
6402 Py_VISIT(traverse_module_state->__pyx_n_s_NotImplementedError);
6403 Py_VISIT(traverse_module_state->__pyx_kp_u_Number);
6404 Py_VISIT(traverse_module_state->__pyx_n_u_Number_2);
6405 Py_VISIT(traverse_module_state->__pyx_n_b_PASS);
6406 Py_VISIT(traverse_module_state->__pyx_n_u_PASS);
6407 Py_VISIT(traverse_module_state->__pyx_n_u_PL);
6408 Py_VISIT(traverse_module_state->__pyx_n_u_POS);
6409 Py_VISIT(traverse_module_state->__pyx_n_s_POS_NOT_NUMERICAL);
6410 Py_VISIT(traverse_module_state->__pyx_kp_u_POS_NOT_NUMERICAL_Position_colum);
6411 Py_VISIT(traverse_module_state->__pyx_n_s_POS_NOT_POSITIVE);
6412 Py_VISIT(traverse_module_state->__pyx_kp_u_POS_NOT_POSITIVE_Position_field);
6413 Py_VISIT(traverse_module_state->__pyx_n_u_PQ);
6414 Py_VISIT(traverse_module_state->__pyx_n_u_PS);
6415 Py_VISIT(traverse_module_state->__pyx_kp_u_Phase_set);
6416 Py_VISIT(traverse_module_state->__pyx_kp_u_Phasing_quality);
6417 Py_VISIT(traverse_module_state->__pyx_kp_u_Phred_scaled_genotype_likelihood);
6418 Py_VISIT(traverse_module_state->__pyx_n_s_PickleError);
6419 Py_VISIT(traverse_module_state->__pyx_n_u_QUAL);
6420 Py_VISIT(traverse_module_state->__pyx_n_s_QUAL_NOT_NUMERICAL);
6421 Py_VISIT(traverse_module_state->__pyx_kp_u_QUAL_NOT_NUMERICAL_Quality_field);
6422 Py_VISIT(traverse_module_state->__pyx_n_u_REF);
6423 Py_VISIT(traverse_module_state->__pyx_kp_u_RMS_mapping_quality);
6424 Py_VISIT(traverse_module_state->__pyx_kp_u_Read_depth_at_this_position_for);
6425 Py_VISIT(traverse_module_state->__pyx_kp_u_Required_key_s_not_found_in_data);
6426 Py_VISIT(traverse_module_state->__pyx_kp_u_Sample_Genotype_Filter);
6427 Py_VISIT(traverse_module_state->__pyx_n_s_StopIteration);
6428 Py_VISIT(traverse_module_state->__pyx_n_u_String);
6429 Py_VISIT(traverse_module_state->__pyx_n_s_Tabixfile);
6430 Py_VISIT(traverse_module_state->__pyx_kp_u_Type);
6431 Py_VISIT(traverse_module_state->__pyx_n_s_TypeError);
6432 Py_VISIT(traverse_module_state->__pyx_n_u_Type_2);
6433 Py_VISIT(traverse_module_state->__pyx_n_s_UNKNOWN_CHAR_IN_REF);
6434 Py_VISIT(traverse_module_state->__pyx_kp_u_UNKNOWN_CHAR_IN_REF_Unknown_char);
6435 Py_VISIT(traverse_module_state->__pyx_n_s_UNKNOWN_FORMAT_STRING);
6436 Py_VISIT(traverse_module_state->__pyx_kp_u_UNKNOWN_FORMAT_STRING_Unknown_fi);
6437 Py_VISIT(traverse_module_state->__pyx_kp_u_Undefined_tag);
6438 Py_VISIT(traverse_module_state->__pyx_kp_u_Unknown_number_type_encountered);
6439 Py_VISIT(traverse_module_state->__pyx_n_s_V33_BAD_ALLELE);
6440 Py_VISIT(traverse_module_state->__pyx_kp_u_V33_BAD_ALLELE_Cannot_interpret);
6441 Py_VISIT(traverse_module_state->__pyx_n_s_V33_BAD_REF);
6442 Py_VISIT(traverse_module_state->__pyx_kp_u_V33_BAD_REF_Reference_should_be);
6443 Py_VISIT(traverse_module_state->__pyx_n_s_V33_UNMATCHED_DELETION);
6444 Py_VISIT(traverse_module_state->__pyx_kp_u_V33_UNMATCHED_DELETION_Deleted_s);
6445 Py_VISIT(traverse_module_state->__pyx_n_s_V40_BAD_ALLELE);
6446 Py_VISIT(traverse_module_state->__pyx_kp_u_V40_BAD_ALLELE_Bad_allele_found);
6447 Py_VISIT(traverse_module_state->__pyx_n_s_V40_FORMAT_MUST_HAVE_NAMED_FIELD);
6448 Py_VISIT(traverse_module_state->__pyx_kp_u_V40_FORMAT_MUST_HAVE_NAMED_FIELD_2);
6449 Py_VISIT(traverse_module_state->__pyx_n_s_V40_MISSING_ANGLE_BRACKETS);
6450 Py_VISIT(traverse_module_state->__pyx_kp_u_V40_MISSING_ANGLE_BRACKETS_Forma);
6451 Py_VISIT(traverse_module_state->__pyx_n_s_VCF);
6452 Py_VISIT(traverse_module_state->__pyx_n_u_VCF);
6453 Py_VISIT(traverse_module_state->__pyx_n_s_VCFRecord);
6454 Py_VISIT(traverse_module_state->__pyx_n_u_VCFRecord);
6455 Py_VISIT(traverse_module_state->__pyx_n_s_VCFRecord___reduce_cython);
6456 Py_VISIT(traverse_module_state->__pyx_n_s_VCFRecord___setstate_cython);
6457 Py_VISIT(traverse_module_state->__pyx_n_s_VCFRecord_error);
6458 Py_VISIT(traverse_module_state->__pyx_n_s_VCF___del);
6459 Py_VISIT(traverse_module_state->__pyx_n_s_VCF___init);
6460 Py_VISIT(traverse_module_state->__pyx_n_s_VCF__add_definition);
6461 Py_VISIT(traverse_module_state->__pyx_n_s_VCF__parse);
6462 Py_VISIT(traverse_module_state->__pyx_n_s_VCF__parse_header);
6463 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_close);
6464 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_compare_calls);
6465 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_connect);
6466 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_convertGT);
6467 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_convertGTback);
6468 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_enter_default_format);
6469 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_error);
6470 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_fetch);
6471 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_format_format);
6472 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_format_formatdata);
6473 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_get_expected);
6474 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_getfilter);
6475 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_getformat);
6476 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_getheader);
6477 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_getinfo);
6478 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_getsamples);
6479 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_ignoreerror);
6480 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_inregion);
6481 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_parse);
6482 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_parse_data);
6483 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_parse_format);
6484 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_parse_formatdata);
6485 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_parse_header);
6486 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_parse_heading);
6487 Py_VISIT(traverse_module_state->__pyx_kp_u_VCF_says);
6488 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_setfilter);
6489 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_setformat);
6490 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_setheader);
6491 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_setinfo);
6492 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_setreference);
6493 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_setregions);
6494 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_setsamples);
6495 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_setversion);
6496 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_validate);
6497 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_warnerror);
6498 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_write);
6499 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_write_data);
6500 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_write_header);
6501 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_write_heading);
6502 Py_VISIT(traverse_module_state->__pyx_n_s_VCF_writeheader);
6503 Py_VISIT(traverse_module_state->__pyx_kp_u_VCFv3_3);
6504 Py_VISIT(traverse_module_state->__pyx_kp_u_VCFv4_0);
6505 Py_VISIT(traverse_module_state->__pyx_kp_u_VCFv4_1);
6506 Py_VISIT(traverse_module_state->__pyx_kp_u_VCFv4_2);
6507 Py_VISIT(traverse_module_state->__pyx_n_s_ValueError);
6508 Py_VISIT(traverse_module_state->__pyx_n_s_WRONG_REF);
6509 Py_VISIT(traverse_module_state->__pyx_kp_u_WRONG_REF_Wrong_reference_s);
6510 Py_VISIT(traverse_module_state->__pyx_n_u_Warning);
6511 Py_VISIT(traverse_module_state->__pyx_n_s_ZERO_FOR_NON_FLAG_FIELD);
6512 Py_VISIT(traverse_module_state->__pyx_kp_u_ZERO_FOR_NON_FLAG_FIELD_number_s);
6513 Py_VISIT(traverse_module_state->__pyx_n_s_ZERO_LENGTH_ALLELE);
6514 Py_VISIT(traverse_module_state->__pyx_kp_u_ZERO_LENGTH_ALLELE_Found_zero_le);
6515 Py_VISIT(traverse_module_state->__pyx_kp_u__10);
6516 Py_VISIT(traverse_module_state->__pyx_kp_u__11);
6517 Py_VISIT(traverse_module_state->__pyx_kp_u__12);
6518 Py_VISIT(traverse_module_state->__pyx_kp_u__13);
6519 Py_VISIT(traverse_module_state->__pyx_n_s__139);
6520 Py_VISIT(traverse_module_state->__pyx_kp_u__14);
6521 Py_VISIT(traverse_module_state->__pyx_kp_u__15);
6522 Py_VISIT(traverse_module_state->__pyx_kp_u__16);
6523 Py_VISIT(traverse_module_state->__pyx_kp_u__19);
6524 Py_VISIT(traverse_module_state->__pyx_kp_u__2);
6525 Py_VISIT(traverse_module_state->__pyx_kp_u__23);
6526 Py_VISIT(traverse_module_state->__pyx_kp_u__24);
6527 Py_VISIT(traverse_module_state->__pyx_kp_u__25);
6528 Py_VISIT(traverse_module_state->__pyx_kp_u__27);
6529 Py_VISIT(traverse_module_state->__pyx_kp_u__3);
6530 Py_VISIT(traverse_module_state->__pyx_n_s__33);
6531 Py_VISIT(traverse_module_state->__pyx_kp_u__34);
6532 Py_VISIT(traverse_module_state->__pyx_kp_u__4);
6533 Py_VISIT(traverse_module_state->__pyx_kp_b__5);
6534 Py_VISIT(traverse_module_state->__pyx_kp_u__5);
6535 Py_VISIT(traverse_module_state->__pyx_kp_u__6);
6536 Py_VISIT(traverse_module_state->__pyx_kp_u__7);
6537 Py_VISIT(traverse_module_state->__pyx_kp_u__8);
6538 Py_VISIT(traverse_module_state->__pyx_n_s_a);
6539 Py_VISIT(traverse_module_state->__pyx_n_s_add);
6540 Py_VISIT(traverse_module_state->__pyx_n_s_add_definition);
6541 Py_VISIT(traverse_module_state->__pyx_n_s_addn);
6542 Py_VISIT(traverse_module_state->__pyx_n_s_addns);
6543 Py_VISIT(traverse_module_state->__pyx_n_s_all);
6544 Py_VISIT(traverse_module_state->__pyx_n_s_allele);
6545 Py_VISIT(traverse_module_state->__pyx_n_s_alleleRegEx);
6546 Py_VISIT(traverse_module_state->__pyx_kp_u_alleles);
6547 Py_VISIT(traverse_module_state->__pyx_n_s_alt);
6548 Py_VISIT(traverse_module_state->__pyx_n_u_alt);
6549 Py_VISIT(traverse_module_state->__pyx_n_s_alt1);
6550 Py_VISIT(traverse_module_state->__pyx_n_s_alt2);
6551 Py_VISIT(traverse_module_state->__pyx_n_s_append);
6552 Py_VISIT(traverse_module_state->__pyx_n_s_args);
6553 Py_VISIT(traverse_module_state->__pyx_n_s_asVCFRecord);
6554 Py_VISIT(traverse_module_state->__pyx_n_s_asVCFRecord___reduce_cython);
6555 Py_VISIT(traverse_module_state->__pyx_n_s_asVCFRecord___setstate_cython);
6556 Py_VISIT(traverse_module_state->__pyx_n_u_ascii);
6557 Py_VISIT(traverse_module_state->__pyx_n_s_asyncio_coroutines);
6558 Py_VISIT(traverse_module_state->__pyx_n_s_bisect);
6559 Py_VISIT(traverse_module_state->__pyx_n_s_blurp);
6560 Py_VISIT(traverse_module_state->__pyx_n_s_c);
6561 Py_VISIT(traverse_module_state->__pyx_n_s_chrom);
6562 Py_VISIT(traverse_module_state->__pyx_n_u_chrom);
6563 Py_VISIT(traverse_module_state->__pyx_n_s_class_getitem);
6564 Py_VISIT(traverse_module_state->__pyx_n_s_cline_in_traceback);
6565 Py_VISIT(traverse_module_state->__pyx_n_s_close);
6566 Py_VISIT(traverse_module_state->__pyx_n_s_collections);
6567 Py_VISIT(traverse_module_state->__pyx_n_s_cols);
6568 Py_VISIT(traverse_module_state->__pyx_n_s_compare_calls);
6569 Py_VISIT(traverse_module_state->__pyx_n_s_compile);
6570 Py_VISIT(traverse_module_state->__pyx_n_s_connect);
6571 Py_VISIT(traverse_module_state->__pyx_n_s_convertGT);
6572 Py_VISIT(traverse_module_state->__pyx_n_s_convertGTback);
6573 Py_VISIT(traverse_module_state->__pyx_n_s_copy);
6574 Py_VISIT(traverse_module_state->__pyx_n_s_copy_2);
6575 Py_VISIT(traverse_module_state->__pyx_n_s_d);
6576 Py_VISIT(traverse_module_state->__pyx_n_s_data);
6577 Py_VISIT(traverse_module_state->__pyx_n_s_datagenerator);
6578 Py_VISIT(traverse_module_state->__pyx_n_s_deepcopy);
6579 Py_VISIT(traverse_module_state->__pyx_n_s_defaultdict);
6580 Py_VISIT(traverse_module_state->__pyx_n_s_del);
6581 Py_VISIT(traverse_module_state->__pyx_kp_u_deletion_is);
6582 Py_VISIT(traverse_module_state->__pyx_n_u_descr);
6583 Py_VISIT(traverse_module_state->__pyx_n_s_description);
6584 Py_VISIT(traverse_module_state->__pyx_n_s_dict);
6585 Py_VISIT(traverse_module_state->__pyx_n_s_dict_2);
6586 Py_VISIT(traverse_module_state->__pyx_n_s_dict_3);
6587 Py_VISIT(traverse_module_state->__pyx_kp_u_disable);
6588 Py_VISIT(traverse_module_state->__pyx_n_s_doc);
6589 Py_VISIT(traverse_module_state->__pyx_n_s_elts);
6590 Py_VISIT(traverse_module_state->__pyx_kp_u_enable);
6591 Py_VISIT(traverse_module_state->__pyx_n_s_encoding);
6592 Py_VISIT(traverse_module_state->__pyx_n_s_end);
6593 Py_VISIT(traverse_module_state->__pyx_n_s_endswith);
6594 Py_VISIT(traverse_module_state->__pyx_n_s_enter_default_format);
6595 Py_VISIT(traverse_module_state->__pyx_n_s_enumerate);
6596 Py_VISIT(traverse_module_state->__pyx_n_s_err);
6597 Py_VISIT(traverse_module_state->__pyx_n_s_error);
6598 Py_VISIT(traverse_module_state->__pyx_n_s_errorlabel);
6599 Py_VISIT(traverse_module_state->__pyx_n_s_errors);
6600 Py_VISIT(traverse_module_state->__pyx_n_s_errorstring);
6601 Py_VISIT(traverse_module_state->__pyx_n_s_errwarn);
6602 Py_VISIT(traverse_module_state->__pyx_kp_u_expected);
6603 Py_VISIT(traverse_module_state->__pyx_kp_u_expected_2);
6604 Py_VISIT(traverse_module_state->__pyx_kp_u_expected_3);
6605 Py_VISIT(traverse_module_state->__pyx_n_s_expected_4);
6606 Py_VISIT(traverse_module_state->__pyx_n_s_f);
6607 Py_VISIT(traverse_module_state->__pyx_n_s_fa);
6608 Py_VISIT(traverse_module_state->__pyx_n_s_faref);
6609 Py_VISIT(traverse_module_state->__pyx_n_s_faref_leftflank);
6610 Py_VISIT(traverse_module_state->__pyx_n_s_fetch);
6611 Py_VISIT(traverse_module_state->__pyx_n_u_fileformat);
6612 Py_VISIT(traverse_module_state->__pyx_kp_u_fileformat_VCFv);
6613 Py_VISIT(traverse_module_state->__pyx_n_s_filename);
6614 Py_VISIT(traverse_module_state->__pyx_n_s_filter);
6615 Py_VISIT(traverse_module_state->__pyx_n_s_filter_2);
6616 Py_VISIT(traverse_module_state->__pyx_n_u_filter_2);
6617 Py_VISIT(traverse_module_state->__pyx_n_s_find);
6618 Py_VISIT(traverse_module_state->__pyx_n_s_first);
6619 Py_VISIT(traverse_module_state->__pyx_n_s_fmt);
6620 Py_VISIT(traverse_module_state->__pyx_kp_u_for);
6621 Py_VISIT(traverse_module_state->__pyx_n_s_format);
6622 Py_VISIT(traverse_module_state->__pyx_n_u_format);
6623 Py_VISIT(traverse_module_state->__pyx_n_s_format_2);
6624 Py_VISIT(traverse_module_state->__pyx_n_s_format_format);
6625 Py_VISIT(traverse_module_state->__pyx_n_s_format_formatdata);
6626 Py_VISIT(traverse_module_state->__pyx_n_s_formatdict);
6627 Py_VISIT(traverse_module_state->__pyx_kp_u_found);
6628 Py_VISIT(traverse_module_state->__pyx_kp_u_gc);
6629 Py_VISIT(traverse_module_state->__pyx_kp_u_genotypes);
6630 Py_VISIT(traverse_module_state->__pyx_n_s_get);
6631 Py_VISIT(traverse_module_state->__pyx_n_s_get_expected);
6632 Py_VISIT(traverse_module_state->__pyx_n_s_get_sequence);
6633 Py_VISIT(traverse_module_state->__pyx_n_s_getfilter);
6634 Py_VISIT(traverse_module_state->__pyx_n_s_getformat);
6635 Py_VISIT(traverse_module_state->__pyx_n_s_getheader);
6636 Py_VISIT(traverse_module_state->__pyx_n_s_getinfo);
6637 Py_VISIT(traverse_module_state->__pyx_n_s_getsamples);
6638 Py_VISIT(traverse_module_state->__pyx_n_s_getstate);
6639 Py_VISIT(traverse_module_state->__pyx_kp_u_got);
6640 Py_VISIT(traverse_module_state->__pyx_n_s_gts);
6641 Py_VISIT(traverse_module_state->__pyx_n_s_gtsRegEx);
6642 Py_VISIT(traverse_module_state->__pyx_n_s_have_deletions);
6643 Py_VISIT(traverse_module_state->__pyx_n_s_header);
6644 Py_VISIT(traverse_module_state->__pyx_n_s_header_2);
6645 Py_VISIT(traverse_module_state->__pyx_n_s_headings);
6646 Py_VISIT(traverse_module_state->__pyx_n_s_i);
6647 Py_VISIT(traverse_module_state->__pyx_kp_u_id);
6648 Py_VISIT(traverse_module_state->__pyx_n_s_id_2);
6649 Py_VISIT(traverse_module_state->__pyx_n_u_id_2);
6650 Py_VISIT(traverse_module_state->__pyx_kp_u_id_numbertype_number_type_descri);
6651 Py_VISIT(traverse_module_state->__pyx_n_s_idx);
6652 Py_VISIT(traverse_module_state->__pyx_n_s_ielts);
6653 Py_VISIT(traverse_module_state->__pyx_n_s_ignored_errors);
6654 Py_VISIT(traverse_module_state->__pyx_n_s_ignoreerror);
6655 Py_VISIT(traverse_module_state->__pyx_n_s_import);
6656 Py_VISIT(traverse_module_state->__pyx_kp_u_in_line);
6657 Py_VISIT(traverse_module_state->__pyx_n_s_info);
6658 Py_VISIT(traverse_module_state->__pyx_n_s_info_2);
6659 Py_VISIT(traverse_module_state->__pyx_n_u_info_2);
6660 Py_VISIT(traverse_module_state->__pyx_n_s_init);
6661 Py_VISIT(traverse_module_state->__pyx_n_s_init_subclass);
6662 Py_VISIT(traverse_module_state->__pyx_n_s_initializing);
6663 Py_VISIT(traverse_module_state->__pyx_n_s_inregion);
6664 Py_VISIT(traverse_module_state->__pyx_n_s_is_coroutine);
6665 Py_VISIT(traverse_module_state->__pyx_kp_u_isenabled);
6666 Py_VISIT(traverse_module_state->__pyx_n_s_itemgetter);
6667 Py_VISIT(traverse_module_state->__pyx_n_s_itervalues);
6668 Py_VISIT(traverse_module_state->__pyx_n_s_join);
6669 Py_VISIT(traverse_module_state->__pyx_n_s_k);
6670 Py_VISIT(traverse_module_state->__pyx_n_s_key);
6671 Py_VISIT(traverse_module_state->__pyx_n_s_keys);
6672 Py_VISIT(traverse_module_state->__pyx_n_s_l);
6673 Py_VISIT(traverse_module_state->__pyx_n_s_label);
6674 Py_VISIT(traverse_module_state->__pyx_n_s_last);
6675 Py_VISIT(traverse_module_state->__pyx_n_s_last_line);
6676 Py_VISIT(traverse_module_state->__pyx_n_s_left);
6677 Py_VISIT(traverse_module_state->__pyx_n_s_leftalign);
6678 Py_VISIT(traverse_module_state->__pyx_n_s_leftalign_2);
6679 Py_VISIT(traverse_module_state->__pyx_n_s_line);
6680 Py_VISIT(traverse_module_state->__pyx_n_s_line_2);
6681 Py_VISIT(traverse_module_state->__pyx_n_s_lineno);
6682 Py_VISIT(traverse_module_state->__pyx_n_s_lineparse);
6683 Py_VISIT(traverse_module_state->__pyx_n_s_lines);
6684 Py_VISIT(traverse_module_state->__pyx_n_s_lines_2);
6685 Py_VISIT(traverse_module_state->__pyx_n_s_longest);
6686 Py_VISIT(traverse_module_state->__pyx_n_s_main);
6687 Py_VISIT(traverse_module_state->__pyx_n_s_map);
6688 Py_VISIT(traverse_module_state->__pyx_n_s_match);
6689 Py_VISIT(traverse_module_state->__pyx_n_s_metaclass);
6690 Py_VISIT(traverse_module_state->__pyx_n_s_min);
6691 Py_VISIT(traverse_module_state->__pyx_n_u_missing);
6692 Py_VISIT(traverse_module_state->__pyx_n_s_missingvalue);
6693 Py_VISIT(traverse_module_state->__pyx_n_s_module);
6694 Py_VISIT(traverse_module_state->__pyx_n_s_movable);
6695 Py_VISIT(traverse_module_state->__pyx_n_s_mro_entries);
6696 Py_VISIT(traverse_module_state->__pyx_n_s_n);
6697 Py_VISIT(traverse_module_state->__pyx_n_s_na);
6698 Py_VISIT(traverse_module_state->__pyx_n_s_name);
6699 Py_VISIT(traverse_module_state->__pyx_n_s_namedtuple);
6700 Py_VISIT(traverse_module_state->__pyx_kp_u_needs_to_be_checked);
6701 Py_VISIT(traverse_module_state->__pyx_n_s_new);
6702 Py_VISIT(traverse_module_state->__pyx_n_s_newalts);
6703 Py_VISIT(traverse_module_state->__pyx_n_s_nmb);
6704 Py_VISIT(traverse_module_state->__pyx_kp_s_no_default___reduce___due_to_non);
6705 Py_VISIT(traverse_module_state->__pyx_kp_u_nonref_alleles);
6706 Py_VISIT(traverse_module_state->__pyx_n_s_number);
6707 Py_VISIT(traverse_module_state->__pyx_n_u_number);
6708 Py_VISIT(traverse_module_state->__pyx_n_s_numbertype);
6709 Py_VISIT(traverse_module_state->__pyx_n_s_object);
6710 Py_VISIT(traverse_module_state->__pyx_n_s_operator);
6711 Py_VISIT(traverse_module_state->__pyx_n_s_opt);
6712 Py_VISIT(traverse_module_state->__pyx_kp_u_output);
6713 Py_VISIT(traverse_module_state->__pyx_n_s_output_2);
6714 Py_VISIT(traverse_module_state->__pyx_kp_u_parameters_got);
6715 Py_VISIT(traverse_module_state->__pyx_n_s_parse);
6716 Py_VISIT(traverse_module_state->__pyx_n_s_parse_2);
6717 Py_VISIT(traverse_module_state->__pyx_n_s_parse_data);
6718 Py_VISIT(traverse_module_state->__pyx_n_s_parse_format);
6719 Py_VISIT(traverse_module_state->__pyx_n_s_parse_formatdata);
6720 Py_VISIT(traverse_module_state->__pyx_n_s_parse_header);
6721 Py_VISIT(traverse_module_state->__pyx_n_s_parse_header_2);
6722 Py_VISIT(traverse_module_state->__pyx_n_s_parse_heading);
6723 Py_VISIT(traverse_module_state->__pyx_n_s_parse_regions);
6724 Py_VISIT(traverse_module_state->__pyx_n_s_parser);
6725 Py_VISIT(traverse_module_state->__pyx_kp_u_phased_genotypes);
6726 Py_VISIT(traverse_module_state->__pyx_n_s_pickle);
6727 Py_VISIT(traverse_module_state->__pyx_n_s_pos);
6728 Py_VISIT(traverse_module_state->__pyx_n_u_pos);
6729 Py_VISIT(traverse_module_state->__pyx_n_s_pos1);
6730 Py_VISIT(traverse_module_state->__pyx_n_s_pos2);
6731 Py_VISIT(traverse_module_state->__pyx_n_s_prepare);
6732 Py_VISIT(traverse_module_state->__pyx_n_s_pysam);
6733 Py_VISIT(traverse_module_state->__pyx_n_s_pysam_libcvcf);
6734 Py_VISIT(traverse_module_state->__pyx_kp_s_pysam_libcvcf_pyx);
6735 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_PickleError);
6736 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_checksum);
6737 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_result);
6738 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_state);
6739 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_type);
6740 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_asVCFRecord);
6741 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_vtable);
6742 Py_VISIT(traverse_module_state->__pyx_n_s_qual);
6743 Py_VISIT(traverse_module_state->__pyx_n_u_qual);
6744 Py_VISIT(traverse_module_state->__pyx_n_s_qualname);
6745 Py_VISIT(traverse_module_state->__pyx_n_s_r);
6746 Py_VISIT(traverse_module_state->__pyx_n_s_range);
6747 Py_VISIT(traverse_module_state->__pyx_n_s_re);
6748 Py_VISIT(traverse_module_state->__pyx_n_s_record);
6749 Py_VISIT(traverse_module_state->__pyx_n_s_reduce);
6750 Py_VISIT(traverse_module_state->__pyx_n_s_reduce_cython);
6751 Py_VISIT(traverse_module_state->__pyx_n_s_reduce_ex);
6752 Py_VISIT(traverse_module_state->__pyx_n_s_ref);
6753 Py_VISIT(traverse_module_state->__pyx_n_u_ref);
6754 Py_VISIT(traverse_module_state->__pyx_n_s_ref1);
6755 Py_VISIT(traverse_module_state->__pyx_n_s_ref2);
6756 Py_VISIT(traverse_module_state->__pyx_n_s_reference);
6757 Py_VISIT(traverse_module_state->__pyx_n_s_reference_2);
6758 Py_VISIT(traverse_module_state->__pyx_kp_u_reference_is);
6759 Py_VISIT(traverse_module_state->__pyx_kp_u_reference_is_2);
6760 Py_VISIT(traverse_module_state->__pyx_n_s_region);
6761 Py_VISIT(traverse_module_state->__pyx_n_s_regions);
6762 Py_VISIT(traverse_module_state->__pyx_n_s_regions_2);
6763 Py_VISIT(traverse_module_state->__pyx_n_s_replace);
6764 Py_VISIT(traverse_module_state->__pyx_n_s_required);
6765 Py_VISIT(traverse_module_state->__pyx_n_s_required_2);
6766 Py_VISIT(traverse_module_state->__pyx_n_s_rest);
6767 Py_VISIT(traverse_module_state->__pyx_n_s_result);
6768 Py_VISIT(traverse_module_state->__pyx_n_s_s);
6769 Py_VISIT(traverse_module_state->__pyx_n_s_sample);
6770 Py_VISIT(traverse_module_state->__pyx_n_s_sample2column);
6771 Py_VISIT(traverse_module_state->__pyx_n_s_samples);
6772 Py_VISIT(traverse_module_state->__pyx_kp_u_samples_2);
6773 Py_VISIT(traverse_module_state->__pyx_n_s_samples_3);
6774 Py_VISIT(traverse_module_state->__pyx_n_s_sdata);
6775 Py_VISIT(traverse_module_state->__pyx_n_s_self);
6776 Py_VISIT(traverse_module_state->__pyx_n_s_send);
6777 Py_VISIT(traverse_module_state->__pyx_n_s_separator);
6778 Py_VISIT(traverse_module_state->__pyx_n_s_sequence);
6779 Py_VISIT(traverse_module_state->__pyx_n_s_set_name);
6780 Py_VISIT(traverse_module_state->__pyx_n_s_setfilter);
6781 Py_VISIT(traverse_module_state->__pyx_n_s_setformat);
6782 Py_VISIT(traverse_module_state->__pyx_n_s_setheader);
6783 Py_VISIT(traverse_module_state->__pyx_n_s_setinfo);
6784 Py_VISIT(traverse_module_state->__pyx_n_s_setreference);
6785 Py_VISIT(traverse_module_state->__pyx_n_s_setregions);
6786 Py_VISIT(traverse_module_state->__pyx_n_s_setsamples);
6787 Py_VISIT(traverse_module_state->__pyx_n_s_setstate);
6788 Py_VISIT(traverse_module_state->__pyx_n_s_setstate_cython);
6789 Py_VISIT(traverse_module_state->__pyx_n_s_setversion);
6790 Py_VISIT(traverse_module_state->__pyx_n_s_shortest);
6791 Py_VISIT(traverse_module_state->__pyx_n_s_spec);
6792 Py_VISIT(traverse_module_state->__pyx_n_s_split);
6793 Py_VISIT(traverse_module_state->__pyx_n_s_start);
6794 Py_VISIT(traverse_module_state->__pyx_n_s_startswith);
6795 Py_VISIT(traverse_module_state->__pyx_n_s_state);
6796 Py_VISIT(traverse_module_state->__pyx_kp_u_sth_entry_not_found);
6797 Py_VISIT(traverse_module_state->__pyx_n_s_stream);
6798 Py_VISIT(traverse_module_state->__pyx_n_s_string);
6799 Py_VISIT(traverse_module_state->__pyx_kp_s_stringsource);
6800 Py_VISIT(traverse_module_state->__pyx_n_s_strip);
6801 Py_VISIT(traverse_module_state->__pyx_n_s_super);
6802 Py_VISIT(traverse_module_state->__pyx_n_s_sys);
6803 Py_VISIT(traverse_module_state->__pyx_n_s_t);
6804 Py_VISIT(traverse_module_state->__pyx_n_s_tabixfile);
6805 Py_VISIT(traverse_module_state->__pyx_n_s_test);
6806 Py_VISIT(traverse_module_state->__pyx_n_s_throw);
6807 Py_VISIT(traverse_module_state->__pyx_n_s_type);
6808 Py_VISIT(traverse_module_state->__pyx_n_u_type);
6809 Py_VISIT(traverse_module_state->__pyx_n_s_update);
6810 Py_VISIT(traverse_module_state->__pyx_n_s_upper);
6811 Py_VISIT(traverse_module_state->__pyx_n_s_use_setstate);
6812 Py_VISIT(traverse_module_state->__pyx_n_s_v);
6813 Py_VISIT(traverse_module_state->__pyx_n_s_validate);
6814 Py_VISIT(traverse_module_state->__pyx_n_s_value);
6815 Py_VISIT(traverse_module_state->__pyx_n_s_values);
6816 Py_VISIT(traverse_module_state->__pyx_kp_u_values_in_element);
6817 Py_VISIT(traverse_module_state->__pyx_n_s_var);
6818 Py_VISIT(traverse_module_state->__pyx_n_s_vcf);
6819 Py_VISIT(traverse_module_state->__pyx_n_s_vcffile);
6820 Py_VISIT(traverse_module_state->__pyx_n_s_version);
6821 Py_VISIT(traverse_module_state->__pyx_n_s_version_2);
6822 Py_VISIT(traverse_module_state->__pyx_n_s_warn_errors);
6823 Py_VISIT(traverse_module_state->__pyx_n_s_warnerror);
6824 Py_VISIT(traverse_module_state->__pyx_n_s_write);
6825 Py_VISIT(traverse_module_state->__pyx_n_s_write_data);
6826 Py_VISIT(traverse_module_state->__pyx_n_s_write_header);
6827 Py_VISIT(traverse_module_state->__pyx_n_s_write_heading);
6828 Py_VISIT(traverse_module_state->__pyx_n_s_writeheader);
6829 Py_VISIT(traverse_module_state->__pyx_n_s_x);
6830 Py_VISIT(traverse_module_state->__pyx_n_s_y);
6831 Py_VISIT(traverse_module_state->__pyx_n_s_zip);
6832 Py_VISIT(traverse_module_state->__pyx_float_0_0);
6833 Py_VISIT(traverse_module_state->__pyx_int_0);
6834 Py_VISIT(traverse_module_state->__pyx_int_1);
6835 Py_VISIT(traverse_module_state->__pyx_int_2);
6836 Py_VISIT(traverse_module_state->__pyx_int_3);
6837 Py_VISIT(traverse_module_state->__pyx_int_4);
6838 Py_VISIT(traverse_module_state->__pyx_int_5);
6839 Py_VISIT(traverse_module_state->__pyx_int_6);
6840 Py_VISIT(traverse_module_state->__pyx_int_7);
6841 Py_VISIT(traverse_module_state->__pyx_int_8);
6842 Py_VISIT(traverse_module_state->__pyx_int_9);
6843 Py_VISIT(traverse_module_state->__pyx_int_10);
6844 Py_VISIT(traverse_module_state->__pyx_int_11);
6845 Py_VISIT(traverse_module_state->__pyx_int_12);
6846 Py_VISIT(traverse_module_state->__pyx_int_13);
6847 Py_VISIT(traverse_module_state->__pyx_int_14);
6848 Py_VISIT(traverse_module_state->__pyx_int_15);
6849 Py_VISIT(traverse_module_state->__pyx_int_16);
6850 Py_VISIT(traverse_module_state->__pyx_int_17);
6851 Py_VISIT(traverse_module_state->__pyx_int_18);
6852 Py_VISIT(traverse_module_state->__pyx_int_19);
6853 Py_VISIT(traverse_module_state->__pyx_int_20);
6854 Py_VISIT(traverse_module_state->__pyx_int_21);
6855 Py_VISIT(traverse_module_state->__pyx_int_22);
6856 Py_VISIT(traverse_module_state->__pyx_int_23);
6857 Py_VISIT(traverse_module_state->__pyx_int_24);
6858 Py_VISIT(traverse_module_state->__pyx_int_25);
6859 Py_VISIT(traverse_module_state->__pyx_int_26);
6860 Py_VISIT(traverse_module_state->__pyx_int_27);
6861 Py_VISIT(traverse_module_state->__pyx_int_28);
6862 Py_VISIT(traverse_module_state->__pyx_int_29);
6863 Py_VISIT(traverse_module_state->__pyx_int_30);
6864 Py_VISIT(traverse_module_state->__pyx_int_31);
6865 Py_VISIT(traverse_module_state->__pyx_int_32);
6866 Py_VISIT(traverse_module_state->__pyx_int_33);
6867 Py_VISIT(traverse_module_state->__pyx_int_40);
6868 Py_VISIT(traverse_module_state->__pyx_int_100);
6869 Py_VISIT(traverse_module_state->__pyx_int_29527880);
6870 Py_VISIT(traverse_module_state->__pyx_int_214161357);
6871 Py_VISIT(traverse_module_state->__pyx_int_239654613);
6872 Py_VISIT(traverse_module_state->__pyx_int_3000000000);
6873 Py_VISIT(traverse_module_state->__pyx_int_neg_1);
6874 Py_VISIT(traverse_module_state->__pyx_slice__9);
6875 Py_VISIT(traverse_module_state->__pyx_slice__17);
6876 Py_VISIT(traverse_module_state->__pyx_slice__18);
6877 Py_VISIT(traverse_module_state->__pyx_slice__20);
6878 Py_VISIT(traverse_module_state->__pyx_slice__26);
6879 Py_VISIT(traverse_module_state->__pyx_slice__28);
6880 Py_VISIT(traverse_module_state->__pyx_tuple__21);
6881 Py_VISIT(traverse_module_state->__pyx_tuple__22);
6882 Py_VISIT(traverse_module_state->__pyx_tuple__30);
6883 Py_VISIT(traverse_module_state->__pyx_tuple__31);
6884 Py_VISIT(traverse_module_state->__pyx_tuple__32);
6885 Py_VISIT(traverse_module_state->__pyx_tuple__35);
6886 Py_VISIT(traverse_module_state->__pyx_tuple__36);
6887 Py_VISIT(traverse_module_state->__pyx_tuple__37);
6888 Py_VISIT(traverse_module_state->__pyx_tuple__39);
6889 Py_VISIT(traverse_module_state->__pyx_tuple__41);
6890 Py_VISIT(traverse_module_state->__pyx_tuple__42);
6891 Py_VISIT(traverse_module_state->__pyx_tuple__44);
6892 Py_VISIT(traverse_module_state->__pyx_tuple__45);
6893 Py_VISIT(traverse_module_state->__pyx_tuple__47);
6894 Py_VISIT(traverse_module_state->__pyx_tuple__49);
6895 Py_VISIT(traverse_module_state->__pyx_tuple__52);
6896 Py_VISIT(traverse_module_state->__pyx_tuple__53);
6897 Py_VISIT(traverse_module_state->__pyx_tuple__54);
6898 Py_VISIT(traverse_module_state->__pyx_tuple__56);
6899 Py_VISIT(traverse_module_state->__pyx_tuple__57);
6900 Py_VISIT(traverse_module_state->__pyx_tuple__59);
6901 Py_VISIT(traverse_module_state->__pyx_tuple__61);
6902 Py_VISIT(traverse_module_state->__pyx_tuple__62);
6903 Py_VISIT(traverse_module_state->__pyx_tuple__64);
6904 Py_VISIT(traverse_module_state->__pyx_tuple__66);
6905 Py_VISIT(traverse_module_state->__pyx_tuple__68);
6906 Py_VISIT(traverse_module_state->__pyx_tuple__70);
6907 Py_VISIT(traverse_module_state->__pyx_tuple__71);
6908 Py_VISIT(traverse_module_state->__pyx_tuple__73);
6909 Py_VISIT(traverse_module_state->__pyx_tuple__75);
6910 Py_VISIT(traverse_module_state->__pyx_tuple__77);
6911 Py_VISIT(traverse_module_state->__pyx_tuple__79);
6912 Py_VISIT(traverse_module_state->__pyx_tuple__81);
6913 Py_VISIT(traverse_module_state->__pyx_tuple__83);
6914 Py_VISIT(traverse_module_state->__pyx_tuple__85);
6915 Py_VISIT(traverse_module_state->__pyx_tuple__87);
6916 Py_VISIT(traverse_module_state->__pyx_tuple__89);
6917 Py_VISIT(traverse_module_state->__pyx_tuple__91);
6918 Py_VISIT(traverse_module_state->__pyx_tuple__93);
6919 Py_VISIT(traverse_module_state->__pyx_tuple__95);
6920 Py_VISIT(traverse_module_state->__pyx_tuple__97);
6921 Py_VISIT(traverse_module_state->__pyx_tuple__100);
6922 Py_VISIT(traverse_module_state->__pyx_tuple__103);
6923 Py_VISIT(traverse_module_state->__pyx_tuple__106);
6924 Py_VISIT(traverse_module_state->__pyx_tuple__109);
6925 Py_VISIT(traverse_module_state->__pyx_tuple__111);
6926 Py_VISIT(traverse_module_state->__pyx_tuple__113);
6927 Py_VISIT(traverse_module_state->__pyx_tuple__115);
6928 Py_VISIT(traverse_module_state->__pyx_tuple__117);
6929 Py_VISIT(traverse_module_state->__pyx_tuple__120);
6930 Py_VISIT(traverse_module_state->__pyx_tuple__122);
6931 Py_VISIT(traverse_module_state->__pyx_tuple__125);
6932 Py_VISIT(traverse_module_state->__pyx_tuple__127);
6933 Py_VISIT(traverse_module_state->__pyx_tuple__129);
6934 Py_VISIT(traverse_module_state->__pyx_tuple__132);
6935 Py_VISIT(traverse_module_state->__pyx_tuple__134);
6936 Py_VISIT(traverse_module_state->__pyx_tuple__135);
6937 Py_VISIT(traverse_module_state->__pyx_tuple__137);
6938 Py_VISIT(traverse_module_state->__pyx_codeobj__29);
6939 Py_VISIT(traverse_module_state->__pyx_codeobj__38);
6940 Py_VISIT(traverse_module_state->__pyx_codeobj__40);
6941 Py_VISIT(traverse_module_state->__pyx_codeobj__43);
6942 Py_VISIT(traverse_module_state->__pyx_codeobj__46);
6943 Py_VISIT(traverse_module_state->__pyx_codeobj__48);
6944 Py_VISIT(traverse_module_state->__pyx_codeobj__50);
6945 Py_VISIT(traverse_module_state->__pyx_codeobj__51);
6946 Py_VISIT(traverse_module_state->__pyx_codeobj__55);
6947 Py_VISIT(traverse_module_state->__pyx_codeobj__58);
6948 Py_VISIT(traverse_module_state->__pyx_codeobj__60);
6949 Py_VISIT(traverse_module_state->__pyx_codeobj__63);
6950 Py_VISIT(traverse_module_state->__pyx_codeobj__65);
6951 Py_VISIT(traverse_module_state->__pyx_codeobj__67);
6952 Py_VISIT(traverse_module_state->__pyx_codeobj__69);
6953 Py_VISIT(traverse_module_state->__pyx_codeobj__72);
6954 Py_VISIT(traverse_module_state->__pyx_codeobj__74);
6955 Py_VISIT(traverse_module_state->__pyx_codeobj__76);
6956 Py_VISIT(traverse_module_state->__pyx_codeobj__78);
6957 Py_VISIT(traverse_module_state->__pyx_codeobj__80);
6958 Py_VISIT(traverse_module_state->__pyx_codeobj__82);
6959 Py_VISIT(traverse_module_state->__pyx_codeobj__84);
6960 Py_VISIT(traverse_module_state->__pyx_codeobj__86);
6961 Py_VISIT(traverse_module_state->__pyx_codeobj__88);
6962 Py_VISIT(traverse_module_state->__pyx_codeobj__90);
6963 Py_VISIT(traverse_module_state->__pyx_codeobj__92);
6964 Py_VISIT(traverse_module_state->__pyx_codeobj__94);
6965 Py_VISIT(traverse_module_state->__pyx_codeobj__96);
6966 Py_VISIT(traverse_module_state->__pyx_codeobj__98);
6967 Py_VISIT(traverse_module_state->__pyx_codeobj__99);
6968 Py_VISIT(traverse_module_state->__pyx_codeobj__101);
6969 Py_VISIT(traverse_module_state->__pyx_codeobj__102);
6970 Py_VISIT(traverse_module_state->__pyx_codeobj__104);
6971 Py_VISIT(traverse_module_state->__pyx_codeobj__105);
6972 Py_VISIT(traverse_module_state->__pyx_codeobj__107);
6973 Py_VISIT(traverse_module_state->__pyx_codeobj__108);
6974 Py_VISIT(traverse_module_state->__pyx_codeobj__110);
6975 Py_VISIT(traverse_module_state->__pyx_codeobj__112);
6976 Py_VISIT(traverse_module_state->__pyx_codeobj__114);
6977 Py_VISIT(traverse_module_state->__pyx_codeobj__116);
6978 Py_VISIT(traverse_module_state->__pyx_codeobj__118);
6979 Py_VISIT(traverse_module_state->__pyx_codeobj__119);
6980 Py_VISIT(traverse_module_state->__pyx_codeobj__121);
6981 Py_VISIT(traverse_module_state->__pyx_codeobj__123);
6982 Py_VISIT(traverse_module_state->__pyx_codeobj__124);
6983 Py_VISIT(traverse_module_state->__pyx_codeobj__126);
6984 Py_VISIT(traverse_module_state->__pyx_codeobj__128);
6985 Py_VISIT(traverse_module_state->__pyx_codeobj__130);
6986 Py_VISIT(traverse_module_state->__pyx_codeobj__131);
6987 Py_VISIT(traverse_module_state->__pyx_codeobj__133);
6988 Py_VISIT(traverse_module_state->__pyx_codeobj__136);
6989 Py_VISIT(traverse_module_state->__pyx_codeobj__138);
6990 return 0;
6991 }
6992 #endif
6993 /* #### Code section: module_state_defines ### */
6994 #define __pyx_d __pyx_mstate_global->__pyx_d
6995 #define __pyx_b __pyx_mstate_global->__pyx_b
6996 #define __pyx_cython_runtime __pyx_mstate_global->__pyx_cython_runtime
6997 #define __pyx_empty_tuple __pyx_mstate_global->__pyx_empty_tuple
6998 #define __pyx_empty_bytes __pyx_mstate_global->__pyx_empty_bytes
6999 #define __pyx_empty_unicode __pyx_mstate_global->__pyx_empty_unicode
7000 #ifdef __Pyx_CyFunction_USED
7001 #define __pyx_CyFunctionType __pyx_mstate_global->__pyx_CyFunctionType
7002 #endif
7003 #ifdef __Pyx_FusedFunction_USED
7004 #define __pyx_FusedFunctionType __pyx_mstate_global->__pyx_FusedFunctionType
7005 #endif
7006 #ifdef __Pyx_Generator_USED
7007 #define __pyx_GeneratorType __pyx_mstate_global->__pyx_GeneratorType
7008 #endif
7009 #ifdef __Pyx_IterableCoroutine_USED
7010 #define __pyx_IterableCoroutineType __pyx_mstate_global->__pyx_IterableCoroutineType
7011 #endif
7012 #ifdef __Pyx_Coroutine_USED
7013 #define __pyx_CoroutineAwaitType __pyx_mstate_global->__pyx_CoroutineAwaitType
7014 #endif
7015 #ifdef __Pyx_Coroutine_USED
7016 #define __pyx_CoroutineType __pyx_mstate_global->__pyx_CoroutineType
7017 #endif
7018 #if CYTHON_USE_MODULE_STATE
7019 #endif
7020 #if CYTHON_USE_MODULE_STATE
7021 #endif
7022 #if CYTHON_USE_MODULE_STATE
7023 #endif
7024 #if CYTHON_USE_MODULE_STATE
7025 #endif
7026 #if CYTHON_USE_MODULE_STATE
7027 #endif
7028 #if CYTHON_USE_MODULE_STATE
7029 #endif
7030 #define __pyx_ptype_5pysam_10libchtslib_HTSFile __pyx_mstate_global->__pyx_ptype_5pysam_10libchtslib_HTSFile
7031 #if CYTHON_USE_MODULE_STATE
7032 #endif
7033 #define __pyx_ptype_5pysam_9libctabix_tabix_file_iterator __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_tabix_file_iterator
7034 #define __pyx_ptype_5pysam_9libctabix_TabixFile __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_TabixFile
7035 #define __pyx_ptype_5pysam_9libctabix_Parser __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_Parser
7036 #define __pyx_ptype_5pysam_9libctabix_asTuple __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asTuple
7037 #define __pyx_ptype_5pysam_9libctabix_asGTF __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asGTF
7038 #define __pyx_ptype_5pysam_9libctabix_asGFF3 __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asGFF3
7039 #define __pyx_ptype_5pysam_9libctabix_asBed __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asBed
7040 #define __pyx_ptype_5pysam_9libctabix_asVCF __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asVCF
7041 #define __pyx_ptype_5pysam_9libctabix_TabixIterator __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_TabixIterator
7042 #define __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed
7043 #define __pyx_ptype_5pysam_9libctabix_GZIterator __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_GZIterator
7044 #define __pyx_ptype_5pysam_9libctabix_GZIteratorHead __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_GZIteratorHead
7045 #define __pyx_ptype_5pysam_9libctabix_GZIteratorParsed __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_GZIteratorParsed
7046 #define __pyx_ptype_5pysam_9libctabix_Tabixfile __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_Tabixfile
7047 #if CYTHON_USE_MODULE_STATE
7048 #endif
7049 #define __pyx_ptype_5pysam_16libctabixproxies_TupleProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_TupleProxy
7050 #define __pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator
7051 #define __pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy
7052 #define __pyx_ptype_5pysam_16libctabixproxies_GTFProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_GTFProxy
7053 #define __pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy
7054 #define __pyx_ptype_5pysam_16libctabixproxies_BedProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_BedProxy
7055 #define __pyx_ptype_5pysam_16libctabixproxies_VCFProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_VCFProxy
7056 #if CYTHON_USE_MODULE_STATE
7057 #endif
7058 #if CYTHON_USE_MODULE_STATE
7059 #endif
7060 #if CYTHON_USE_MODULE_STATE
7061 #endif
7062 #if CYTHON_USE_MODULE_STATE
7063 #endif
7064 #define __pyx_ptype_7cpython_4type_type __pyx_mstate_global->__pyx_ptype_7cpython_4type_type
7065 #if CYTHON_USE_MODULE_STATE
7066 #endif
7067 #if CYTHON_USE_MODULE_STATE
7068 #endif
7069 #if CYTHON_USE_MODULE_STATE
7070 #endif
7071 #if CYTHON_USE_MODULE_STATE
7072 #endif
7073 #if CYTHON_USE_MODULE_STATE
7074 #endif
7075 #if CYTHON_USE_MODULE_STATE
7076 #endif
7077 #if CYTHON_USE_MODULE_STATE
7078 #endif
7079 #if CYTHON_USE_MODULE_STATE
7080 #endif
7081 #if CYTHON_USE_MODULE_STATE
7082 #endif
7083 #if CYTHON_USE_MODULE_STATE
7084 #endif
7085 #if CYTHON_USE_MODULE_STATE
7086 #endif
7087 #if CYTHON_USE_MODULE_STATE
7088 #endif
7089 #if CYTHON_USE_MODULE_STATE
7090 #endif
7091 #if CYTHON_USE_MODULE_STATE
7092 #endif
7093 #define __pyx_ptype_7cpython_4bool_bool __pyx_mstate_global->__pyx_ptype_7cpython_4bool_bool
7094 #if CYTHON_USE_MODULE_STATE
7095 #endif
7096 #if CYTHON_USE_MODULE_STATE
7097 #endif
7098 #if CYTHON_USE_MODULE_STATE
7099 #endif
7100 #if CYTHON_USE_MODULE_STATE
7101 #endif
7102 #define __pyx_ptype_7cpython_7complex_complex __pyx_mstate_global->__pyx_ptype_7cpython_7complex_complex
7103 #if CYTHON_USE_MODULE_STATE
7104 #endif
7105 #if CYTHON_USE_MODULE_STATE
7106 #endif
7107 #if CYTHON_USE_MODULE_STATE
7108 #endif
7109 #if CYTHON_USE_MODULE_STATE
7110 #endif
7111 #if CYTHON_USE_MODULE_STATE
7112 #endif
7113 #if CYTHON_USE_MODULE_STATE
7114 #endif
7115 #if CYTHON_USE_MODULE_STATE
7116 #endif
7117 #if CYTHON_USE_MODULE_STATE
7118 #endif
7119 #if CYTHON_USE_MODULE_STATE
7120 #endif
7121 #if CYTHON_USE_MODULE_STATE
7122 #endif
7123 #if CYTHON_USE_MODULE_STATE
7124 #endif
7125 #if CYTHON_USE_MODULE_STATE
7126 #endif
7127 #if CYTHON_USE_MODULE_STATE
7128 #endif
7129 #if CYTHON_USE_MODULE_STATE
7130 #endif
7131 #if CYTHON_USE_MODULE_STATE
7132 #endif
7133 #if CYTHON_USE_MODULE_STATE
7134 #endif
7135 #if CYTHON_USE_MODULE_STATE
7136 #endif
7137 #if CYTHON_USE_MODULE_STATE
7138 #endif
7139 #if CYTHON_USE_MODULE_STATE
7140 #endif
7141 #if CYTHON_USE_MODULE_STATE
7142 #endif
7143 #if CYTHON_USE_MODULE_STATE
7144 #endif
7145 #if CYTHON_USE_MODULE_STATE
7146 #endif
7147 #define __pyx_ptype_7cpython_5array_array __pyx_mstate_global->__pyx_ptype_7cpython_5array_array
7148 #if CYTHON_USE_MODULE_STATE
7149 #endif
7150 #if CYTHON_USE_MODULE_STATE
7151 #define __pyx_type_5pysam_7libcvcf_VCFRecord __pyx_mstate_global->__pyx_type_5pysam_7libcvcf_VCFRecord
7152 #define __pyx_type_5pysam_7libcvcf_asVCFRecord __pyx_mstate_global->__pyx_type_5pysam_7libcvcf_asVCFRecord
7153 #define __pyx_type_5pysam_7libcvcf___pyx_scope_struct___parse __pyx_mstate_global->__pyx_type_5pysam_7libcvcf___pyx_scope_struct___parse
7154 #endif
7155 #define __pyx_ptype_5pysam_7libcvcf_VCFRecord __pyx_mstate_global->__pyx_ptype_5pysam_7libcvcf_VCFRecord
7156 #define __pyx_ptype_5pysam_7libcvcf_asVCFRecord __pyx_mstate_global->__pyx_ptype_5pysam_7libcvcf_asVCFRecord
7157 #define __pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse __pyx_mstate_global->__pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse
7158 #define __pyx_kp_u_ __pyx_mstate_global->__pyx_kp_u_
7159 #define __pyx_kp_b_0 __pyx_mstate_global->__pyx_kp_b_0
7160 #define __pyx_kp_u_0 __pyx_mstate_global->__pyx_kp_u_0
7161 #define __pyx_n_u_A __pyx_mstate_global->__pyx_n_u_A
7162 #define __pyx_n_u_ACGTN __pyx_mstate_global->__pyx_n_u_ACGTN
7163 #define __pyx_kp_u_ACGTN_2 __pyx_mstate_global->__pyx_kp_u_ACGTN_2
7164 #define __pyx_n_u_ALT __pyx_mstate_global->__pyx_n_u_ALT
7165 #define __pyx_n_s_AssertionError __pyx_mstate_global->__pyx_n_s_AssertionError
7166 #define __pyx_n_s_BADLY_FORMATTED_FORMAT_STRING __pyx_mstate_global->__pyx_n_s_BADLY_FORMATTED_FORMAT_STRING
7167 #define __pyx_kp_u_BADLY_FORMATTED_FORMAT_STRING_Fo __pyx_mstate_global->__pyx_kp_u_BADLY_FORMATTED_FORMAT_STRING_Fo
7168 #define __pyx_n_s_BADLY_FORMATTED_HEADING __pyx_mstate_global->__pyx_n_s_BADLY_FORMATTED_HEADING
7169 #define __pyx_kp_u_BADLY_FORMATTED_HEADING_Did_not __pyx_mstate_global->__pyx_kp_u_BADLY_FORMATTED_HEADING_Did_not
7170 #define __pyx_kp_u_BAD_CHR_TAG_Error_calculating_ch __pyx_mstate_global->__pyx_kp_u_BAD_CHR_TAG_Error_calculating_ch
7171 #define __pyx_n_s_BAD_GENOTYPE __pyx_mstate_global->__pyx_n_s_BAD_GENOTYPE
7172 #define __pyx_kp_u_BAD_GENOTYPE_Cannot_parse_genoty __pyx_mstate_global->__pyx_kp_u_BAD_GENOTYPE_Cannot_parse_genoty
7173 #define __pyx_n_s_BAD_NUMBER_OF_COLUMNS __pyx_mstate_global->__pyx_n_s_BAD_NUMBER_OF_COLUMNS
7174 #define __pyx_kp_u_BAD_NUMBER_OF_COLUMNS_Wrong_numb __pyx_mstate_global->__pyx_kp_u_BAD_NUMBER_OF_COLUMNS_Wrong_numb
7175 #define __pyx_n_s_BAD_NUMBER_OF_PARAMETERS __pyx_mstate_global->__pyx_n_s_BAD_NUMBER_OF_PARAMETERS
7176 #define __pyx_kp_u_BAD_NUMBER_OF_PARAMETERS_Found_u __pyx_mstate_global->__pyx_kp_u_BAD_NUMBER_OF_PARAMETERS_Found_u
7177 #define __pyx_n_s_BAD_NUMBER_OF_VALUES __pyx_mstate_global->__pyx_n_s_BAD_NUMBER_OF_VALUES
7178 #define __pyx_kp_u_BAD_NUMBER_OF_VALUES_Found_too_m __pyx_mstate_global->__pyx_kp_u_BAD_NUMBER_OF_VALUES_Found_too_m
7179 #define __pyx_n_u_CHROM __pyx_mstate_global->__pyx_n_u_CHROM
7180 #define __pyx_kp_u_Can_only_handle_v3_3_and_v4_0_VC __pyx_mstate_global->__pyx_kp_u_Can_only_handle_v3_3_and_v4_0_VC
7181 #define __pyx_n_u_Character __pyx_mstate_global->__pyx_n_u_Character
7182 #define __pyx_kp_u_Conditional_genotype_quality __pyx_mstate_global->__pyx_kp_u_Conditional_genotype_quality
7183 #define __pyx_n_u_D __pyx_mstate_global->__pyx_n_u_D
7184 #define __pyx_n_u_DP __pyx_mstate_global->__pyx_n_u_DP
7185 #define __pyx_kp_u_Description __pyx_mstate_global->__pyx_kp_u_Description
7186 #define __pyx_n_u_Description_2 __pyx_mstate_global->__pyx_n_u_Description_2
7187 #define __pyx_kp_u_Don_t_understand_region_string_s __pyx_mstate_global->__pyx_kp_u_Don_t_understand_region_string_s
7188 #define __pyx_n_u_EC __pyx_mstate_global->__pyx_n_u_EC
7189 #define __pyx_n_s_ERROR_FLAG_HAS_VALUE __pyx_mstate_global->__pyx_n_s_ERROR_FLAG_HAS_VALUE
7190 #define __pyx_kp_u_ERROR_FLAG_HAS_VALUE_Flag_fields __pyx_mstate_global->__pyx_kp_u_ERROR_FLAG_HAS_VALUE_Flag_fields
7191 #define __pyx_n_s_ERROR_FORMAT_NOT_CHAR __pyx_mstate_global->__pyx_n_s_ERROR_FORMAT_NOT_CHAR
7192 #define __pyx_kp_u_ERROR_FORMAT_NOT_CHAR_Eexpected __pyx_mstate_global->__pyx_kp_u_ERROR_FORMAT_NOT_CHAR_Eexpected
7193 #define __pyx_n_s_ERROR_FORMAT_NOT_INTEGER __pyx_mstate_global->__pyx_n_s_ERROR_FORMAT_NOT_INTEGER
7194 #define __pyx_kp_u_ERROR_FORMAT_NOT_INTEGER_Expecte __pyx_mstate_global->__pyx_kp_u_ERROR_FORMAT_NOT_INTEGER_Expecte
7195 #define __pyx_n_s_ERROR_FORMAT_NOT_NUMERICAL __pyx_mstate_global->__pyx_n_s_ERROR_FORMAT_NOT_NUMERICAL
7196 #define __pyx_kp_u_ERROR_FORMAT_NOT_NUMERICAL_Expec __pyx_mstate_global->__pyx_kp_u_ERROR_FORMAT_NOT_NUMERICAL_Expec
7197 #define __pyx_n_s_ERROR_INFO_STRING __pyx_mstate_global->__pyx_n_s_ERROR_INFO_STRING
7198 #define __pyx_kp_u_ERROR_INFO_STRING_Error_while_pa __pyx_mstate_global->__pyx_kp_u_ERROR_INFO_STRING_Error_while_pa
7199 #define __pyx_n_s_ERROR_TRAILING_DATA __pyx_mstate_global->__pyx_n_s_ERROR_TRAILING_DATA
7200 #define __pyx_kp_u_ERROR_TRAILING_DATA_Numerical_fi __pyx_mstate_global->__pyx_kp_u_ERROR_TRAILING_DATA_Numerical_fi
7201 #define __pyx_n_s_ERROR_UNKNOWN_KEY __pyx_mstate_global->__pyx_n_s_ERROR_UNKNOWN_KEY
7202 #define __pyx_kp_u_ERROR_UNKNOWN_KEY_Unknown_key_s __pyx_mstate_global->__pyx_kp_u_ERROR_UNKNOWN_KEY_Unknown_key_s
7203 #define __pyx_n_u_Error __pyx_mstate_global->__pyx_n_u_Error
7204 #define __pyx_kp_u_Expected_alternate_allel_counts __pyx_mstate_global->__pyx_kp_u_Expected_alternate_allel_counts
7205 #define __pyx_n_u_FILTER __pyx_mstate_global->__pyx_n_u_FILTER
7206 #define __pyx_n_s_FILTER_NOT_DEFINED __pyx_mstate_global->__pyx_n_s_FILTER_NOT_DEFINED
7207 #define __pyx_kp_u_FILTER_NOT_DEFINED_Identifier_s __pyx_mstate_global->__pyx_kp_u_FILTER_NOT_DEFINED_Identifier_s
7208 #define __pyx_n_s_FORMAT __pyx_mstate_global->__pyx_n_s_FORMAT
7209 #define __pyx_n_u_FORMAT __pyx_mstate_global->__pyx_n_u_FORMAT
7210 #define __pyx_n_s_FORMAT_MISSING_QUOTES __pyx_mstate_global->__pyx_n_s_FORMAT_MISSING_QUOTES
7211 #define __pyx_kp_u_FORMAT_MISSING_QUOTES_Descriptio __pyx_mstate_global->__pyx_kp_u_FORMAT_MISSING_QUOTES_Descriptio
7212 #define __pyx_n_s_FORMAT_NOT_DEFINED __pyx_mstate_global->__pyx_n_s_FORMAT_NOT_DEFINED
7213 #define __pyx_kp_u_FORMAT_NOT_DEFINED_Identifier_s __pyx_mstate_global->__pyx_kp_u_FORMAT_NOT_DEFINED_Identifier_s
7214 #define __pyx_n_u_FT __pyx_mstate_global->__pyx_n_u_FT
7215 #define __pyx_n_u_Flag __pyx_mstate_global->__pyx_n_u_Flag
7216 #define __pyx_n_u_Float __pyx_mstate_global->__pyx_n_u_Float
7217 #define __pyx_n_u_G __pyx_mstate_global->__pyx_n_u_G
7218 #define __pyx_n_u_GL __pyx_mstate_global->__pyx_n_u_GL
7219 #define __pyx_n_u_GLE __pyx_mstate_global->__pyx_n_u_GLE
7220 #define __pyx_n_u_GP __pyx_mstate_global->__pyx_n_u_GP
7221 #define __pyx_n_u_GQ __pyx_mstate_global->__pyx_n_u_GQ
7222 #define __pyx_n_u_GT __pyx_mstate_global->__pyx_n_u_GT
7223 #define __pyx_n_s_GTdata __pyx_mstate_global->__pyx_n_s_GTdata
7224 #define __pyx_n_s_GTstring __pyx_mstate_global->__pyx_n_s_GTstring
7225 #define __pyx_n_u_Genotype __pyx_mstate_global->__pyx_n_u_Genotype
7226 #define __pyx_kp_u_Genotype_Quality __pyx_mstate_global->__pyx_kp_u_Genotype_Quality
7227 #define __pyx_kp_u_Genotype_likelihoods __pyx_mstate_global->__pyx_kp_u_Genotype_likelihoods
7228 #define __pyx_kp_u_Genotype_posterior_probabilities __pyx_mstate_global->__pyx_kp_u_Genotype_posterior_probabilities
7229 #define __pyx_n_s_HEADING_NOT_SEPARATED_BY_TABS __pyx_mstate_global->__pyx_n_s_HEADING_NOT_SEPARATED_BY_TABS
7230 #define __pyx_kp_u_HEADING_NOT_SEPARATED_BY_TABS_He __pyx_mstate_global->__pyx_kp_u_HEADING_NOT_SEPARATED_BY_TABS_He
7231 #define __pyx_n_u_HQ __pyx_mstate_global->__pyx_n_u_HQ
7232 #define __pyx_kp_u_Haplotype_Quality __pyx_mstate_global->__pyx_kp_u_Haplotype_Quality
7233 #define __pyx_n_u_I __pyx_mstate_global->__pyx_n_u_I
7234 #define __pyx_kp_u_ID __pyx_mstate_global->__pyx_kp_u_ID
7235 #define __pyx_n_u_ID_2 __pyx_mstate_global->__pyx_n_u_ID_2
7236 #define __pyx_n_u_INFO __pyx_mstate_global->__pyx_n_u_INFO
7237 #define __pyx_kp_s_Incompatible_checksums_0x_x_vs_0 __pyx_mstate_global->__pyx_kp_s_Incompatible_checksums_0x_x_vs_0
7238 #define __pyx_n_u_Integer __pyx_mstate_global->__pyx_n_u_Integer
7239 #define __pyx_kp_u_Invalid_error_string_s __pyx_mstate_global->__pyx_kp_u_Invalid_error_string_s
7240 #define __pyx_n_s_KeyError __pyx_mstate_global->__pyx_n_s_KeyError
7241 #define __pyx_n_s_MISSING_INDEL_ALLELE_REF_BASE __pyx_mstate_global->__pyx_n_s_MISSING_INDEL_ALLELE_REF_BASE
7242 #define __pyx_kp_u_MISSING_INDEL_ALLELE_REF_BASE_In __pyx_mstate_global->__pyx_kp_u_MISSING_INDEL_ALLELE_REF_BASE_In
7243 #define __pyx_n_s_MISSING_REF __pyx_mstate_global->__pyx_n_s_MISSING_REF
7244 #define __pyx_kp_u_MISSING_REF_Reference_allele_mis __pyx_mstate_global->__pyx_kp_u_MISSING_REF_Reference_allele_mis
7245 #define __pyx_n_u_MQ __pyx_mstate_global->__pyx_n_u_MQ
7246 #define __pyx_n_s_MemoryError __pyx_mstate_global->__pyx_n_s_MemoryError
7247 #define __pyx_n_u_N __pyx_mstate_global->__pyx_n_u_N
7248 #define __pyx_n_s_NT_ALLELES __pyx_mstate_global->__pyx_n_s_NT_ALLELES
7249 #define __pyx_n_s_NT_GENOTYPES __pyx_mstate_global->__pyx_n_s_NT_GENOTYPES
7250 #define __pyx_n_s_NT_NR_ALLELES __pyx_mstate_global->__pyx_n_s_NT_NR_ALLELES
7251 #define __pyx_n_s_NT_NUMBER __pyx_mstate_global->__pyx_n_s_NT_NUMBER
7252 #define __pyx_n_s_NT_PHASED_GENOTYPES __pyx_mstate_global->__pyx_n_s_NT_PHASED_GENOTYPES
7253 #define __pyx_n_s_NT_UNKNOWN __pyx_mstate_global->__pyx_n_s_NT_UNKNOWN
7254 #define __pyx_n_s_NotImplementedError __pyx_mstate_global->__pyx_n_s_NotImplementedError
7255 #define __pyx_kp_u_Number __pyx_mstate_global->__pyx_kp_u_Number
7256 #define __pyx_n_u_Number_2 __pyx_mstate_global->__pyx_n_u_Number_2
7257 #define __pyx_n_b_PASS __pyx_mstate_global->__pyx_n_b_PASS
7258 #define __pyx_n_u_PASS __pyx_mstate_global->__pyx_n_u_PASS
7259 #define __pyx_n_u_PL __pyx_mstate_global->__pyx_n_u_PL
7260 #define __pyx_n_u_POS __pyx_mstate_global->__pyx_n_u_POS
7261 #define __pyx_n_s_POS_NOT_NUMERICAL __pyx_mstate_global->__pyx_n_s_POS_NOT_NUMERICAL
7262 #define __pyx_kp_u_POS_NOT_NUMERICAL_Position_colum __pyx_mstate_global->__pyx_kp_u_POS_NOT_NUMERICAL_Position_colum
7263 #define __pyx_n_s_POS_NOT_POSITIVE __pyx_mstate_global->__pyx_n_s_POS_NOT_POSITIVE
7264 #define __pyx_kp_u_POS_NOT_POSITIVE_Position_field __pyx_mstate_global->__pyx_kp_u_POS_NOT_POSITIVE_Position_field
7265 #define __pyx_n_u_PQ __pyx_mstate_global->__pyx_n_u_PQ
7266 #define __pyx_n_u_PS __pyx_mstate_global->__pyx_n_u_PS
7267 #define __pyx_kp_u_Phase_set __pyx_mstate_global->__pyx_kp_u_Phase_set
7268 #define __pyx_kp_u_Phasing_quality __pyx_mstate_global->__pyx_kp_u_Phasing_quality
7269 #define __pyx_kp_u_Phred_scaled_genotype_likelihood __pyx_mstate_global->__pyx_kp_u_Phred_scaled_genotype_likelihood
7270 #define __pyx_n_s_PickleError __pyx_mstate_global->__pyx_n_s_PickleError
7271 #define __pyx_n_u_QUAL __pyx_mstate_global->__pyx_n_u_QUAL
7272 #define __pyx_n_s_QUAL_NOT_NUMERICAL __pyx_mstate_global->__pyx_n_s_QUAL_NOT_NUMERICAL
7273 #define __pyx_kp_u_QUAL_NOT_NUMERICAL_Quality_field __pyx_mstate_global->__pyx_kp_u_QUAL_NOT_NUMERICAL_Quality_field
7274 #define __pyx_n_u_REF __pyx_mstate_global->__pyx_n_u_REF
7275 #define __pyx_kp_u_RMS_mapping_quality __pyx_mstate_global->__pyx_kp_u_RMS_mapping_quality
7276 #define __pyx_kp_u_Read_depth_at_this_position_for __pyx_mstate_global->__pyx_kp_u_Read_depth_at_this_position_for
7277 #define __pyx_kp_u_Required_key_s_not_found_in_data __pyx_mstate_global->__pyx_kp_u_Required_key_s_not_found_in_data
7278 #define __pyx_kp_u_Sample_Genotype_Filter __pyx_mstate_global->__pyx_kp_u_Sample_Genotype_Filter
7279 #define __pyx_n_s_StopIteration __pyx_mstate_global->__pyx_n_s_StopIteration
7280 #define __pyx_n_u_String __pyx_mstate_global->__pyx_n_u_String
7281 #define __pyx_n_s_Tabixfile __pyx_mstate_global->__pyx_n_s_Tabixfile
7282 #define __pyx_kp_u_Type __pyx_mstate_global->__pyx_kp_u_Type
7283 #define __pyx_n_s_TypeError __pyx_mstate_global->__pyx_n_s_TypeError
7284 #define __pyx_n_u_Type_2 __pyx_mstate_global->__pyx_n_u_Type_2
7285 #define __pyx_n_s_UNKNOWN_CHAR_IN_REF __pyx_mstate_global->__pyx_n_s_UNKNOWN_CHAR_IN_REF
7286 #define __pyx_kp_u_UNKNOWN_CHAR_IN_REF_Unknown_char __pyx_mstate_global->__pyx_kp_u_UNKNOWN_CHAR_IN_REF_Unknown_char
7287 #define __pyx_n_s_UNKNOWN_FORMAT_STRING __pyx_mstate_global->__pyx_n_s_UNKNOWN_FORMAT_STRING
7288 #define __pyx_kp_u_UNKNOWN_FORMAT_STRING_Unknown_fi __pyx_mstate_global->__pyx_kp_u_UNKNOWN_FORMAT_STRING_Unknown_fi
7289 #define __pyx_kp_u_Undefined_tag __pyx_mstate_global->__pyx_kp_u_Undefined_tag
7290 #define __pyx_kp_u_Unknown_number_type_encountered __pyx_mstate_global->__pyx_kp_u_Unknown_number_type_encountered
7291 #define __pyx_n_s_V33_BAD_ALLELE __pyx_mstate_global->__pyx_n_s_V33_BAD_ALLELE
7292 #define __pyx_kp_u_V33_BAD_ALLELE_Cannot_interpret __pyx_mstate_global->__pyx_kp_u_V33_BAD_ALLELE_Cannot_interpret
7293 #define __pyx_n_s_V33_BAD_REF __pyx_mstate_global->__pyx_n_s_V33_BAD_REF
7294 #define __pyx_kp_u_V33_BAD_REF_Reference_should_be __pyx_mstate_global->__pyx_kp_u_V33_BAD_REF_Reference_should_be
7295 #define __pyx_n_s_V33_UNMATCHED_DELETION __pyx_mstate_global->__pyx_n_s_V33_UNMATCHED_DELETION
7296 #define __pyx_kp_u_V33_UNMATCHED_DELETION_Deleted_s __pyx_mstate_global->__pyx_kp_u_V33_UNMATCHED_DELETION_Deleted_s
7297 #define __pyx_n_s_V40_BAD_ALLELE __pyx_mstate_global->__pyx_n_s_V40_BAD_ALLELE
7298 #define __pyx_kp_u_V40_BAD_ALLELE_Bad_allele_found __pyx_mstate_global->__pyx_kp_u_V40_BAD_ALLELE_Bad_allele_found
7299 #define __pyx_n_s_V40_FORMAT_MUST_HAVE_NAMED_FIELD __pyx_mstate_global->__pyx_n_s_V40_FORMAT_MUST_HAVE_NAMED_FIELD
7300 #define __pyx_kp_u_V40_FORMAT_MUST_HAVE_NAMED_FIELD_2 __pyx_mstate_global->__pyx_kp_u_V40_FORMAT_MUST_HAVE_NAMED_FIELD_2
7301 #define __pyx_n_s_V40_MISSING_ANGLE_BRACKETS __pyx_mstate_global->__pyx_n_s_V40_MISSING_ANGLE_BRACKETS
7302 #define __pyx_kp_u_V40_MISSING_ANGLE_BRACKETS_Forma __pyx_mstate_global->__pyx_kp_u_V40_MISSING_ANGLE_BRACKETS_Forma
7303 #define __pyx_n_s_VCF __pyx_mstate_global->__pyx_n_s_VCF
7304 #define __pyx_n_u_VCF __pyx_mstate_global->__pyx_n_u_VCF
7305 #define __pyx_n_s_VCFRecord __pyx_mstate_global->__pyx_n_s_VCFRecord
7306 #define __pyx_n_u_VCFRecord __pyx_mstate_global->__pyx_n_u_VCFRecord
7307 #define __pyx_n_s_VCFRecord___reduce_cython __pyx_mstate_global->__pyx_n_s_VCFRecord___reduce_cython
7308 #define __pyx_n_s_VCFRecord___setstate_cython __pyx_mstate_global->__pyx_n_s_VCFRecord___setstate_cython
7309 #define __pyx_n_s_VCFRecord_error __pyx_mstate_global->__pyx_n_s_VCFRecord_error
7310 #define __pyx_n_s_VCF___del __pyx_mstate_global->__pyx_n_s_VCF___del
7311 #define __pyx_n_s_VCF___init __pyx_mstate_global->__pyx_n_s_VCF___init
7312 #define __pyx_n_s_VCF__add_definition __pyx_mstate_global->__pyx_n_s_VCF__add_definition
7313 #define __pyx_n_s_VCF__parse __pyx_mstate_global->__pyx_n_s_VCF__parse
7314 #define __pyx_n_s_VCF__parse_header __pyx_mstate_global->__pyx_n_s_VCF__parse_header
7315 #define __pyx_n_s_VCF_close __pyx_mstate_global->__pyx_n_s_VCF_close
7316 #define __pyx_n_s_VCF_compare_calls __pyx_mstate_global->__pyx_n_s_VCF_compare_calls
7317 #define __pyx_n_s_VCF_connect __pyx_mstate_global->__pyx_n_s_VCF_connect
7318 #define __pyx_n_s_VCF_convertGT __pyx_mstate_global->__pyx_n_s_VCF_convertGT
7319 #define __pyx_n_s_VCF_convertGTback __pyx_mstate_global->__pyx_n_s_VCF_convertGTback
7320 #define __pyx_n_s_VCF_enter_default_format __pyx_mstate_global->__pyx_n_s_VCF_enter_default_format
7321 #define __pyx_n_s_VCF_error __pyx_mstate_global->__pyx_n_s_VCF_error
7322 #define __pyx_n_s_VCF_fetch __pyx_mstate_global->__pyx_n_s_VCF_fetch
7323 #define __pyx_n_s_VCF_format_format __pyx_mstate_global->__pyx_n_s_VCF_format_format
7324 #define __pyx_n_s_VCF_format_formatdata __pyx_mstate_global->__pyx_n_s_VCF_format_formatdata
7325 #define __pyx_n_s_VCF_get_expected __pyx_mstate_global->__pyx_n_s_VCF_get_expected
7326 #define __pyx_n_s_VCF_getfilter __pyx_mstate_global->__pyx_n_s_VCF_getfilter
7327 #define __pyx_n_s_VCF_getformat __pyx_mstate_global->__pyx_n_s_VCF_getformat
7328 #define __pyx_n_s_VCF_getheader __pyx_mstate_global->__pyx_n_s_VCF_getheader
7329 #define __pyx_n_s_VCF_getinfo __pyx_mstate_global->__pyx_n_s_VCF_getinfo
7330 #define __pyx_n_s_VCF_getsamples __pyx_mstate_global->__pyx_n_s_VCF_getsamples
7331 #define __pyx_n_s_VCF_ignoreerror __pyx_mstate_global->__pyx_n_s_VCF_ignoreerror
7332 #define __pyx_n_s_VCF_inregion __pyx_mstate_global->__pyx_n_s_VCF_inregion
7333 #define __pyx_n_s_VCF_parse __pyx_mstate_global->__pyx_n_s_VCF_parse
7334 #define __pyx_n_s_VCF_parse_data __pyx_mstate_global->__pyx_n_s_VCF_parse_data
7335 #define __pyx_n_s_VCF_parse_format __pyx_mstate_global->__pyx_n_s_VCF_parse_format
7336 #define __pyx_n_s_VCF_parse_formatdata __pyx_mstate_global->__pyx_n_s_VCF_parse_formatdata
7337 #define __pyx_n_s_VCF_parse_header __pyx_mstate_global->__pyx_n_s_VCF_parse_header
7338 #define __pyx_n_s_VCF_parse_heading __pyx_mstate_global->__pyx_n_s_VCF_parse_heading
7339 #define __pyx_kp_u_VCF_says __pyx_mstate_global->__pyx_kp_u_VCF_says
7340 #define __pyx_n_s_VCF_setfilter __pyx_mstate_global->__pyx_n_s_VCF_setfilter
7341 #define __pyx_n_s_VCF_setformat __pyx_mstate_global->__pyx_n_s_VCF_setformat
7342 #define __pyx_n_s_VCF_setheader __pyx_mstate_global->__pyx_n_s_VCF_setheader
7343 #define __pyx_n_s_VCF_setinfo __pyx_mstate_global->__pyx_n_s_VCF_setinfo
7344 #define __pyx_n_s_VCF_setreference __pyx_mstate_global->__pyx_n_s_VCF_setreference
7345 #define __pyx_n_s_VCF_setregions __pyx_mstate_global->__pyx_n_s_VCF_setregions
7346 #define __pyx_n_s_VCF_setsamples __pyx_mstate_global->__pyx_n_s_VCF_setsamples
7347 #define __pyx_n_s_VCF_setversion __pyx_mstate_global->__pyx_n_s_VCF_setversion
7348 #define __pyx_n_s_VCF_validate __pyx_mstate_global->__pyx_n_s_VCF_validate
7349 #define __pyx_n_s_VCF_warnerror __pyx_mstate_global->__pyx_n_s_VCF_warnerror
7350 #define __pyx_n_s_VCF_write __pyx_mstate_global->__pyx_n_s_VCF_write
7351 #define __pyx_n_s_VCF_write_data __pyx_mstate_global->__pyx_n_s_VCF_write_data
7352 #define __pyx_n_s_VCF_write_header __pyx_mstate_global->__pyx_n_s_VCF_write_header
7353 #define __pyx_n_s_VCF_write_heading __pyx_mstate_global->__pyx_n_s_VCF_write_heading
7354 #define __pyx_n_s_VCF_writeheader __pyx_mstate_global->__pyx_n_s_VCF_writeheader
7355 #define __pyx_kp_u_VCFv3_3 __pyx_mstate_global->__pyx_kp_u_VCFv3_3
7356 #define __pyx_kp_u_VCFv4_0 __pyx_mstate_global->__pyx_kp_u_VCFv4_0
7357 #define __pyx_kp_u_VCFv4_1 __pyx_mstate_global->__pyx_kp_u_VCFv4_1
7358 #define __pyx_kp_u_VCFv4_2 __pyx_mstate_global->__pyx_kp_u_VCFv4_2
7359 #define __pyx_n_s_ValueError __pyx_mstate_global->__pyx_n_s_ValueError
7360 #define __pyx_n_s_WRONG_REF __pyx_mstate_global->__pyx_n_s_WRONG_REF
7361 #define __pyx_kp_u_WRONG_REF_Wrong_reference_s __pyx_mstate_global->__pyx_kp_u_WRONG_REF_Wrong_reference_s
7362 #define __pyx_n_u_Warning __pyx_mstate_global->__pyx_n_u_Warning
7363 #define __pyx_n_s_ZERO_FOR_NON_FLAG_FIELD __pyx_mstate_global->__pyx_n_s_ZERO_FOR_NON_FLAG_FIELD
7364 #define __pyx_kp_u_ZERO_FOR_NON_FLAG_FIELD_number_s __pyx_mstate_global->__pyx_kp_u_ZERO_FOR_NON_FLAG_FIELD_number_s
7365 #define __pyx_n_s_ZERO_LENGTH_ALLELE __pyx_mstate_global->__pyx_n_s_ZERO_LENGTH_ALLELE
7366 #define __pyx_kp_u_ZERO_LENGTH_ALLELE_Found_zero_le __pyx_mstate_global->__pyx_kp_u_ZERO_LENGTH_ALLELE_Found_zero_le
7367 #define __pyx_kp_u__10 __pyx_mstate_global->__pyx_kp_u__10
7368 #define __pyx_kp_u__11 __pyx_mstate_global->__pyx_kp_u__11
7369 #define __pyx_kp_u__12 __pyx_mstate_global->__pyx_kp_u__12
7370 #define __pyx_kp_u__13 __pyx_mstate_global->__pyx_kp_u__13
7371 #define __pyx_n_s__139 __pyx_mstate_global->__pyx_n_s__139
7372 #define __pyx_kp_u__14 __pyx_mstate_global->__pyx_kp_u__14
7373 #define __pyx_kp_u__15 __pyx_mstate_global->__pyx_kp_u__15
7374 #define __pyx_kp_u__16 __pyx_mstate_global->__pyx_kp_u__16
7375 #define __pyx_kp_u__19 __pyx_mstate_global->__pyx_kp_u__19
7376 #define __pyx_kp_u__2 __pyx_mstate_global->__pyx_kp_u__2
7377 #define __pyx_kp_u__23 __pyx_mstate_global->__pyx_kp_u__23
7378 #define __pyx_kp_u__24 __pyx_mstate_global->__pyx_kp_u__24
7379 #define __pyx_kp_u__25 __pyx_mstate_global->__pyx_kp_u__25
7380 #define __pyx_kp_u__27 __pyx_mstate_global->__pyx_kp_u__27
7381 #define __pyx_kp_u__3 __pyx_mstate_global->__pyx_kp_u__3
7382 #define __pyx_n_s__33 __pyx_mstate_global->__pyx_n_s__33
7383 #define __pyx_kp_u__34 __pyx_mstate_global->__pyx_kp_u__34
7384 #define __pyx_kp_u__4 __pyx_mstate_global->__pyx_kp_u__4
7385 #define __pyx_kp_b__5 __pyx_mstate_global->__pyx_kp_b__5
7386 #define __pyx_kp_u__5 __pyx_mstate_global->__pyx_kp_u__5
7387 #define __pyx_kp_u__6 __pyx_mstate_global->__pyx_kp_u__6
7388 #define __pyx_kp_u__7 __pyx_mstate_global->__pyx_kp_u__7
7389 #define __pyx_kp_u__8 __pyx_mstate_global->__pyx_kp_u__8
7390 #define __pyx_n_s_a __pyx_mstate_global->__pyx_n_s_a
7391 #define __pyx_n_s_add __pyx_mstate_global->__pyx_n_s_add
7392 #define __pyx_n_s_add_definition __pyx_mstate_global->__pyx_n_s_add_definition
7393 #define __pyx_n_s_addn __pyx_mstate_global->__pyx_n_s_addn
7394 #define __pyx_n_s_addns __pyx_mstate_global->__pyx_n_s_addns
7395 #define __pyx_n_s_all __pyx_mstate_global->__pyx_n_s_all
7396 #define __pyx_n_s_allele __pyx_mstate_global->__pyx_n_s_allele
7397 #define __pyx_n_s_alleleRegEx __pyx_mstate_global->__pyx_n_s_alleleRegEx
7398 #define __pyx_kp_u_alleles __pyx_mstate_global->__pyx_kp_u_alleles
7399 #define __pyx_n_s_alt __pyx_mstate_global->__pyx_n_s_alt
7400 #define __pyx_n_u_alt __pyx_mstate_global->__pyx_n_u_alt
7401 #define __pyx_n_s_alt1 __pyx_mstate_global->__pyx_n_s_alt1
7402 #define __pyx_n_s_alt2 __pyx_mstate_global->__pyx_n_s_alt2
7403 #define __pyx_n_s_append __pyx_mstate_global->__pyx_n_s_append
7404 #define __pyx_n_s_args __pyx_mstate_global->__pyx_n_s_args
7405 #define __pyx_n_s_asVCFRecord __pyx_mstate_global->__pyx_n_s_asVCFRecord
7406 #define __pyx_n_s_asVCFRecord___reduce_cython __pyx_mstate_global->__pyx_n_s_asVCFRecord___reduce_cython
7407 #define __pyx_n_s_asVCFRecord___setstate_cython __pyx_mstate_global->__pyx_n_s_asVCFRecord___setstate_cython
7408 #define __pyx_n_u_ascii __pyx_mstate_global->__pyx_n_u_ascii
7409 #define __pyx_n_s_asyncio_coroutines __pyx_mstate_global->__pyx_n_s_asyncio_coroutines
7410 #define __pyx_n_s_bisect __pyx_mstate_global->__pyx_n_s_bisect
7411 #define __pyx_n_s_blurp __pyx_mstate_global->__pyx_n_s_blurp
7412 #define __pyx_n_s_c __pyx_mstate_global->__pyx_n_s_c
7413 #define __pyx_n_s_chrom __pyx_mstate_global->__pyx_n_s_chrom
7414 #define __pyx_n_u_chrom __pyx_mstate_global->__pyx_n_u_chrom
7415 #define __pyx_n_s_class_getitem __pyx_mstate_global->__pyx_n_s_class_getitem
7416 #define __pyx_n_s_cline_in_traceback __pyx_mstate_global->__pyx_n_s_cline_in_traceback
7417 #define __pyx_n_s_close __pyx_mstate_global->__pyx_n_s_close
7418 #define __pyx_n_s_collections __pyx_mstate_global->__pyx_n_s_collections
7419 #define __pyx_n_s_cols __pyx_mstate_global->__pyx_n_s_cols
7420 #define __pyx_n_s_compare_calls __pyx_mstate_global->__pyx_n_s_compare_calls
7421 #define __pyx_n_s_compile __pyx_mstate_global->__pyx_n_s_compile
7422 #define __pyx_n_s_connect __pyx_mstate_global->__pyx_n_s_connect
7423 #define __pyx_n_s_convertGT __pyx_mstate_global->__pyx_n_s_convertGT
7424 #define __pyx_n_s_convertGTback __pyx_mstate_global->__pyx_n_s_convertGTback
7425 #define __pyx_n_s_copy __pyx_mstate_global->__pyx_n_s_copy
7426 #define __pyx_n_s_copy_2 __pyx_mstate_global->__pyx_n_s_copy_2
7427 #define __pyx_n_s_d __pyx_mstate_global->__pyx_n_s_d
7428 #define __pyx_n_s_data __pyx_mstate_global->__pyx_n_s_data
7429 #define __pyx_n_s_datagenerator __pyx_mstate_global->__pyx_n_s_datagenerator
7430 #define __pyx_n_s_deepcopy __pyx_mstate_global->__pyx_n_s_deepcopy
7431 #define __pyx_n_s_defaultdict __pyx_mstate_global->__pyx_n_s_defaultdict
7432 #define __pyx_n_s_del __pyx_mstate_global->__pyx_n_s_del
7433 #define __pyx_kp_u_deletion_is __pyx_mstate_global->__pyx_kp_u_deletion_is
7434 #define __pyx_n_u_descr __pyx_mstate_global->__pyx_n_u_descr
7435 #define __pyx_n_s_description __pyx_mstate_global->__pyx_n_s_description
7436 #define __pyx_n_s_dict __pyx_mstate_global->__pyx_n_s_dict
7437 #define __pyx_n_s_dict_2 __pyx_mstate_global->__pyx_n_s_dict_2
7438 #define __pyx_n_s_dict_3 __pyx_mstate_global->__pyx_n_s_dict_3
7439 #define __pyx_kp_u_disable __pyx_mstate_global->__pyx_kp_u_disable
7440 #define __pyx_n_s_doc __pyx_mstate_global->__pyx_n_s_doc
7441 #define __pyx_n_s_elts __pyx_mstate_global->__pyx_n_s_elts
7442 #define __pyx_kp_u_enable __pyx_mstate_global->__pyx_kp_u_enable
7443 #define __pyx_n_s_encoding __pyx_mstate_global->__pyx_n_s_encoding
7444 #define __pyx_n_s_end __pyx_mstate_global->__pyx_n_s_end
7445 #define __pyx_n_s_endswith __pyx_mstate_global->__pyx_n_s_endswith
7446 #define __pyx_n_s_enter_default_format __pyx_mstate_global->__pyx_n_s_enter_default_format
7447 #define __pyx_n_s_enumerate __pyx_mstate_global->__pyx_n_s_enumerate
7448 #define __pyx_n_s_err __pyx_mstate_global->__pyx_n_s_err
7449 #define __pyx_n_s_error __pyx_mstate_global->__pyx_n_s_error
7450 #define __pyx_n_s_errorlabel __pyx_mstate_global->__pyx_n_s_errorlabel
7451 #define __pyx_n_s_errors __pyx_mstate_global->__pyx_n_s_errors
7452 #define __pyx_n_s_errorstring __pyx_mstate_global->__pyx_n_s_errorstring
7453 #define __pyx_n_s_errwarn __pyx_mstate_global->__pyx_n_s_errwarn
7454 #define __pyx_kp_u_expected __pyx_mstate_global->__pyx_kp_u_expected
7455 #define __pyx_kp_u_expected_2 __pyx_mstate_global->__pyx_kp_u_expected_2
7456 #define __pyx_kp_u_expected_3 __pyx_mstate_global->__pyx_kp_u_expected_3
7457 #define __pyx_n_s_expected_4 __pyx_mstate_global->__pyx_n_s_expected_4
7458 #define __pyx_n_s_f __pyx_mstate_global->__pyx_n_s_f
7459 #define __pyx_n_s_fa __pyx_mstate_global->__pyx_n_s_fa
7460 #define __pyx_n_s_faref __pyx_mstate_global->__pyx_n_s_faref
7461 #define __pyx_n_s_faref_leftflank __pyx_mstate_global->__pyx_n_s_faref_leftflank
7462 #define __pyx_n_s_fetch __pyx_mstate_global->__pyx_n_s_fetch
7463 #define __pyx_n_u_fileformat __pyx_mstate_global->__pyx_n_u_fileformat
7464 #define __pyx_kp_u_fileformat_VCFv __pyx_mstate_global->__pyx_kp_u_fileformat_VCFv
7465 #define __pyx_n_s_filename __pyx_mstate_global->__pyx_n_s_filename
7466 #define __pyx_n_s_filter __pyx_mstate_global->__pyx_n_s_filter
7467 #define __pyx_n_s_filter_2 __pyx_mstate_global->__pyx_n_s_filter_2
7468 #define __pyx_n_u_filter_2 __pyx_mstate_global->__pyx_n_u_filter_2
7469 #define __pyx_n_s_find __pyx_mstate_global->__pyx_n_s_find
7470 #define __pyx_n_s_first __pyx_mstate_global->__pyx_n_s_first
7471 #define __pyx_n_s_fmt __pyx_mstate_global->__pyx_n_s_fmt
7472 #define __pyx_kp_u_for __pyx_mstate_global->__pyx_kp_u_for
7473 #define __pyx_n_s_format __pyx_mstate_global->__pyx_n_s_format
7474 #define __pyx_n_u_format __pyx_mstate_global->__pyx_n_u_format
7475 #define __pyx_n_s_format_2 __pyx_mstate_global->__pyx_n_s_format_2
7476 #define __pyx_n_s_format_format __pyx_mstate_global->__pyx_n_s_format_format
7477 #define __pyx_n_s_format_formatdata __pyx_mstate_global->__pyx_n_s_format_formatdata
7478 #define __pyx_n_s_formatdict __pyx_mstate_global->__pyx_n_s_formatdict
7479 #define __pyx_kp_u_found __pyx_mstate_global->__pyx_kp_u_found
7480 #define __pyx_kp_u_gc __pyx_mstate_global->__pyx_kp_u_gc
7481 #define __pyx_kp_u_genotypes __pyx_mstate_global->__pyx_kp_u_genotypes
7482 #define __pyx_n_s_get __pyx_mstate_global->__pyx_n_s_get
7483 #define __pyx_n_s_get_expected __pyx_mstate_global->__pyx_n_s_get_expected
7484 #define __pyx_n_s_get_sequence __pyx_mstate_global->__pyx_n_s_get_sequence
7485 #define __pyx_n_s_getfilter __pyx_mstate_global->__pyx_n_s_getfilter
7486 #define __pyx_n_s_getformat __pyx_mstate_global->__pyx_n_s_getformat
7487 #define __pyx_n_s_getheader __pyx_mstate_global->__pyx_n_s_getheader
7488 #define __pyx_n_s_getinfo __pyx_mstate_global->__pyx_n_s_getinfo
7489 #define __pyx_n_s_getsamples __pyx_mstate_global->__pyx_n_s_getsamples
7490 #define __pyx_n_s_getstate __pyx_mstate_global->__pyx_n_s_getstate
7491 #define __pyx_kp_u_got __pyx_mstate_global->__pyx_kp_u_got
7492 #define __pyx_n_s_gts __pyx_mstate_global->__pyx_n_s_gts
7493 #define __pyx_n_s_gtsRegEx __pyx_mstate_global->__pyx_n_s_gtsRegEx
7494 #define __pyx_n_s_have_deletions __pyx_mstate_global->__pyx_n_s_have_deletions
7495 #define __pyx_n_s_header __pyx_mstate_global->__pyx_n_s_header
7496 #define __pyx_n_s_header_2 __pyx_mstate_global->__pyx_n_s_header_2
7497 #define __pyx_n_s_headings __pyx_mstate_global->__pyx_n_s_headings
7498 #define __pyx_n_s_i __pyx_mstate_global->__pyx_n_s_i
7499 #define __pyx_kp_u_id __pyx_mstate_global->__pyx_kp_u_id
7500 #define __pyx_n_s_id_2 __pyx_mstate_global->__pyx_n_s_id_2
7501 #define __pyx_n_u_id_2 __pyx_mstate_global->__pyx_n_u_id_2
7502 #define __pyx_kp_u_id_numbertype_number_type_descri __pyx_mstate_global->__pyx_kp_u_id_numbertype_number_type_descri
7503 #define __pyx_n_s_idx __pyx_mstate_global->__pyx_n_s_idx
7504 #define __pyx_n_s_ielts __pyx_mstate_global->__pyx_n_s_ielts
7505 #define __pyx_n_s_ignored_errors __pyx_mstate_global->__pyx_n_s_ignored_errors
7506 #define __pyx_n_s_ignoreerror __pyx_mstate_global->__pyx_n_s_ignoreerror
7507 #define __pyx_n_s_import __pyx_mstate_global->__pyx_n_s_import
7508 #define __pyx_kp_u_in_line __pyx_mstate_global->__pyx_kp_u_in_line
7509 #define __pyx_n_s_info __pyx_mstate_global->__pyx_n_s_info
7510 #define __pyx_n_s_info_2 __pyx_mstate_global->__pyx_n_s_info_2
7511 #define __pyx_n_u_info_2 __pyx_mstate_global->__pyx_n_u_info_2
7512 #define __pyx_n_s_init __pyx_mstate_global->__pyx_n_s_init
7513 #define __pyx_n_s_init_subclass __pyx_mstate_global->__pyx_n_s_init_subclass
7514 #define __pyx_n_s_initializing __pyx_mstate_global->__pyx_n_s_initializing
7515 #define __pyx_n_s_inregion __pyx_mstate_global->__pyx_n_s_inregion
7516 #define __pyx_n_s_is_coroutine __pyx_mstate_global->__pyx_n_s_is_coroutine
7517 #define __pyx_kp_u_isenabled __pyx_mstate_global->__pyx_kp_u_isenabled
7518 #define __pyx_n_s_itemgetter __pyx_mstate_global->__pyx_n_s_itemgetter
7519 #define __pyx_n_s_itervalues __pyx_mstate_global->__pyx_n_s_itervalues
7520 #define __pyx_n_s_join __pyx_mstate_global->__pyx_n_s_join
7521 #define __pyx_n_s_k __pyx_mstate_global->__pyx_n_s_k
7522 #define __pyx_n_s_key __pyx_mstate_global->__pyx_n_s_key
7523 #define __pyx_n_s_keys __pyx_mstate_global->__pyx_n_s_keys
7524 #define __pyx_n_s_l __pyx_mstate_global->__pyx_n_s_l
7525 #define __pyx_n_s_label __pyx_mstate_global->__pyx_n_s_label
7526 #define __pyx_n_s_last __pyx_mstate_global->__pyx_n_s_last
7527 #define __pyx_n_s_last_line __pyx_mstate_global->__pyx_n_s_last_line
7528 #define __pyx_n_s_left __pyx_mstate_global->__pyx_n_s_left
7529 #define __pyx_n_s_leftalign __pyx_mstate_global->__pyx_n_s_leftalign
7530 #define __pyx_n_s_leftalign_2 __pyx_mstate_global->__pyx_n_s_leftalign_2
7531 #define __pyx_n_s_line __pyx_mstate_global->__pyx_n_s_line
7532 #define __pyx_n_s_line_2 __pyx_mstate_global->__pyx_n_s_line_2
7533 #define __pyx_n_s_lineno __pyx_mstate_global->__pyx_n_s_lineno
7534 #define __pyx_n_s_lineparse __pyx_mstate_global->__pyx_n_s_lineparse
7535 #define __pyx_n_s_lines __pyx_mstate_global->__pyx_n_s_lines
7536 #define __pyx_n_s_lines_2 __pyx_mstate_global->__pyx_n_s_lines_2
7537 #define __pyx_n_s_longest __pyx_mstate_global->__pyx_n_s_longest
7538 #define __pyx_n_s_main __pyx_mstate_global->__pyx_n_s_main
7539 #define __pyx_n_s_map __pyx_mstate_global->__pyx_n_s_map
7540 #define __pyx_n_s_match __pyx_mstate_global->__pyx_n_s_match
7541 #define __pyx_n_s_metaclass __pyx_mstate_global->__pyx_n_s_metaclass
7542 #define __pyx_n_s_min __pyx_mstate_global->__pyx_n_s_min
7543 #define __pyx_n_u_missing __pyx_mstate_global->__pyx_n_u_missing
7544 #define __pyx_n_s_missingvalue __pyx_mstate_global->__pyx_n_s_missingvalue
7545 #define __pyx_n_s_module __pyx_mstate_global->__pyx_n_s_module
7546 #define __pyx_n_s_movable __pyx_mstate_global->__pyx_n_s_movable
7547 #define __pyx_n_s_mro_entries __pyx_mstate_global->__pyx_n_s_mro_entries
7548 #define __pyx_n_s_n __pyx_mstate_global->__pyx_n_s_n
7549 #define __pyx_n_s_na __pyx_mstate_global->__pyx_n_s_na
7550 #define __pyx_n_s_name __pyx_mstate_global->__pyx_n_s_name
7551 #define __pyx_n_s_namedtuple __pyx_mstate_global->__pyx_n_s_namedtuple
7552 #define __pyx_kp_u_needs_to_be_checked __pyx_mstate_global->__pyx_kp_u_needs_to_be_checked
7553 #define __pyx_n_s_new __pyx_mstate_global->__pyx_n_s_new
7554 #define __pyx_n_s_newalts __pyx_mstate_global->__pyx_n_s_newalts
7555 #define __pyx_n_s_nmb __pyx_mstate_global->__pyx_n_s_nmb
7556 #define __pyx_kp_s_no_default___reduce___due_to_non __pyx_mstate_global->__pyx_kp_s_no_default___reduce___due_to_non
7557 #define __pyx_kp_u_nonref_alleles __pyx_mstate_global->__pyx_kp_u_nonref_alleles
7558 #define __pyx_n_s_number __pyx_mstate_global->__pyx_n_s_number
7559 #define __pyx_n_u_number __pyx_mstate_global->__pyx_n_u_number
7560 #define __pyx_n_s_numbertype __pyx_mstate_global->__pyx_n_s_numbertype
7561 #define __pyx_n_s_object __pyx_mstate_global->__pyx_n_s_object
7562 #define __pyx_n_s_operator __pyx_mstate_global->__pyx_n_s_operator
7563 #define __pyx_n_s_opt __pyx_mstate_global->__pyx_n_s_opt
7564 #define __pyx_kp_u_output __pyx_mstate_global->__pyx_kp_u_output
7565 #define __pyx_n_s_output_2 __pyx_mstate_global->__pyx_n_s_output_2
7566 #define __pyx_kp_u_parameters_got __pyx_mstate_global->__pyx_kp_u_parameters_got
7567 #define __pyx_n_s_parse __pyx_mstate_global->__pyx_n_s_parse
7568 #define __pyx_n_s_parse_2 __pyx_mstate_global->__pyx_n_s_parse_2
7569 #define __pyx_n_s_parse_data __pyx_mstate_global->__pyx_n_s_parse_data
7570 #define __pyx_n_s_parse_format __pyx_mstate_global->__pyx_n_s_parse_format
7571 #define __pyx_n_s_parse_formatdata __pyx_mstate_global->__pyx_n_s_parse_formatdata
7572 #define __pyx_n_s_parse_header __pyx_mstate_global->__pyx_n_s_parse_header
7573 #define __pyx_n_s_parse_header_2 __pyx_mstate_global->__pyx_n_s_parse_header_2
7574 #define __pyx_n_s_parse_heading __pyx_mstate_global->__pyx_n_s_parse_heading
7575 #define __pyx_n_s_parse_regions __pyx_mstate_global->__pyx_n_s_parse_regions
7576 #define __pyx_n_s_parser __pyx_mstate_global->__pyx_n_s_parser
7577 #define __pyx_kp_u_phased_genotypes __pyx_mstate_global->__pyx_kp_u_phased_genotypes
7578 #define __pyx_n_s_pickle __pyx_mstate_global->__pyx_n_s_pickle
7579 #define __pyx_n_s_pos __pyx_mstate_global->__pyx_n_s_pos
7580 #define __pyx_n_u_pos __pyx_mstate_global->__pyx_n_u_pos
7581 #define __pyx_n_s_pos1 __pyx_mstate_global->__pyx_n_s_pos1
7582 #define __pyx_n_s_pos2 __pyx_mstate_global->__pyx_n_s_pos2
7583 #define __pyx_n_s_prepare __pyx_mstate_global->__pyx_n_s_prepare
7584 #define __pyx_n_s_pysam __pyx_mstate_global->__pyx_n_s_pysam
7585 #define __pyx_n_s_pysam_libcvcf __pyx_mstate_global->__pyx_n_s_pysam_libcvcf
7586 #define __pyx_kp_s_pysam_libcvcf_pyx __pyx_mstate_global->__pyx_kp_s_pysam_libcvcf_pyx
7587 #define __pyx_n_s_pyx_PickleError __pyx_mstate_global->__pyx_n_s_pyx_PickleError
7588 #define __pyx_n_s_pyx_checksum __pyx_mstate_global->__pyx_n_s_pyx_checksum
7589 #define __pyx_n_s_pyx_result __pyx_mstate_global->__pyx_n_s_pyx_result
7590 #define __pyx_n_s_pyx_state __pyx_mstate_global->__pyx_n_s_pyx_state
7591 #define __pyx_n_s_pyx_type __pyx_mstate_global->__pyx_n_s_pyx_type
7592 #define __pyx_n_s_pyx_unpickle_asVCFRecord __pyx_mstate_global->__pyx_n_s_pyx_unpickle_asVCFRecord
7593 #define __pyx_n_s_pyx_vtable __pyx_mstate_global->__pyx_n_s_pyx_vtable
7594 #define __pyx_n_s_qual __pyx_mstate_global->__pyx_n_s_qual
7595 #define __pyx_n_u_qual __pyx_mstate_global->__pyx_n_u_qual
7596 #define __pyx_n_s_qualname __pyx_mstate_global->__pyx_n_s_qualname
7597 #define __pyx_n_s_r __pyx_mstate_global->__pyx_n_s_r
7598 #define __pyx_n_s_range __pyx_mstate_global->__pyx_n_s_range
7599 #define __pyx_n_s_re __pyx_mstate_global->__pyx_n_s_re
7600 #define __pyx_n_s_record __pyx_mstate_global->__pyx_n_s_record
7601 #define __pyx_n_s_reduce __pyx_mstate_global->__pyx_n_s_reduce
7602 #define __pyx_n_s_reduce_cython __pyx_mstate_global->__pyx_n_s_reduce_cython
7603 #define __pyx_n_s_reduce_ex __pyx_mstate_global->__pyx_n_s_reduce_ex
7604 #define __pyx_n_s_ref __pyx_mstate_global->__pyx_n_s_ref
7605 #define __pyx_n_u_ref __pyx_mstate_global->__pyx_n_u_ref
7606 #define __pyx_n_s_ref1 __pyx_mstate_global->__pyx_n_s_ref1
7607 #define __pyx_n_s_ref2 __pyx_mstate_global->__pyx_n_s_ref2
7608 #define __pyx_n_s_reference __pyx_mstate_global->__pyx_n_s_reference
7609 #define __pyx_n_s_reference_2 __pyx_mstate_global->__pyx_n_s_reference_2
7610 #define __pyx_kp_u_reference_is __pyx_mstate_global->__pyx_kp_u_reference_is
7611 #define __pyx_kp_u_reference_is_2 __pyx_mstate_global->__pyx_kp_u_reference_is_2
7612 #define __pyx_n_s_region __pyx_mstate_global->__pyx_n_s_region
7613 #define __pyx_n_s_regions __pyx_mstate_global->__pyx_n_s_regions
7614 #define __pyx_n_s_regions_2 __pyx_mstate_global->__pyx_n_s_regions_2
7615 #define __pyx_n_s_replace __pyx_mstate_global->__pyx_n_s_replace
7616 #define __pyx_n_s_required __pyx_mstate_global->__pyx_n_s_required
7617 #define __pyx_n_s_required_2 __pyx_mstate_global->__pyx_n_s_required_2
7618 #define __pyx_n_s_rest __pyx_mstate_global->__pyx_n_s_rest
7619 #define __pyx_n_s_result __pyx_mstate_global->__pyx_n_s_result
7620 #define __pyx_n_s_s __pyx_mstate_global->__pyx_n_s_s
7621 #define __pyx_n_s_sample __pyx_mstate_global->__pyx_n_s_sample
7622 #define __pyx_n_s_sample2column __pyx_mstate_global->__pyx_n_s_sample2column
7623 #define __pyx_n_s_samples __pyx_mstate_global->__pyx_n_s_samples
7624 #define __pyx_kp_u_samples_2 __pyx_mstate_global->__pyx_kp_u_samples_2
7625 #define __pyx_n_s_samples_3 __pyx_mstate_global->__pyx_n_s_samples_3
7626 #define __pyx_n_s_sdata __pyx_mstate_global->__pyx_n_s_sdata
7627 #define __pyx_n_s_self __pyx_mstate_global->__pyx_n_s_self
7628 #define __pyx_n_s_send __pyx_mstate_global->__pyx_n_s_send
7629 #define __pyx_n_s_separator __pyx_mstate_global->__pyx_n_s_separator
7630 #define __pyx_n_s_sequence __pyx_mstate_global->__pyx_n_s_sequence
7631 #define __pyx_n_s_set_name __pyx_mstate_global->__pyx_n_s_set_name
7632 #define __pyx_n_s_setfilter __pyx_mstate_global->__pyx_n_s_setfilter
7633 #define __pyx_n_s_setformat __pyx_mstate_global->__pyx_n_s_setformat
7634 #define __pyx_n_s_setheader __pyx_mstate_global->__pyx_n_s_setheader
7635 #define __pyx_n_s_setinfo __pyx_mstate_global->__pyx_n_s_setinfo
7636 #define __pyx_n_s_setreference __pyx_mstate_global->__pyx_n_s_setreference
7637 #define __pyx_n_s_setregions __pyx_mstate_global->__pyx_n_s_setregions
7638 #define __pyx_n_s_setsamples __pyx_mstate_global->__pyx_n_s_setsamples
7639 #define __pyx_n_s_setstate __pyx_mstate_global->__pyx_n_s_setstate
7640 #define __pyx_n_s_setstate_cython __pyx_mstate_global->__pyx_n_s_setstate_cython
7641 #define __pyx_n_s_setversion __pyx_mstate_global->__pyx_n_s_setversion
7642 #define __pyx_n_s_shortest __pyx_mstate_global->__pyx_n_s_shortest
7643 #define __pyx_n_s_spec __pyx_mstate_global->__pyx_n_s_spec
7644 #define __pyx_n_s_split __pyx_mstate_global->__pyx_n_s_split
7645 #define __pyx_n_s_start __pyx_mstate_global->__pyx_n_s_start
7646 #define __pyx_n_s_startswith __pyx_mstate_global->__pyx_n_s_startswith
7647 #define __pyx_n_s_state __pyx_mstate_global->__pyx_n_s_state
7648 #define __pyx_kp_u_sth_entry_not_found __pyx_mstate_global->__pyx_kp_u_sth_entry_not_found
7649 #define __pyx_n_s_stream __pyx_mstate_global->__pyx_n_s_stream
7650 #define __pyx_n_s_string __pyx_mstate_global->__pyx_n_s_string
7651 #define __pyx_kp_s_stringsource __pyx_mstate_global->__pyx_kp_s_stringsource
7652 #define __pyx_n_s_strip __pyx_mstate_global->__pyx_n_s_strip
7653 #define __pyx_n_s_super __pyx_mstate_global->__pyx_n_s_super
7654 #define __pyx_n_s_sys __pyx_mstate_global->__pyx_n_s_sys
7655 #define __pyx_n_s_t __pyx_mstate_global->__pyx_n_s_t
7656 #define __pyx_n_s_tabixfile __pyx_mstate_global->__pyx_n_s_tabixfile
7657 #define __pyx_n_s_test __pyx_mstate_global->__pyx_n_s_test
7658 #define __pyx_n_s_throw __pyx_mstate_global->__pyx_n_s_throw
7659 #define __pyx_n_s_type __pyx_mstate_global->__pyx_n_s_type
7660 #define __pyx_n_u_type __pyx_mstate_global->__pyx_n_u_type
7661 #define __pyx_n_s_update __pyx_mstate_global->__pyx_n_s_update
7662 #define __pyx_n_s_upper __pyx_mstate_global->__pyx_n_s_upper
7663 #define __pyx_n_s_use_setstate __pyx_mstate_global->__pyx_n_s_use_setstate
7664 #define __pyx_n_s_v __pyx_mstate_global->__pyx_n_s_v
7665 #define __pyx_n_s_validate __pyx_mstate_global->__pyx_n_s_validate
7666 #define __pyx_n_s_value __pyx_mstate_global->__pyx_n_s_value
7667 #define __pyx_n_s_values __pyx_mstate_global->__pyx_n_s_values
7668 #define __pyx_kp_u_values_in_element __pyx_mstate_global->__pyx_kp_u_values_in_element
7669 #define __pyx_n_s_var __pyx_mstate_global->__pyx_n_s_var
7670 #define __pyx_n_s_vcf __pyx_mstate_global->__pyx_n_s_vcf
7671 #define __pyx_n_s_vcffile __pyx_mstate_global->__pyx_n_s_vcffile
7672 #define __pyx_n_s_version __pyx_mstate_global->__pyx_n_s_version
7673 #define __pyx_n_s_version_2 __pyx_mstate_global->__pyx_n_s_version_2
7674 #define __pyx_n_s_warn_errors __pyx_mstate_global->__pyx_n_s_warn_errors
7675 #define __pyx_n_s_warnerror __pyx_mstate_global->__pyx_n_s_warnerror
7676 #define __pyx_n_s_write __pyx_mstate_global->__pyx_n_s_write
7677 #define __pyx_n_s_write_data __pyx_mstate_global->__pyx_n_s_write_data
7678 #define __pyx_n_s_write_header __pyx_mstate_global->__pyx_n_s_write_header
7679 #define __pyx_n_s_write_heading __pyx_mstate_global->__pyx_n_s_write_heading
7680 #define __pyx_n_s_writeheader __pyx_mstate_global->__pyx_n_s_writeheader
7681 #define __pyx_n_s_x __pyx_mstate_global->__pyx_n_s_x
7682 #define __pyx_n_s_y __pyx_mstate_global->__pyx_n_s_y
7683 #define __pyx_n_s_zip __pyx_mstate_global->__pyx_n_s_zip
7684 #define __pyx_float_0_0 __pyx_mstate_global->__pyx_float_0_0
7685 #define __pyx_int_0 __pyx_mstate_global->__pyx_int_0
7686 #define __pyx_int_1 __pyx_mstate_global->__pyx_int_1
7687 #define __pyx_int_2 __pyx_mstate_global->__pyx_int_2
7688 #define __pyx_int_3 __pyx_mstate_global->__pyx_int_3
7689 #define __pyx_int_4 __pyx_mstate_global->__pyx_int_4
7690 #define __pyx_int_5 __pyx_mstate_global->__pyx_int_5
7691 #define __pyx_int_6 __pyx_mstate_global->__pyx_int_6
7692 #define __pyx_int_7 __pyx_mstate_global->__pyx_int_7
7693 #define __pyx_int_8 __pyx_mstate_global->__pyx_int_8
7694 #define __pyx_int_9 __pyx_mstate_global->__pyx_int_9
7695 #define __pyx_int_10 __pyx_mstate_global->__pyx_int_10
7696 #define __pyx_int_11 __pyx_mstate_global->__pyx_int_11
7697 #define __pyx_int_12 __pyx_mstate_global->__pyx_int_12
7698 #define __pyx_int_13 __pyx_mstate_global->__pyx_int_13
7699 #define __pyx_int_14 __pyx_mstate_global->__pyx_int_14
7700 #define __pyx_int_15 __pyx_mstate_global->__pyx_int_15
7701 #define __pyx_int_16 __pyx_mstate_global->__pyx_int_16
7702 #define __pyx_int_17 __pyx_mstate_global->__pyx_int_17
7703 #define __pyx_int_18 __pyx_mstate_global->__pyx_int_18
7704 #define __pyx_int_19 __pyx_mstate_global->__pyx_int_19
7705 #define __pyx_int_20 __pyx_mstate_global->__pyx_int_20
7706 #define __pyx_int_21 __pyx_mstate_global->__pyx_int_21
7707 #define __pyx_int_22 __pyx_mstate_global->__pyx_int_22
7708 #define __pyx_int_23 __pyx_mstate_global->__pyx_int_23
7709 #define __pyx_int_24 __pyx_mstate_global->__pyx_int_24
7710 #define __pyx_int_25 __pyx_mstate_global->__pyx_int_25
7711 #define __pyx_int_26 __pyx_mstate_global->__pyx_int_26
7712 #define __pyx_int_27 __pyx_mstate_global->__pyx_int_27
7713 #define __pyx_int_28 __pyx_mstate_global->__pyx_int_28
7714 #define __pyx_int_29 __pyx_mstate_global->__pyx_int_29
7715 #define __pyx_int_30 __pyx_mstate_global->__pyx_int_30
7716 #define __pyx_int_31 __pyx_mstate_global->__pyx_int_31
7717 #define __pyx_int_32 __pyx_mstate_global->__pyx_int_32
7718 #define __pyx_int_33 __pyx_mstate_global->__pyx_int_33
7719 #define __pyx_int_40 __pyx_mstate_global->__pyx_int_40
7720 #define __pyx_int_100 __pyx_mstate_global->__pyx_int_100
7721 #define __pyx_int_29527880 __pyx_mstate_global->__pyx_int_29527880
7722 #define __pyx_int_214161357 __pyx_mstate_global->__pyx_int_214161357
7723 #define __pyx_int_239654613 __pyx_mstate_global->__pyx_int_239654613
7724 #define __pyx_int_3000000000 __pyx_mstate_global->__pyx_int_3000000000
7725 #define __pyx_int_neg_1 __pyx_mstate_global->__pyx_int_neg_1
7726 #define __pyx_slice__9 __pyx_mstate_global->__pyx_slice__9
7727 #define __pyx_slice__17 __pyx_mstate_global->__pyx_slice__17
7728 #define __pyx_slice__18 __pyx_mstate_global->__pyx_slice__18
7729 #define __pyx_slice__20 __pyx_mstate_global->__pyx_slice__20
7730 #define __pyx_slice__26 __pyx_mstate_global->__pyx_slice__26
7731 #define __pyx_slice__28 __pyx_mstate_global->__pyx_slice__28
7732 #define __pyx_tuple__21 __pyx_mstate_global->__pyx_tuple__21
7733 #define __pyx_tuple__22 __pyx_mstate_global->__pyx_tuple__22
7734 #define __pyx_tuple__30 __pyx_mstate_global->__pyx_tuple__30
7735 #define __pyx_tuple__31 __pyx_mstate_global->__pyx_tuple__31
7736 #define __pyx_tuple__32 __pyx_mstate_global->__pyx_tuple__32
7737 #define __pyx_tuple__35 __pyx_mstate_global->__pyx_tuple__35
7738 #define __pyx_tuple__36 __pyx_mstate_global->__pyx_tuple__36
7739 #define __pyx_tuple__37 __pyx_mstate_global->__pyx_tuple__37
7740 #define __pyx_tuple__39 __pyx_mstate_global->__pyx_tuple__39
7741 #define __pyx_tuple__41 __pyx_mstate_global->__pyx_tuple__41
7742 #define __pyx_tuple__42 __pyx_mstate_global->__pyx_tuple__42
7743 #define __pyx_tuple__44 __pyx_mstate_global->__pyx_tuple__44
7744 #define __pyx_tuple__45 __pyx_mstate_global->__pyx_tuple__45
7745 #define __pyx_tuple__47 __pyx_mstate_global->__pyx_tuple__47
7746 #define __pyx_tuple__49 __pyx_mstate_global->__pyx_tuple__49
7747 #define __pyx_tuple__52 __pyx_mstate_global->__pyx_tuple__52
7748 #define __pyx_tuple__53 __pyx_mstate_global->__pyx_tuple__53
7749 #define __pyx_tuple__54 __pyx_mstate_global->__pyx_tuple__54
7750 #define __pyx_tuple__56 __pyx_mstate_global->__pyx_tuple__56
7751 #define __pyx_tuple__57 __pyx_mstate_global->__pyx_tuple__57
7752 #define __pyx_tuple__59 __pyx_mstate_global->__pyx_tuple__59
7753 #define __pyx_tuple__61 __pyx_mstate_global->__pyx_tuple__61
7754 #define __pyx_tuple__62 __pyx_mstate_global->__pyx_tuple__62
7755 #define __pyx_tuple__64 __pyx_mstate_global->__pyx_tuple__64
7756 #define __pyx_tuple__66 __pyx_mstate_global->__pyx_tuple__66
7757 #define __pyx_tuple__68 __pyx_mstate_global->__pyx_tuple__68
7758 #define __pyx_tuple__70 __pyx_mstate_global->__pyx_tuple__70
7759 #define __pyx_tuple__71 __pyx_mstate_global->__pyx_tuple__71
7760 #define __pyx_tuple__73 __pyx_mstate_global->__pyx_tuple__73
7761 #define __pyx_tuple__75 __pyx_mstate_global->__pyx_tuple__75
7762 #define __pyx_tuple__77 __pyx_mstate_global->__pyx_tuple__77
7763 #define __pyx_tuple__79 __pyx_mstate_global->__pyx_tuple__79
7764 #define __pyx_tuple__81 __pyx_mstate_global->__pyx_tuple__81
7765 #define __pyx_tuple__83 __pyx_mstate_global->__pyx_tuple__83
7766 #define __pyx_tuple__85 __pyx_mstate_global->__pyx_tuple__85
7767 #define __pyx_tuple__87 __pyx_mstate_global->__pyx_tuple__87
7768 #define __pyx_tuple__89 __pyx_mstate_global->__pyx_tuple__89
7769 #define __pyx_tuple__91 __pyx_mstate_global->__pyx_tuple__91
7770 #define __pyx_tuple__93 __pyx_mstate_global->__pyx_tuple__93
7771 #define __pyx_tuple__95 __pyx_mstate_global->__pyx_tuple__95
7772 #define __pyx_tuple__97 __pyx_mstate_global->__pyx_tuple__97
7773 #define __pyx_tuple__100 __pyx_mstate_global->__pyx_tuple__100
7774 #define __pyx_tuple__103 __pyx_mstate_global->__pyx_tuple__103
7775 #define __pyx_tuple__106 __pyx_mstate_global->__pyx_tuple__106
7776 #define __pyx_tuple__109 __pyx_mstate_global->__pyx_tuple__109
7777 #define __pyx_tuple__111 __pyx_mstate_global->__pyx_tuple__111
7778 #define __pyx_tuple__113 __pyx_mstate_global->__pyx_tuple__113
7779 #define __pyx_tuple__115 __pyx_mstate_global->__pyx_tuple__115
7780 #define __pyx_tuple__117 __pyx_mstate_global->__pyx_tuple__117
7781 #define __pyx_tuple__120 __pyx_mstate_global->__pyx_tuple__120
7782 #define __pyx_tuple__122 __pyx_mstate_global->__pyx_tuple__122
7783 #define __pyx_tuple__125 __pyx_mstate_global->__pyx_tuple__125
7784 #define __pyx_tuple__127 __pyx_mstate_global->__pyx_tuple__127
7785 #define __pyx_tuple__129 __pyx_mstate_global->__pyx_tuple__129
7786 #define __pyx_tuple__132 __pyx_mstate_global->__pyx_tuple__132
7787 #define __pyx_tuple__134 __pyx_mstate_global->__pyx_tuple__134
7788 #define __pyx_tuple__135 __pyx_mstate_global->__pyx_tuple__135
7789 #define __pyx_tuple__137 __pyx_mstate_global->__pyx_tuple__137
7790 #define __pyx_codeobj__29 __pyx_mstate_global->__pyx_codeobj__29
7791 #define __pyx_codeobj__38 __pyx_mstate_global->__pyx_codeobj__38
7792 #define __pyx_codeobj__40 __pyx_mstate_global->__pyx_codeobj__40
7793 #define __pyx_codeobj__43 __pyx_mstate_global->__pyx_codeobj__43
7794 #define __pyx_codeobj__46 __pyx_mstate_global->__pyx_codeobj__46
7795 #define __pyx_codeobj__48 __pyx_mstate_global->__pyx_codeobj__48
7796 #define __pyx_codeobj__50 __pyx_mstate_global->__pyx_codeobj__50
7797 #define __pyx_codeobj__51 __pyx_mstate_global->__pyx_codeobj__51
7798 #define __pyx_codeobj__55 __pyx_mstate_global->__pyx_codeobj__55
7799 #define __pyx_codeobj__58 __pyx_mstate_global->__pyx_codeobj__58
7800 #define __pyx_codeobj__60 __pyx_mstate_global->__pyx_codeobj__60
7801 #define __pyx_codeobj__63 __pyx_mstate_global->__pyx_codeobj__63
7802 #define __pyx_codeobj__65 __pyx_mstate_global->__pyx_codeobj__65
7803 #define __pyx_codeobj__67 __pyx_mstate_global->__pyx_codeobj__67
7804 #define __pyx_codeobj__69 __pyx_mstate_global->__pyx_codeobj__69
7805 #define __pyx_codeobj__72 __pyx_mstate_global->__pyx_codeobj__72
7806 #define __pyx_codeobj__74 __pyx_mstate_global->__pyx_codeobj__74
7807 #define __pyx_codeobj__76 __pyx_mstate_global->__pyx_codeobj__76
7808 #define __pyx_codeobj__78 __pyx_mstate_global->__pyx_codeobj__78
7809 #define __pyx_codeobj__80 __pyx_mstate_global->__pyx_codeobj__80
7810 #define __pyx_codeobj__82 __pyx_mstate_global->__pyx_codeobj__82
7811 #define __pyx_codeobj__84 __pyx_mstate_global->__pyx_codeobj__84
7812 #define __pyx_codeobj__86 __pyx_mstate_global->__pyx_codeobj__86
7813 #define __pyx_codeobj__88 __pyx_mstate_global->__pyx_codeobj__88
7814 #define __pyx_codeobj__90 __pyx_mstate_global->__pyx_codeobj__90
7815 #define __pyx_codeobj__92 __pyx_mstate_global->__pyx_codeobj__92
7816 #define __pyx_codeobj__94 __pyx_mstate_global->__pyx_codeobj__94
7817 #define __pyx_codeobj__96 __pyx_mstate_global->__pyx_codeobj__96
7818 #define __pyx_codeobj__98 __pyx_mstate_global->__pyx_codeobj__98
7819 #define __pyx_codeobj__99 __pyx_mstate_global->__pyx_codeobj__99
7820 #define __pyx_codeobj__101 __pyx_mstate_global->__pyx_codeobj__101
7821 #define __pyx_codeobj__102 __pyx_mstate_global->__pyx_codeobj__102
7822 #define __pyx_codeobj__104 __pyx_mstate_global->__pyx_codeobj__104
7823 #define __pyx_codeobj__105 __pyx_mstate_global->__pyx_codeobj__105
7824 #define __pyx_codeobj__107 __pyx_mstate_global->__pyx_codeobj__107
7825 #define __pyx_codeobj__108 __pyx_mstate_global->__pyx_codeobj__108
7826 #define __pyx_codeobj__110 __pyx_mstate_global->__pyx_codeobj__110
7827 #define __pyx_codeobj__112 __pyx_mstate_global->__pyx_codeobj__112
7828 #define __pyx_codeobj__114 __pyx_mstate_global->__pyx_codeobj__114
7829 #define __pyx_codeobj__116 __pyx_mstate_global->__pyx_codeobj__116
7830 #define __pyx_codeobj__118 __pyx_mstate_global->__pyx_codeobj__118
7831 #define __pyx_codeobj__119 __pyx_mstate_global->__pyx_codeobj__119
7832 #define __pyx_codeobj__121 __pyx_mstate_global->__pyx_codeobj__121
7833 #define __pyx_codeobj__123 __pyx_mstate_global->__pyx_codeobj__123
7834 #define __pyx_codeobj__124 __pyx_mstate_global->__pyx_codeobj__124
7835 #define __pyx_codeobj__126 __pyx_mstate_global->__pyx_codeobj__126
7836 #define __pyx_codeobj__128 __pyx_mstate_global->__pyx_codeobj__128
7837 #define __pyx_codeobj__130 __pyx_mstate_global->__pyx_codeobj__130
7838 #define __pyx_codeobj__131 __pyx_mstate_global->__pyx_codeobj__131
7839 #define __pyx_codeobj__133 __pyx_mstate_global->__pyx_codeobj__133
7840 #define __pyx_codeobj__136 __pyx_mstate_global->__pyx_codeobj__136
7841 #define __pyx_codeobj__138 __pyx_mstate_global->__pyx_codeobj__138
7842 /* #### Code section: module_code ### */
7843
7844 /* "cpython/complex.pxd":19
7845 *
7846 * @property
7847 * cdef inline double real(self) noexcept: # <<<<<<<<<<<<<<
7848 * return self.cval.real
7849 *
7850 */
7851
7852 static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4real_real(PyComplexObject *__pyx_v_self) {
7853 double __pyx_r;
7854
7855 /* "cpython/complex.pxd":20
7856 * @property
7857 * cdef inline double real(self) noexcept:
7858 * return self.cval.real # <<<<<<<<<<<<<<
7859 *
7860 * @property
7861 */
7862 __pyx_r = __pyx_v_self->cval.real;
7863 goto __pyx_L0;
7864
7865 /* "cpython/complex.pxd":19
7866 *
7867 * @property
7868 * cdef inline double real(self) noexcept: # <<<<<<<<<<<<<<
7869 * return self.cval.real
7870 *
7871 */
7872
7873 /* function exit code */
7874 __pyx_L0:;
7875 return __pyx_r;
7876 }
7877
7878 /* "cpython/complex.pxd":23
7879 *
7880 * @property
7881 * cdef inline double imag(self) noexcept: # <<<<<<<<<<<<<<
7882 * return self.cval.imag
7883 *
7884 */
7885
7886 static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4imag_imag(PyComplexObject *__pyx_v_self) {
7887 double __pyx_r;
7888
7889 /* "cpython/complex.pxd":24
7890 * @property
7891 * cdef inline double imag(self) noexcept:
7892 * return self.cval.imag # <<<<<<<<<<<<<<
7893 *
7894 * # PyTypeObject PyComplex_Type
7895 */
7896 __pyx_r = __pyx_v_self->cval.imag;
7897 goto __pyx_L0;
7898
7899 /* "cpython/complex.pxd":23
7900 *
7901 * @property
7902 * cdef inline double imag(self) noexcept: # <<<<<<<<<<<<<<
7903 * return self.cval.imag
7904 *
7905 */
7906
7907 /* function exit code */
7908 __pyx_L0:;
7909 return __pyx_r;
7910 }
7911
7912 /* "cpython/contextvars.pxd":112
7913 *
7914 *
7915 * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<<
7916 * """Return a new reference to the value of the context variable,
7917 * or the default value of the context variable,
7918 */
7919
7920 static CYTHON_INLINE PyObject *__pyx_f_7cpython_11contextvars_get_value(PyObject *__pyx_v_var, struct __pyx_opt_args_7cpython_11contextvars_get_value *__pyx_optional_args) {
7921 PyObject *__pyx_v_default_value = ((PyObject *)Py_None);
7922 PyObject *__pyx_v_value;
7923 PyObject *__pyx_v_pyvalue = NULL;
7924 PyObject *__pyx_r = NULL;
7925 __Pyx_RefNannyDeclarations
7926 int __pyx_t_1;
7927 int __pyx_t_2;
7928 PyObject *__pyx_t_3 = NULL;
7929 int __pyx_lineno = 0;
7930 const char *__pyx_filename = NULL;
7931 int __pyx_clineno = 0;
7932 __Pyx_RefNannySetupContext("get_value", 1);
7933 if (__pyx_optional_args) {
7934 if (__pyx_optional_args->__pyx_n > 0) {
7935 __pyx_v_default_value = __pyx_optional_args->default_value;
7936 }
7937 }
7938
7939 /* "cpython/contextvars.pxd":117
7940 * or None if no such value or default was found.
7941 * """
7942 * cdef PyObject *value = NULL # <<<<<<<<<<<<<<
7943 * PyContextVar_Get(var, NULL, &value)
7944 * if value is NULL:
7945 */
7946 __pyx_v_value = NULL;
7947
7948 /* "cpython/contextvars.pxd":118
7949 * """
7950 * cdef PyObject *value = NULL
7951 * PyContextVar_Get(var, NULL, &value) # <<<<<<<<<<<<<<
7952 * if value is NULL:
7953 * # context variable does not have a default
7954 */
7955 __pyx_t_1 = PyContextVar_Get(__pyx_v_var, NULL, (&__pyx_v_value)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(2, 118, __pyx_L1_error)
7956
7957 /* "cpython/contextvars.pxd":119
7958 * cdef PyObject *value = NULL
7959 * PyContextVar_Get(var, NULL, &value)
7960 * if value is NULL: # <<<<<<<<<<<<<<
7961 * # context variable does not have a default
7962 * pyvalue = default_value
7963 */
7964 __pyx_t_2 = (__pyx_v_value == NULL);
7965 if (__pyx_t_2) {
7966
7967 /* "cpython/contextvars.pxd":121
7968 * if value is NULL:
7969 * # context variable does not have a default
7970 * pyvalue = default_value # <<<<<<<<<<<<<<
7971 * else:
7972 * # value or default value of context variable
7973 */
7974 __Pyx_INCREF(__pyx_v_default_value);
7975 __pyx_v_pyvalue = __pyx_v_default_value;
7976
7977 /* "cpython/contextvars.pxd":119
7978 * cdef PyObject *value = NULL
7979 * PyContextVar_Get(var, NULL, &value)
7980 * if value is NULL: # <<<<<<<<<<<<<<
7981 * # context variable does not have a default
7982 * pyvalue = default_value
7983 */
7984 goto __pyx_L3;
7985 }
7986
7987 /* "cpython/contextvars.pxd":124
7988 * else:
7989 * # value or default value of context variable
7990 * pyvalue = <object>value # <<<<<<<<<<<<<<
7991 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*'
7992 * return pyvalue
7993 */
7994 /*else*/ {
7995 __pyx_t_3 = ((PyObject *)__pyx_v_value);
7996 __Pyx_INCREF(__pyx_t_3);
7997 __pyx_v_pyvalue = __pyx_t_3;
7998 __pyx_t_3 = 0;
7999
8000 /* "cpython/contextvars.pxd":125
8001 * # value or default value of context variable
8002 * pyvalue = <object>value
8003 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' # <<<<<<<<<<<<<<
8004 * return pyvalue
8005 *
8006 */
8007 Py_XDECREF(__pyx_v_value);
8008 }
8009 __pyx_L3:;
8010
8011 /* "cpython/contextvars.pxd":126
8012 * pyvalue = <object>value
8013 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*'
8014 * return pyvalue # <<<<<<<<<<<<<<
8015 *
8016 *
8017 */
8018 __Pyx_XDECREF(__pyx_r);
8019 __Pyx_INCREF(__pyx_v_pyvalue);
8020 __pyx_r = __pyx_v_pyvalue;
8021 goto __pyx_L0;
8022
8023 /* "cpython/contextvars.pxd":112
8024 *
8025 *
8026 * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<<
8027 * """Return a new reference to the value of the context variable,
8028 * or the default value of the context variable,
8029 */
8030
8031 /* function exit code */
8032 __pyx_L1_error:;
8033 __Pyx_XDECREF(__pyx_t_3);
8034 __Pyx_AddTraceback("cpython.contextvars.get_value", __pyx_clineno, __pyx_lineno, __pyx_filename);
8035 __pyx_r = 0;
8036 __pyx_L0:;
8037 __Pyx_XDECREF(__pyx_v_pyvalue);
8038 __Pyx_XGIVEREF(__pyx_r);
8039 __Pyx_RefNannyFinishContext();
8040 return __pyx_r;
8041 }
8042
8043 /* "cpython/contextvars.pxd":129
8044 *
8045 *
8046 * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<<
8047 * """Return a new reference to the value of the context variable,
8048 * or the provided default value if no such value was found.
8049 */
8050
8051 static CYTHON_INLINE PyObject *__pyx_f_7cpython_11contextvars_get_value_no_default(PyObject *__pyx_v_var, struct __pyx_opt_args_7cpython_11contextvars_get_value_no_default *__pyx_optional_args) {
8052 PyObject *__pyx_v_default_value = ((PyObject *)Py_None);
8053 PyObject *__pyx_v_value;
8054 PyObject *__pyx_v_pyvalue = NULL;
8055 PyObject *__pyx_r = NULL;
8056 __Pyx_RefNannyDeclarations
8057 int __pyx_t_1;
8058 PyObject *__pyx_t_2 = NULL;
8059 int __pyx_lineno = 0;
8060 const char *__pyx_filename = NULL;
8061 int __pyx_clineno = 0;
8062 __Pyx_RefNannySetupContext("get_value_no_default", 1);
8063 if (__pyx_optional_args) {
8064 if (__pyx_optional_args->__pyx_n > 0) {
8065 __pyx_v_default_value = __pyx_optional_args->default_value;
8066 }
8067 }
8068
8069 /* "cpython/contextvars.pxd":135
8070 * Ignores the default value of the context variable, if any.
8071 * """
8072 * cdef PyObject *value = NULL # <<<<<<<<<<<<<<
8073 * PyContextVar_Get(var, <PyObject*>default_value, &value)
8074 * # value of context variable or 'default_value'
8075 */
8076 __pyx_v_value = NULL;
8077
8078 /* "cpython/contextvars.pxd":136
8079 * """
8080 * cdef PyObject *value = NULL
8081 * PyContextVar_Get(var, <PyObject*>default_value, &value) # <<<<<<<<<<<<<<
8082 * # value of context variable or 'default_value'
8083 * pyvalue = <object>value
8084 */
8085 __pyx_t_1 = PyContextVar_Get(__pyx_v_var, ((PyObject *)__pyx_v_default_value), (&__pyx_v_value)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(2, 136, __pyx_L1_error)
8086
8087 /* "cpython/contextvars.pxd":138
8088 * PyContextVar_Get(var, <PyObject*>default_value, &value)
8089 * # value of context variable or 'default_value'
8090 * pyvalue = <object>value # <<<<<<<<<<<<<<
8091 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*'
8092 * return pyvalue
8093 */
8094 __pyx_t_2 = ((PyObject *)__pyx_v_value);
8095 __Pyx_INCREF(__pyx_t_2);
8096 __pyx_v_pyvalue = __pyx_t_2;
8097 __pyx_t_2 = 0;
8098
8099 /* "cpython/contextvars.pxd":139
8100 * # value of context variable or 'default_value'
8101 * pyvalue = <object>value
8102 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' # <<<<<<<<<<<<<<
8103 * return pyvalue
8104 */
8105 Py_XDECREF(__pyx_v_value);
8106
8107 /* "cpython/contextvars.pxd":140
8108 * pyvalue = <object>value
8109 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*'
8110 * return pyvalue # <<<<<<<<<<<<<<
8111 */
8112 __Pyx_XDECREF(__pyx_r);
8113 __Pyx_INCREF(__pyx_v_pyvalue);
8114 __pyx_r = __pyx_v_pyvalue;
8115 goto __pyx_L0;
8116
8117 /* "cpython/contextvars.pxd":129
8118 *
8119 *
8120 * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<<
8121 * """Return a new reference to the value of the context variable,
8122 * or the provided default value if no such value was found.
8123 */
8124
8125 /* function exit code */
8126 __pyx_L1_error:;
8127 __Pyx_XDECREF(__pyx_t_2);
8128 __Pyx_AddTraceback("cpython.contextvars.get_value_no_default", __pyx_clineno, __pyx_lineno, __pyx_filename);
8129 __pyx_r = 0;
8130 __pyx_L0:;
8131 __Pyx_XDECREF(__pyx_v_pyvalue);
8132 __Pyx_XGIVEREF(__pyx_r);
8133 __Pyx_RefNannyFinishContext();
8134 return __pyx_r;
8135 }
8136
8137 /* "array.pxd":104
8138 * __data_union data
8139 *
8140 * def __getbuffer__(self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
8141 * # This implementation of getbuffer is geared towards Cython
8142 * # requirements, and does not yet fulfill the PEP.
8143 */
8144
8145 /* Python wrapper */
8146 CYTHON_UNUSED static int __pyx_pw_7cpython_5array_5array_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/
8147 CYTHON_UNUSED static int __pyx_pw_7cpython_5array_5array_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) {
8148 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
8149 int __pyx_r;
8150 __Pyx_RefNannyDeclarations
8151 __Pyx_RefNannySetupContext("__getbuffer__ (wrapper)", 0);
8152 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
8153 __pyx_r = __pyx_pf_7cpython_5array_5array___getbuffer__(((arrayobject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info), ((int)__pyx_v_flags));
8154
8155 /* function exit code */
8156 __Pyx_RefNannyFinishContext();
8157 return __pyx_r;
8158 }
8159
8160 static int __pyx_pf_7cpython_5array_5array___getbuffer__(arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info, CYTHON_UNUSED int __pyx_v_flags) {
8161 PyObject *__pyx_v_item_count = NULL;
8162 int __pyx_r;
8163 __Pyx_RefNannyDeclarations
8164 PyObject *__pyx_t_1 = NULL;
8165 char *__pyx_t_2;
8166 int __pyx_t_3;
8167 PyObject *__pyx_t_4 = NULL;
8168 Py_ssize_t __pyx_t_5;
8169 int __pyx_t_6;
8170 char __pyx_t_7;
8171 int __pyx_lineno = 0;
8172 const char *__pyx_filename = NULL;
8173 int __pyx_clineno = 0;
8174 if (unlikely(__pyx_v_info == NULL)) {
8175 PyErr_SetString(PyExc_BufferError, "PyObject_GetBuffer: view==NULL argument is obsolete");
8176 return -1;
8177 }
8178 __Pyx_RefNannySetupContext("__getbuffer__", 0);
8179 __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None);
8180 __Pyx_GIVEREF(__pyx_v_info->obj);
8181
8182 /* "array.pxd":109
8183 * # In particular strided access is always provided regardless
8184 * # of flags
8185 * item_count = Py_SIZE(self) # <<<<<<<<<<<<<<
8186 *
8187 * info.suboffsets = NULL
8188 */
8189 __pyx_t_1 = PyInt_FromSsize_t(Py_SIZE(((PyObject *)__pyx_v_self))); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 109, __pyx_L1_error)
8190 __Pyx_GOTREF(__pyx_t_1);
8191 __pyx_v_item_count = __pyx_t_1;
8192 __pyx_t_1 = 0;
8193
8194 /* "array.pxd":111
8195 * item_count = Py_SIZE(self)
8196 *
8197 * info.suboffsets = NULL # <<<<<<<<<<<<<<
8198 * info.buf = self.data.as_chars
8199 * info.readonly = 0
8200 */
8201 __pyx_v_info->suboffsets = NULL;
8202
8203 /* "array.pxd":112
8204 *
8205 * info.suboffsets = NULL
8206 * info.buf = self.data.as_chars # <<<<<<<<<<<<<<
8207 * info.readonly = 0
8208 * info.ndim = 1
8209 */
8210 __pyx_t_2 = __pyx_v_self->data.as_chars;
8211 __pyx_v_info->buf = __pyx_t_2;
8212
8213 /* "array.pxd":113
8214 * info.suboffsets = NULL
8215 * info.buf = self.data.as_chars
8216 * info.readonly = 0 # <<<<<<<<<<<<<<
8217 * info.ndim = 1
8218 * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float)
8219 */
8220 __pyx_v_info->readonly = 0;
8221
8222 /* "array.pxd":114
8223 * info.buf = self.data.as_chars
8224 * info.readonly = 0
8225 * info.ndim = 1 # <<<<<<<<<<<<<<
8226 * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float)
8227 * info.len = info.itemsize * item_count
8228 */
8229 __pyx_v_info->ndim = 1;
8230
8231 /* "array.pxd":115
8232 * info.readonly = 0
8233 * info.ndim = 1
8234 * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float) # <<<<<<<<<<<<<<
8235 * info.len = info.itemsize * item_count
8236 *
8237 */
8238 __pyx_t_3 = __pyx_v_self->ob_descr->itemsize;
8239 __pyx_v_info->itemsize = __pyx_t_3;
8240
8241 /* "array.pxd":116
8242 * info.ndim = 1
8243 * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float)
8244 * info.len = info.itemsize * item_count # <<<<<<<<<<<<<<
8245 *
8246 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2)
8247 */
8248 __pyx_t_1 = PyInt_FromSsize_t(__pyx_v_info->itemsize); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 116, __pyx_L1_error)
8249 __Pyx_GOTREF(__pyx_t_1);
8250 __pyx_t_4 = PyNumber_Multiply(__pyx_t_1, __pyx_v_item_count); if (unlikely(!__pyx_t_4)) __PYX_ERR(3, 116, __pyx_L1_error)
8251 __Pyx_GOTREF(__pyx_t_4);
8252 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
8253 __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(3, 116, __pyx_L1_error)
8254 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
8255 __pyx_v_info->len = __pyx_t_5;
8256
8257 /* "array.pxd":118
8258 * info.len = info.itemsize * item_count
8259 *
8260 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2) # <<<<<<<<<<<<<<
8261 * if not info.shape:
8262 * raise MemoryError()
8263 */
8264 __pyx_v_info->shape = ((Py_ssize_t *)PyObject_Malloc(((sizeof(Py_ssize_t)) + 2)));
8265
8266 /* "array.pxd":119
8267 *
8268 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2)
8269 * if not info.shape: # <<<<<<<<<<<<<<
8270 * raise MemoryError()
8271 * info.shape[0] = item_count # constant regardless of resizing
8272 */
8273 __pyx_t_6 = (!(__pyx_v_info->shape != 0));
8274 if (unlikely(__pyx_t_6)) {
8275
8276 /* "array.pxd":120
8277 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2)
8278 * if not info.shape:
8279 * raise MemoryError() # <<<<<<<<<<<<<<
8280 * info.shape[0] = item_count # constant regardless of resizing
8281 * info.strides = &info.itemsize
8282 */
8283 PyErr_NoMemory(); __PYX_ERR(3, 120, __pyx_L1_error)
8284
8285 /* "array.pxd":119
8286 *
8287 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2)
8288 * if not info.shape: # <<<<<<<<<<<<<<
8289 * raise MemoryError()
8290 * info.shape[0] = item_count # constant regardless of resizing
8291 */
8292 }
8293
8294 /* "array.pxd":121
8295 * if not info.shape:
8296 * raise MemoryError()
8297 * info.shape[0] = item_count # constant regardless of resizing # <<<<<<<<<<<<<<
8298 * info.strides = &info.itemsize
8299 *
8300 */
8301 __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_v_item_count); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(3, 121, __pyx_L1_error)
8302 (__pyx_v_info->shape[0]) = __pyx_t_5;
8303
8304 /* "array.pxd":122
8305 * raise MemoryError()
8306 * info.shape[0] = item_count # constant regardless of resizing
8307 * info.strides = &info.itemsize # <<<<<<<<<<<<<<
8308 *
8309 * info.format = <char*> (info.shape + 1)
8310 */
8311 __pyx_v_info->strides = (&__pyx_v_info->itemsize);
8312
8313 /* "array.pxd":124
8314 * info.strides = &info.itemsize
8315 *
8316 * info.format = <char*> (info.shape + 1) # <<<<<<<<<<<<<<
8317 * info.format[0] = self.ob_descr.typecode
8318 * info.format[1] = 0
8319 */
8320 __pyx_v_info->format = ((char *)(__pyx_v_info->shape + 1));
8321
8322 /* "array.pxd":125
8323 *
8324 * info.format = <char*> (info.shape + 1)
8325 * info.format[0] = self.ob_descr.typecode # <<<<<<<<<<<<<<
8326 * info.format[1] = 0
8327 * info.obj = self
8328 */
8329 __pyx_t_7 = __pyx_v_self->ob_descr->typecode;
8330 (__pyx_v_info->format[0]) = __pyx_t_7;
8331
8332 /* "array.pxd":126
8333 * info.format = <char*> (info.shape + 1)
8334 * info.format[0] = self.ob_descr.typecode
8335 * info.format[1] = 0 # <<<<<<<<<<<<<<
8336 * info.obj = self
8337 *
8338 */
8339 (__pyx_v_info->format[1]) = 0;
8340
8341 /* "array.pxd":127
8342 * info.format[0] = self.ob_descr.typecode
8343 * info.format[1] = 0
8344 * info.obj = self # <<<<<<<<<<<<<<
8345 *
8346 * def __releasebuffer__(self, Py_buffer* info):
8347 */
8348 __Pyx_INCREF((PyObject *)__pyx_v_self);
8349 __Pyx_GIVEREF((PyObject *)__pyx_v_self);
8350 __Pyx_GOTREF(__pyx_v_info->obj);
8351 __Pyx_DECREF(__pyx_v_info->obj);
8352 __pyx_v_info->obj = ((PyObject *)__pyx_v_self);
8353
8354 /* "array.pxd":104
8355 * __data_union data
8356 *
8357 * def __getbuffer__(self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
8358 * # This implementation of getbuffer is geared towards Cython
8359 * # requirements, and does not yet fulfill the PEP.
8360 */
8361
8362 /* function exit code */
8363 __pyx_r = 0;
8364 goto __pyx_L0;
8365 __pyx_L1_error:;
8366 __Pyx_XDECREF(__pyx_t_1);
8367 __Pyx_XDECREF(__pyx_t_4);
8368 __Pyx_AddTraceback("cpython.array.array.__getbuffer__", __pyx_clineno, __pyx_lineno, __pyx_filename);
8369 __pyx_r = -1;
8370 if (__pyx_v_info->obj != NULL) {
8371 __Pyx_GOTREF(__pyx_v_info->obj);
8372 __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = 0;
8373 }
8374 goto __pyx_L2;
8375 __pyx_L0:;
8376 if (__pyx_v_info->obj == Py_None) {
8377 __Pyx_GOTREF(__pyx_v_info->obj);
8378 __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = 0;
8379 }
8380 __pyx_L2:;
8381 __Pyx_XDECREF(__pyx_v_item_count);
8382 __Pyx_RefNannyFinishContext();
8383 return __pyx_r;
8384 }
8385
8386 /* "array.pxd":129
8387 * info.obj = self
8388 *
8389 * def __releasebuffer__(self, Py_buffer* info): # <<<<<<<<<<<<<<
8390 * PyObject_Free(info.shape)
8391 *
8392 */
8393
8394 /* Python wrapper */
8395 CYTHON_UNUSED static void __pyx_pw_7cpython_5array_5array_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info); /*proto*/
8396 CYTHON_UNUSED static void __pyx_pw_7cpython_5array_5array_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) {
8397 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
8398 __Pyx_RefNannyDeclarations
8399 __Pyx_RefNannySetupContext("__releasebuffer__ (wrapper)", 0);
8400 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
8401 __pyx_pf_7cpython_5array_5array_2__releasebuffer__(((arrayobject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info));
8402
8403 /* function exit code */
8404 __Pyx_RefNannyFinishContext();
8405 }
8406
8407 static void __pyx_pf_7cpython_5array_5array_2__releasebuffer__(CYTHON_UNUSED arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info) {
8408
8409 /* "array.pxd":130
8410 *
8411 * def __releasebuffer__(self, Py_buffer* info):
8412 * PyObject_Free(info.shape) # <<<<<<<<<<<<<<
8413 *
8414 * array newarrayobject(PyTypeObject* type, Py_ssize_t size, arraydescr *descr)
8415 */
8416 PyObject_Free(__pyx_v_info->shape);
8417
8418 /* "array.pxd":129
8419 * info.obj = self
8420 *
8421 * def __releasebuffer__(self, Py_buffer* info): # <<<<<<<<<<<<<<
8422 * PyObject_Free(info.shape)
8423 *
8424 */
8425
8426 /* function exit code */
8427 }
8428
8429 /* "array.pxd":141
8430 *
8431 *
8432 * cdef inline array clone(array template, Py_ssize_t length, bint zero): # <<<<<<<<<<<<<<
8433 * """ fast creation of a new array, given a template array.
8434 * type will be same as template.
8435 */
8436
8437 static CYTHON_INLINE arrayobject *__pyx_f_7cpython_5array_clone(arrayobject *__pyx_v_template, Py_ssize_t __pyx_v_length, int __pyx_v_zero) {
8438 arrayobject *__pyx_v_op = 0;
8439 arrayobject *__pyx_r = NULL;
8440 __Pyx_RefNannyDeclarations
8441 PyObject *__pyx_t_1 = NULL;
8442 int __pyx_t_2;
8443 int __pyx_t_3;
8444 int __pyx_lineno = 0;
8445 const char *__pyx_filename = NULL;
8446 int __pyx_clineno = 0;
8447 __Pyx_RefNannySetupContext("clone", 1);
8448
8449 /* "array.pxd":145
8450 * type will be same as template.
8451 * if zero is true, new array will be initialized with zeroes."""
8452 * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr) # <<<<<<<<<<<<<<
8453 * if zero and op is not None:
8454 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize)
8455 */
8456 __pyx_t_1 = ((PyObject *)newarrayobject(Py_TYPE(((PyObject *)__pyx_v_template)), __pyx_v_length, __pyx_v_template->ob_descr)); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 145, __pyx_L1_error)
8457 __Pyx_GOTREF(__pyx_t_1);
8458 __pyx_v_op = ((arrayobject *)__pyx_t_1);
8459 __pyx_t_1 = 0;
8460
8461 /* "array.pxd":146
8462 * if zero is true, new array will be initialized with zeroes."""
8463 * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr)
8464 * if zero and op is not None: # <<<<<<<<<<<<<<
8465 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize)
8466 * return op
8467 */
8468 if (__pyx_v_zero) {
8469 } else {
8470 __pyx_t_2 = __pyx_v_zero;
8471 goto __pyx_L4_bool_binop_done;
8472 }
8473 __pyx_t_3 = (((PyObject *)__pyx_v_op) != Py_None);
8474 __pyx_t_2 = __pyx_t_3;
8475 __pyx_L4_bool_binop_done:;
8476 if (__pyx_t_2) {
8477
8478 /* "array.pxd":147
8479 * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr)
8480 * if zero and op is not None:
8481 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) # <<<<<<<<<<<<<<
8482 * return op
8483 *
8484 */
8485 (void)(memset(__pyx_v_op->data.as_chars, 0, (__pyx_v_length * __pyx_v_op->ob_descr->itemsize)));
8486
8487 /* "array.pxd":146
8488 * if zero is true, new array will be initialized with zeroes."""
8489 * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr)
8490 * if zero and op is not None: # <<<<<<<<<<<<<<
8491 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize)
8492 * return op
8493 */
8494 }
8495
8496 /* "array.pxd":148
8497 * if zero and op is not None:
8498 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize)
8499 * return op # <<<<<<<<<<<<<<
8500 *
8501 * cdef inline array copy(array self):
8502 */
8503 __Pyx_XDECREF((PyObject *)__pyx_r);
8504 __Pyx_INCREF((PyObject *)__pyx_v_op);
8505 __pyx_r = __pyx_v_op;
8506 goto __pyx_L0;
8507
8508 /* "array.pxd":141
8509 *
8510 *
8511 * cdef inline array clone(array template, Py_ssize_t length, bint zero): # <<<<<<<<<<<<<<
8512 * """ fast creation of a new array, given a template array.
8513 * type will be same as template.
8514 */
8515
8516 /* function exit code */
8517 __pyx_L1_error:;
8518 __Pyx_XDECREF(__pyx_t_1);
8519 __Pyx_AddTraceback("cpython.array.clone", __pyx_clineno, __pyx_lineno, __pyx_filename);
8520 __pyx_r = 0;
8521 __pyx_L0:;
8522 __Pyx_XDECREF((PyObject *)__pyx_v_op);
8523 __Pyx_XGIVEREF((PyObject *)__pyx_r);
8524 __Pyx_RefNannyFinishContext();
8525 return __pyx_r;
8526 }
8527
8528 /* "array.pxd":150
8529 * return op
8530 *
8531 * cdef inline array copy(array self): # <<<<<<<<<<<<<<
8532 * """ make a copy of an array. """
8533 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr)
8534 */
8535
8536 static CYTHON_INLINE arrayobject *__pyx_f_7cpython_5array_copy(arrayobject *__pyx_v_self) {
8537 arrayobject *__pyx_v_op = 0;
8538 arrayobject *__pyx_r = NULL;
8539 __Pyx_RefNannyDeclarations
8540 PyObject *__pyx_t_1 = NULL;
8541 int __pyx_lineno = 0;
8542 const char *__pyx_filename = NULL;
8543 int __pyx_clineno = 0;
8544 __Pyx_RefNannySetupContext("copy", 1);
8545
8546 /* "array.pxd":152
8547 * cdef inline array copy(array self):
8548 * """ make a copy of an array. """
8549 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) # <<<<<<<<<<<<<<
8550 * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize)
8551 * return op
8552 */
8553 __pyx_t_1 = ((PyObject *)newarrayobject(Py_TYPE(((PyObject *)__pyx_v_self)), Py_SIZE(((PyObject *)__pyx_v_self)), __pyx_v_self->ob_descr)); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 152, __pyx_L1_error)
8554 __Pyx_GOTREF(__pyx_t_1);
8555 __pyx_v_op = ((arrayobject *)__pyx_t_1);
8556 __pyx_t_1 = 0;
8557
8558 /* "array.pxd":153
8559 * """ make a copy of an array. """
8560 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr)
8561 * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize) # <<<<<<<<<<<<<<
8562 * return op
8563 *
8564 */
8565 (void)(memcpy(__pyx_v_op->data.as_chars, __pyx_v_self->data.as_chars, (Py_SIZE(((PyObject *)__pyx_v_op)) * __pyx_v_op->ob_descr->itemsize)));
8566
8567 /* "array.pxd":154
8568 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr)
8569 * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize)
8570 * return op # <<<<<<<<<<<<<<
8571 *
8572 * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1:
8573 */
8574 __Pyx_XDECREF((PyObject *)__pyx_r);
8575 __Pyx_INCREF((PyObject *)__pyx_v_op);
8576 __pyx_r = __pyx_v_op;
8577 goto __pyx_L0;
8578
8579 /* "array.pxd":150
8580 * return op
8581 *
8582 * cdef inline array copy(array self): # <<<<<<<<<<<<<<
8583 * """ make a copy of an array. """
8584 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr)
8585 */
8586
8587 /* function exit code */
8588 __pyx_L1_error:;
8589 __Pyx_XDECREF(__pyx_t_1);
8590 __Pyx_AddTraceback("cpython.array.copy", __pyx_clineno, __pyx_lineno, __pyx_filename);
8591 __pyx_r = 0;
8592 __pyx_L0:;
8593 __Pyx_XDECREF((PyObject *)__pyx_v_op);
8594 __Pyx_XGIVEREF((PyObject *)__pyx_r);
8595 __Pyx_RefNannyFinishContext();
8596 return __pyx_r;
8597 }
8598
8599 /* "array.pxd":156
8600 * return op
8601 *
8602 * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1: # <<<<<<<<<<<<<<
8603 * """ efficient appending of new stuff of same type
8604 * (e.g. of same array type)
8605 */
8606
8607 static CYTHON_INLINE int __pyx_f_7cpython_5array_extend_buffer(arrayobject *__pyx_v_self, char *__pyx_v_stuff, Py_ssize_t __pyx_v_n) {
8608 Py_ssize_t __pyx_v_itemsize;
8609 Py_ssize_t __pyx_v_origsize;
8610 int __pyx_r;
8611 int __pyx_t_1;
8612 int __pyx_lineno = 0;
8613 const char *__pyx_filename = NULL;
8614 int __pyx_clineno = 0;
8615
8616 /* "array.pxd":160
8617 * (e.g. of same array type)
8618 * n: number of elements (not number of bytes!) """
8619 * cdef Py_ssize_t itemsize = self.ob_descr.itemsize # <<<<<<<<<<<<<<
8620 * cdef Py_ssize_t origsize = Py_SIZE(self)
8621 * resize_smart(self, origsize + n)
8622 */
8623 __pyx_t_1 = __pyx_v_self->ob_descr->itemsize;
8624 __pyx_v_itemsize = __pyx_t_1;
8625
8626 /* "array.pxd":161
8627 * n: number of elements (not number of bytes!) """
8628 * cdef Py_ssize_t itemsize = self.ob_descr.itemsize
8629 * cdef Py_ssize_t origsize = Py_SIZE(self) # <<<<<<<<<<<<<<
8630 * resize_smart(self, origsize + n)
8631 * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize)
8632 */
8633 __pyx_v_origsize = Py_SIZE(((PyObject *)__pyx_v_self));
8634
8635 /* "array.pxd":162
8636 * cdef Py_ssize_t itemsize = self.ob_descr.itemsize
8637 * cdef Py_ssize_t origsize = Py_SIZE(self)
8638 * resize_smart(self, origsize + n) # <<<<<<<<<<<<<<
8639 * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize)
8640 * return 0
8641 */
8642 __pyx_t_1 = resize_smart(__pyx_v_self, (__pyx_v_origsize + __pyx_v_n)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(3, 162, __pyx_L1_error)
8643
8644 /* "array.pxd":163
8645 * cdef Py_ssize_t origsize = Py_SIZE(self)
8646 * resize_smart(self, origsize + n)
8647 * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize) # <<<<<<<<<<<<<<
8648 * return 0
8649 *
8650 */
8651 (void)(memcpy((__pyx_v_self->data.as_chars + (__pyx_v_origsize * __pyx_v_itemsize)), __pyx_v_stuff, (__pyx_v_n * __pyx_v_itemsize)));
8652
8653 /* "array.pxd":164
8654 * resize_smart(self, origsize + n)
8655 * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize)
8656 * return 0 # <<<<<<<<<<<<<<
8657 *
8658 * cdef inline int extend(array self, array other) except -1:
8659 */
8660 __pyx_r = 0;
8661 goto __pyx_L0;
8662
8663 /* "array.pxd":156
8664 * return op
8665 *
8666 * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1: # <<<<<<<<<<<<<<
8667 * """ efficient appending of new stuff of same type
8668 * (e.g. of same array type)
8669 */
8670
8671 /* function exit code */
8672 __pyx_L1_error:;
8673 __Pyx_AddTraceback("cpython.array.extend_buffer", __pyx_clineno, __pyx_lineno, __pyx_filename);
8674 __pyx_r = -1;
8675 __pyx_L0:;
8676 return __pyx_r;
8677 }
8678
8679 /* "array.pxd":166
8680 * return 0
8681 *
8682 * cdef inline int extend(array self, array other) except -1: # <<<<<<<<<<<<<<
8683 * """ extend array with data from another array; types must match. """
8684 * if self.ob_descr.typecode != other.ob_descr.typecode:
8685 */
8686
8687 static CYTHON_INLINE int __pyx_f_7cpython_5array_extend(arrayobject *__pyx_v_self, arrayobject *__pyx_v_other) {
8688 int __pyx_r;
8689 int __pyx_t_1;
8690 int __pyx_t_2;
8691 int __pyx_lineno = 0;
8692 const char *__pyx_filename = NULL;
8693 int __pyx_clineno = 0;
8694
8695 /* "array.pxd":168
8696 * cdef inline int extend(array self, array other) except -1:
8697 * """ extend array with data from another array; types must match. """
8698 * if self.ob_descr.typecode != other.ob_descr.typecode: # <<<<<<<<<<<<<<
8699 * PyErr_BadArgument()
8700 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
8701 */
8702 __pyx_t_1 = (__pyx_v_self->ob_descr->typecode != __pyx_v_other->ob_descr->typecode);
8703 if (__pyx_t_1) {
8704
8705 /* "array.pxd":169
8706 * """ extend array with data from another array; types must match. """
8707 * if self.ob_descr.typecode != other.ob_descr.typecode:
8708 * PyErr_BadArgument() # <<<<<<<<<<<<<<
8709 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
8710 *
8711 */
8712 __pyx_t_2 = PyErr_BadArgument(); if (unlikely(__pyx_t_2 == ((int)0))) __PYX_ERR(3, 169, __pyx_L1_error)
8713
8714 /* "array.pxd":168
8715 * cdef inline int extend(array self, array other) except -1:
8716 * """ extend array with data from another array; types must match. """
8717 * if self.ob_descr.typecode != other.ob_descr.typecode: # <<<<<<<<<<<<<<
8718 * PyErr_BadArgument()
8719 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
8720 */
8721 }
8722
8723 /* "array.pxd":170
8724 * if self.ob_descr.typecode != other.ob_descr.typecode:
8725 * PyErr_BadArgument()
8726 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) # <<<<<<<<<<<<<<
8727 *
8728 * cdef inline void zero(array self) noexcept:
8729 */
8730 __pyx_t_2 = __pyx_f_7cpython_5array_extend_buffer(__pyx_v_self, __pyx_v_other->data.as_chars, Py_SIZE(((PyObject *)__pyx_v_other))); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(3, 170, __pyx_L1_error)
8731 __pyx_r = __pyx_t_2;
8732 goto __pyx_L0;
8733
8734 /* "array.pxd":166
8735 * return 0
8736 *
8737 * cdef inline int extend(array self, array other) except -1: # <<<<<<<<<<<<<<
8738 * """ extend array with data from another array; types must match. """
8739 * if self.ob_descr.typecode != other.ob_descr.typecode:
8740 */
8741
8742 /* function exit code */
8743 __pyx_L1_error:;
8744 __Pyx_AddTraceback("cpython.array.extend", __pyx_clineno, __pyx_lineno, __pyx_filename);
8745 __pyx_r = -1;
8746 __pyx_L0:;
8747 return __pyx_r;
8748 }
8749
8750 /* "array.pxd":172
8751 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
8752 *
8753 * cdef inline void zero(array self) noexcept: # <<<<<<<<<<<<<<
8754 * """ set all elements of array to zero. """
8755 * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize)
8756 */
8757
8758 static CYTHON_INLINE void __pyx_f_7cpython_5array_zero(arrayobject *__pyx_v_self) {
8759
8760 /* "array.pxd":174
8761 * cdef inline void zero(array self) noexcept:
8762 * """ set all elements of array to zero. """
8763 * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize) # <<<<<<<<<<<<<<
8764 */
8765 (void)(memset(__pyx_v_self->data.as_chars, 0, (Py_SIZE(((PyObject *)__pyx_v_self)) * __pyx_v_self->ob_descr->itemsize)));
8766
8767 /* "array.pxd":172
8768 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
8769 *
8770 * cdef inline void zero(array self) noexcept: # <<<<<<<<<<<<<<
8771 * """ set all elements of array to zero. """
8772 * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize)
8773 */
8774
8775 /* function exit code */
8776 }
8777
8778 /* "pysam/libcvcf.pyx":68
8779 *
8780 * # Utility function. Uses 0-based coordinates
8781 * def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<<
8782 * # obtain sequence from .fa file, without truncation
8783 * if end<=start: return ""
8784 */
8785
8786 /* Python wrapper */
8787 static PyObject *__pyx_pw_5pysam_7libcvcf_1get_sequence(PyObject *__pyx_self,
8788 #if CYTHON_METH_FASTCALL
8789 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
8790 #else
8791 PyObject *__pyx_args, PyObject *__pyx_kwds
8792 #endif
8793 ); /*proto*/
8794 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_get_sequence, "get_sequence(chrom, start, end, fa)");
8795 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_1get_sequence = {"get_sequence", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_1get_sequence, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_get_sequence};
8796 static PyObject *__pyx_pw_5pysam_7libcvcf_1get_sequence(PyObject *__pyx_self,
8797 #if CYTHON_METH_FASTCALL
8798 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
8799 #else
8800 PyObject *__pyx_args, PyObject *__pyx_kwds
8801 #endif
8802 ) {
8803 PyObject *__pyx_v_chrom = 0;
8804 PyObject *__pyx_v_start = 0;
8805 PyObject *__pyx_v_end = 0;
8806 PyObject *__pyx_v_fa = 0;
8807 #if !CYTHON_METH_FASTCALL
8808 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
8809 #endif
8810 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
8811 PyObject* values[4] = {0,0,0,0};
8812 int __pyx_lineno = 0;
8813 const char *__pyx_filename = NULL;
8814 int __pyx_clineno = 0;
8815 PyObject *__pyx_r = 0;
8816 __Pyx_RefNannyDeclarations
8817 __Pyx_RefNannySetupContext("get_sequence (wrapper)", 0);
8818 #if !CYTHON_METH_FASTCALL
8819 #if CYTHON_ASSUME_SAFE_MACROS
8820 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
8821 #else
8822 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
8823 #endif
8824 #endif
8825 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
8826 {
8827 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_chrom,&__pyx_n_s_start,&__pyx_n_s_end,&__pyx_n_s_fa,0};
8828 if (__pyx_kwds) {
8829 Py_ssize_t kw_args;
8830 switch (__pyx_nargs) {
8831 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
8832 CYTHON_FALLTHROUGH;
8833 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
8834 CYTHON_FALLTHROUGH;
8835 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
8836 CYTHON_FALLTHROUGH;
8837 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
8838 CYTHON_FALLTHROUGH;
8839 case 0: break;
8840 default: goto __pyx_L5_argtuple_error;
8841 }
8842 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
8843 switch (__pyx_nargs) {
8844 case 0:
8845 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_chrom)) != 0)) {
8846 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
8847 kw_args--;
8848 }
8849 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 68, __pyx_L3_error)
8850 else goto __pyx_L5_argtuple_error;
8851 CYTHON_FALLTHROUGH;
8852 case 1:
8853 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_start)) != 0)) {
8854 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
8855 kw_args--;
8856 }
8857 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 68, __pyx_L3_error)
8858 else {
8859 __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 1); __PYX_ERR(0, 68, __pyx_L3_error)
8860 }
8861 CYTHON_FALLTHROUGH;
8862 case 2:
8863 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_end)) != 0)) {
8864 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
8865 kw_args--;
8866 }
8867 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 68, __pyx_L3_error)
8868 else {
8869 __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 2); __PYX_ERR(0, 68, __pyx_L3_error)
8870 }
8871 CYTHON_FALLTHROUGH;
8872 case 3:
8873 if (likely((values[3] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_fa)) != 0)) {
8874 (void)__Pyx_Arg_NewRef_FASTCALL(values[3]);
8875 kw_args--;
8876 }
8877 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 68, __pyx_L3_error)
8878 else {
8879 __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 3); __PYX_ERR(0, 68, __pyx_L3_error)
8880 }
8881 }
8882 if (unlikely(kw_args > 0)) {
8883 const Py_ssize_t kwd_pos_args = __pyx_nargs;
8884 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "get_sequence") < 0)) __PYX_ERR(0, 68, __pyx_L3_error)
8885 }
8886 } else if (unlikely(__pyx_nargs != 4)) {
8887 goto __pyx_L5_argtuple_error;
8888 } else {
8889 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
8890 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
8891 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
8892 values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
8893 }
8894 __pyx_v_chrom = values[0];
8895 __pyx_v_start = values[1];
8896 __pyx_v_end = values[2];
8897 __pyx_v_fa = values[3];
8898 }
8899 goto __pyx_L6_skip;
8900 __pyx_L5_argtuple_error:;
8901 __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, __pyx_nargs); __PYX_ERR(0, 68, __pyx_L3_error)
8902 __pyx_L6_skip:;
8903 goto __pyx_L4_argument_unpacking_done;
8904 __pyx_L3_error:;
8905 {
8906 Py_ssize_t __pyx_temp;
8907 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
8908 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
8909 }
8910 }
8911 __Pyx_AddTraceback("pysam.libcvcf.get_sequence", __pyx_clineno, __pyx_lineno, __pyx_filename);
8912 __Pyx_RefNannyFinishContext();
8913 return NULL;
8914 __pyx_L4_argument_unpacking_done:;
8915 __pyx_r = __pyx_pf_5pysam_7libcvcf_get_sequence(__pyx_self, __pyx_v_chrom, __pyx_v_start, __pyx_v_end, __pyx_v_fa);
8916
8917 /* function exit code */
8918 {
8919 Py_ssize_t __pyx_temp;
8920 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
8921 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
8922 }
8923 }
8924 __Pyx_RefNannyFinishContext();
8925 return __pyx_r;
8926 }
8927
8928 static PyObject *__pyx_pf_5pysam_7libcvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_fa) {
8929 PyObject *__pyx_v_sequence = NULL;
8930 PyObject *__pyx_r = NULL;
8931 __Pyx_RefNannyDeclarations
8932 PyObject *__pyx_t_1 = NULL;
8933 int __pyx_t_2;
8934 int __pyx_t_3;
8935 PyObject *__pyx_t_4 = NULL;
8936 PyObject *__pyx_t_5 = NULL;
8937 PyObject *__pyx_t_6 = NULL;
8938 PyObject *__pyx_t_7 = NULL;
8939 unsigned int __pyx_t_8;
8940 Py_ssize_t __pyx_t_9;
8941 int __pyx_lineno = 0;
8942 const char *__pyx_filename = NULL;
8943 int __pyx_clineno = 0;
8944 __Pyx_RefNannySetupContext("get_sequence", 1);
8945
8946 /* "pysam/libcvcf.pyx":70
8947 * def get_sequence(chrom, start, end, fa):
8948 * # obtain sequence from .fa file, without truncation
8949 * if end<=start: return "" # <<<<<<<<<<<<<<
8950 * if not fa: return "N"*(end-start)
8951 * if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
8952 */
8953 __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_v_start, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 70, __pyx_L1_error)
8954 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 70, __pyx_L1_error)
8955 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
8956 if (__pyx_t_2) {
8957 __Pyx_XDECREF(__pyx_r);
8958 __Pyx_INCREF(__pyx_kp_u_);
8959 __pyx_r = __pyx_kp_u_;
8960 goto __pyx_L0;
8961 }
8962
8963 /* "pysam/libcvcf.pyx":71
8964 * # obtain sequence from .fa file, without truncation
8965 * if end<=start: return ""
8966 * if not fa: return "N"*(end-start) # <<<<<<<<<<<<<<
8967 * if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
8968 * sequence = fa.fetch(chrom, start, end).upper()
8969 */
8970 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_fa); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 71, __pyx_L1_error)
8971 __pyx_t_3 = (!__pyx_t_2);
8972 if (__pyx_t_3) {
8973 __Pyx_XDECREF(__pyx_r);
8974 __pyx_t_1 = PyNumber_Subtract(__pyx_v_end, __pyx_v_start); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 71, __pyx_L1_error)
8975 __Pyx_GOTREF(__pyx_t_1);
8976 __pyx_t_4 = PyNumber_Multiply(__pyx_n_u_N, __pyx_t_1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 71, __pyx_L1_error)
8977 __Pyx_GOTREF(__pyx_t_4);
8978 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
8979 __pyx_r = __pyx_t_4;
8980 __pyx_t_4 = 0;
8981 goto __pyx_L0;
8982 }
8983
8984 /* "pysam/libcvcf.pyx":72
8985 * if end<=start: return ""
8986 * if not fa: return "N"*(end-start)
8987 * if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper() # <<<<<<<<<<<<<<
8988 * sequence = fa.fetch(chrom, start, end).upper()
8989 * if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
8990 */
8991 __pyx_t_4 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 72, __pyx_L1_error)
8992 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 72, __pyx_L1_error)
8993 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
8994 if (__pyx_t_3) {
8995 __Pyx_XDECREF(__pyx_r);
8996 __pyx_t_4 = PyNumber_Negative(__pyx_v_start); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 72, __pyx_L1_error)
8997 __Pyx_GOTREF(__pyx_t_4);
8998 __pyx_t_1 = PyNumber_Multiply(__pyx_n_u_N, __pyx_t_4); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 72, __pyx_L1_error)
8999 __Pyx_GOTREF(__pyx_t_1);
9000 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
9001 __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_get_sequence); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 72, __pyx_L1_error)
9002 __Pyx_GOTREF(__pyx_t_6);
9003 __pyx_t_7 = NULL;
9004 __pyx_t_8 = 0;
9005 #if CYTHON_UNPACK_METHODS
9006 if (unlikely(PyMethod_Check(__pyx_t_6))) {
9007 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6);
9008 if (likely(__pyx_t_7)) {
9009 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
9010 __Pyx_INCREF(__pyx_t_7);
9011 __Pyx_INCREF(function);
9012 __Pyx_DECREF_SET(__pyx_t_6, function);
9013 __pyx_t_8 = 1;
9014 }
9015 }
9016 #endif
9017 {
9018 PyObject *__pyx_callargs[5] = {__pyx_t_7, __pyx_v_chrom, __pyx_int_0, __pyx_v_end, __pyx_v_fa};
9019 __pyx_t_5 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 4+__pyx_t_8);
9020 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
9021 if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 72, __pyx_L1_error)
9022 __Pyx_GOTREF(__pyx_t_5);
9023 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
9024 }
9025 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_upper); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 72, __pyx_L1_error)
9026 __Pyx_GOTREF(__pyx_t_6);
9027 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
9028 __pyx_t_5 = NULL;
9029 __pyx_t_8 = 0;
9030 #if CYTHON_UNPACK_METHODS
9031 if (likely(PyMethod_Check(__pyx_t_6))) {
9032 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_6);
9033 if (likely(__pyx_t_5)) {
9034 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
9035 __Pyx_INCREF(__pyx_t_5);
9036 __Pyx_INCREF(function);
9037 __Pyx_DECREF_SET(__pyx_t_6, function);
9038 __pyx_t_8 = 1;
9039 }
9040 }
9041 #endif
9042 {
9043 PyObject *__pyx_callargs[2] = {__pyx_t_5, NULL};
9044 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 0+__pyx_t_8);
9045 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
9046 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 72, __pyx_L1_error)
9047 __Pyx_GOTREF(__pyx_t_4);
9048 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
9049 }
9050 __pyx_t_6 = PyNumber_Add(__pyx_t_1, __pyx_t_4); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 72, __pyx_L1_error)
9051 __Pyx_GOTREF(__pyx_t_6);
9052 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
9053 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
9054 __pyx_r = __pyx_t_6;
9055 __pyx_t_6 = 0;
9056 goto __pyx_L0;
9057 }
9058
9059 /* "pysam/libcvcf.pyx":73
9060 * if not fa: return "N"*(end-start)
9061 * if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
9062 * sequence = fa.fetch(chrom, start, end).upper() # <<<<<<<<<<<<<<
9063 * if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
9064 * return sequence
9065 */
9066 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_fa, __pyx_n_s_fetch); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 73, __pyx_L1_error)
9067 __Pyx_GOTREF(__pyx_t_1);
9068 __pyx_t_5 = NULL;
9069 __pyx_t_8 = 0;
9070 #if CYTHON_UNPACK_METHODS
9071 if (likely(PyMethod_Check(__pyx_t_1))) {
9072 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_1);
9073 if (likely(__pyx_t_5)) {
9074 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
9075 __Pyx_INCREF(__pyx_t_5);
9076 __Pyx_INCREF(function);
9077 __Pyx_DECREF_SET(__pyx_t_1, function);
9078 __pyx_t_8 = 1;
9079 }
9080 }
9081 #endif
9082 {
9083 PyObject *__pyx_callargs[4] = {__pyx_t_5, __pyx_v_chrom, __pyx_v_start, __pyx_v_end};
9084 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_8, 3+__pyx_t_8);
9085 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
9086 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 73, __pyx_L1_error)
9087 __Pyx_GOTREF(__pyx_t_4);
9088 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
9089 }
9090 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_upper); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 73, __pyx_L1_error)
9091 __Pyx_GOTREF(__pyx_t_1);
9092 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
9093 __pyx_t_4 = NULL;
9094 __pyx_t_8 = 0;
9095 #if CYTHON_UNPACK_METHODS
9096 if (likely(PyMethod_Check(__pyx_t_1))) {
9097 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_1);
9098 if (likely(__pyx_t_4)) {
9099 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
9100 __Pyx_INCREF(__pyx_t_4);
9101 __Pyx_INCREF(function);
9102 __Pyx_DECREF_SET(__pyx_t_1, function);
9103 __pyx_t_8 = 1;
9104 }
9105 }
9106 #endif
9107 {
9108 PyObject *__pyx_callargs[2] = {__pyx_t_4, NULL};
9109 __pyx_t_6 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_8, 0+__pyx_t_8);
9110 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
9111 if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 73, __pyx_L1_error)
9112 __Pyx_GOTREF(__pyx_t_6);
9113 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
9114 }
9115 __pyx_v_sequence = __pyx_t_6;
9116 __pyx_t_6 = 0;
9117
9118 /* "pysam/libcvcf.pyx":74
9119 * if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
9120 * sequence = fa.fetch(chrom, start, end).upper()
9121 * if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence)) # <<<<<<<<<<<<<<
9122 * return sequence
9123 *
9124 */
9125 __pyx_t_9 = PyObject_Length(__pyx_v_sequence); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 74, __pyx_L1_error)
9126 __pyx_t_6 = PyInt_FromSsize_t(__pyx_t_9); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 74, __pyx_L1_error)
9127 __Pyx_GOTREF(__pyx_t_6);
9128 __pyx_t_1 = PyNumber_Subtract(__pyx_v_end, __pyx_v_start); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 74, __pyx_L1_error)
9129 __Pyx_GOTREF(__pyx_t_1);
9130 __pyx_t_4 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 74, __pyx_L1_error)
9131 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
9132 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
9133 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 74, __pyx_L1_error)
9134 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
9135 if (__pyx_t_3) {
9136 __pyx_t_4 = PyNumber_Subtract(__pyx_v_end, __pyx_v_start); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 74, __pyx_L1_error)
9137 __Pyx_GOTREF(__pyx_t_4);
9138 __pyx_t_9 = PyObject_Length(__pyx_v_sequence); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 74, __pyx_L1_error)
9139 __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_9); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 74, __pyx_L1_error)
9140 __Pyx_GOTREF(__pyx_t_1);
9141 __pyx_t_6 = PyNumber_Subtract(__pyx_t_4, __pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 74, __pyx_L1_error)
9142 __Pyx_GOTREF(__pyx_t_6);
9143 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
9144 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
9145 __pyx_t_1 = PyNumber_Multiply(__pyx_n_u_N, __pyx_t_6); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 74, __pyx_L1_error)
9146 __Pyx_GOTREF(__pyx_t_1);
9147 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
9148 __pyx_t_6 = PyNumber_InPlaceAdd(__pyx_v_sequence, __pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 74, __pyx_L1_error)
9149 __Pyx_GOTREF(__pyx_t_6);
9150 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
9151 __Pyx_DECREF_SET(__pyx_v_sequence, __pyx_t_6);
9152 __pyx_t_6 = 0;
9153 }
9154
9155 /* "pysam/libcvcf.pyx":75
9156 * sequence = fa.fetch(chrom, start, end).upper()
9157 * if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
9158 * return sequence # <<<<<<<<<<<<<<
9159 *
9160 * # Utility function. Parses a region string
9161 */
9162 __Pyx_XDECREF(__pyx_r);
9163 __Pyx_INCREF(__pyx_v_sequence);
9164 __pyx_r = __pyx_v_sequence;
9165 goto __pyx_L0;
9166
9167 /* "pysam/libcvcf.pyx":68
9168 *
9169 * # Utility function. Uses 0-based coordinates
9170 * def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<<
9171 * # obtain sequence from .fa file, without truncation
9172 * if end<=start: return ""
9173 */
9174
9175 /* function exit code */
9176 __pyx_L1_error:;
9177 __Pyx_XDECREF(__pyx_t_1);
9178 __Pyx_XDECREF(__pyx_t_4);
9179 __Pyx_XDECREF(__pyx_t_5);
9180 __Pyx_XDECREF(__pyx_t_6);
9181 __Pyx_XDECREF(__pyx_t_7);
9182 __Pyx_AddTraceback("pysam.libcvcf.get_sequence", __pyx_clineno, __pyx_lineno, __pyx_filename);
9183 __pyx_r = NULL;
9184 __pyx_L0:;
9185 __Pyx_XDECREF(__pyx_v_sequence);
9186 __Pyx_XGIVEREF(__pyx_r);
9187 __Pyx_RefNannyFinishContext();
9188 return __pyx_r;
9189 }
9190
9191 /* "pysam/libcvcf.pyx":78
9192 *
9193 * # Utility function. Parses a region string
9194 * def parse_regions( string ): # <<<<<<<<<<<<<<
9195 * result = []
9196 * for r in string.split(','):
9197 */
9198
9199 /* Python wrapper */
9200 static PyObject *__pyx_pw_5pysam_7libcvcf_3parse_regions(PyObject *__pyx_self,
9201 #if CYTHON_METH_FASTCALL
9202 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
9203 #else
9204 PyObject *__pyx_args, PyObject *__pyx_kwds
9205 #endif
9206 ); /*proto*/
9207 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_2parse_regions, "parse_regions(string)");
9208 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3parse_regions = {"parse_regions", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3parse_regions, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_2parse_regions};
9209 static PyObject *__pyx_pw_5pysam_7libcvcf_3parse_regions(PyObject *__pyx_self,
9210 #if CYTHON_METH_FASTCALL
9211 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
9212 #else
9213 PyObject *__pyx_args, PyObject *__pyx_kwds
9214 #endif
9215 ) {
9216 PyObject *__pyx_v_string = 0;
9217 #if !CYTHON_METH_FASTCALL
9218 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
9219 #endif
9220 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
9221 PyObject* values[1] = {0};
9222 int __pyx_lineno = 0;
9223 const char *__pyx_filename = NULL;
9224 int __pyx_clineno = 0;
9225 PyObject *__pyx_r = 0;
9226 __Pyx_RefNannyDeclarations
9227 __Pyx_RefNannySetupContext("parse_regions (wrapper)", 0);
9228 #if !CYTHON_METH_FASTCALL
9229 #if CYTHON_ASSUME_SAFE_MACROS
9230 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
9231 #else
9232 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
9233 #endif
9234 #endif
9235 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
9236 {
9237 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_string,0};
9238 if (__pyx_kwds) {
9239 Py_ssize_t kw_args;
9240 switch (__pyx_nargs) {
9241 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
9242 CYTHON_FALLTHROUGH;
9243 case 0: break;
9244 default: goto __pyx_L5_argtuple_error;
9245 }
9246 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
9247 switch (__pyx_nargs) {
9248 case 0:
9249 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_string)) != 0)) {
9250 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
9251 kw_args--;
9252 }
9253 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 78, __pyx_L3_error)
9254 else goto __pyx_L5_argtuple_error;
9255 }
9256 if (unlikely(kw_args > 0)) {
9257 const Py_ssize_t kwd_pos_args = __pyx_nargs;
9258 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "parse_regions") < 0)) __PYX_ERR(0, 78, __pyx_L3_error)
9259 }
9260 } else if (unlikely(__pyx_nargs != 1)) {
9261 goto __pyx_L5_argtuple_error;
9262 } else {
9263 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
9264 }
9265 __pyx_v_string = values[0];
9266 }
9267 goto __pyx_L6_skip;
9268 __pyx_L5_argtuple_error:;
9269 __Pyx_RaiseArgtupleInvalid("parse_regions", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 78, __pyx_L3_error)
9270 __pyx_L6_skip:;
9271 goto __pyx_L4_argument_unpacking_done;
9272 __pyx_L3_error:;
9273 {
9274 Py_ssize_t __pyx_temp;
9275 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
9276 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
9277 }
9278 }
9279 __Pyx_AddTraceback("pysam.libcvcf.parse_regions", __pyx_clineno, __pyx_lineno, __pyx_filename);
9280 __Pyx_RefNannyFinishContext();
9281 return NULL;
9282 __pyx_L4_argument_unpacking_done:;
9283 __pyx_r = __pyx_pf_5pysam_7libcvcf_2parse_regions(__pyx_self, __pyx_v_string);
9284
9285 /* function exit code */
9286 {
9287 Py_ssize_t __pyx_temp;
9288 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
9289 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
9290 }
9291 }
9292 __Pyx_RefNannyFinishContext();
9293 return __pyx_r;
9294 }
9295
9296 static PyObject *__pyx_pf_5pysam_7libcvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string) {
9297 PyObject *__pyx_v_result = NULL;
9298 PyObject *__pyx_v_r = NULL;
9299 PyObject *__pyx_v_elts = NULL;
9300 PyObject *__pyx_v_chrom = NULL;
9301 PyObject *__pyx_v_start = NULL;
9302 PyObject *__pyx_v_end = NULL;
9303 PyObject *__pyx_v_ielts = NULL;
9304 PyObject *__pyx_r = NULL;
9305 __Pyx_RefNannyDeclarations
9306 PyObject *__pyx_t_1 = NULL;
9307 PyObject *__pyx_t_2 = NULL;
9308 PyObject *__pyx_t_3 = NULL;
9309 unsigned int __pyx_t_4;
9310 Py_ssize_t __pyx_t_5;
9311 PyObject *(*__pyx_t_6)(PyObject *);
9312 PyObject *__pyx_t_7 = NULL;
9313 Py_ssize_t __pyx_t_8;
9314 int __pyx_t_9;
9315 PyObject *__pyx_t_10 = NULL;
9316 PyObject *__pyx_t_11 = NULL;
9317 PyObject *__pyx_t_12 = NULL;
9318 PyObject *__pyx_t_13 = NULL;
9319 PyObject *__pyx_t_14 = NULL;
9320 int __pyx_t_15;
9321 int __pyx_lineno = 0;
9322 const char *__pyx_filename = NULL;
9323 int __pyx_clineno = 0;
9324 __Pyx_RefNannySetupContext("parse_regions", 1);
9325
9326 /* "pysam/libcvcf.pyx":79
9327 * # Utility function. Parses a region string
9328 * def parse_regions( string ):
9329 * result = [] # <<<<<<<<<<<<<<
9330 * for r in string.split(','):
9331 * elts = r.split(':')
9332 */
9333 __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 79, __pyx_L1_error)
9334 __Pyx_GOTREF(__pyx_t_1);
9335 __pyx_v_result = ((PyObject*)__pyx_t_1);
9336 __pyx_t_1 = 0;
9337
9338 /* "pysam/libcvcf.pyx":80
9339 * def parse_regions( string ):
9340 * result = []
9341 * for r in string.split(','): # <<<<<<<<<<<<<<
9342 * elts = r.split(':')
9343 * chrom, start, end = elts[0], 0, 3000000000
9344 */
9345 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_string, __pyx_n_s_split); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 80, __pyx_L1_error)
9346 __Pyx_GOTREF(__pyx_t_2);
9347 __pyx_t_3 = NULL;
9348 __pyx_t_4 = 0;
9349 #if CYTHON_UNPACK_METHODS
9350 if (likely(PyMethod_Check(__pyx_t_2))) {
9351 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
9352 if (likely(__pyx_t_3)) {
9353 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
9354 __Pyx_INCREF(__pyx_t_3);
9355 __Pyx_INCREF(function);
9356 __Pyx_DECREF_SET(__pyx_t_2, function);
9357 __pyx_t_4 = 1;
9358 }
9359 }
9360 #endif
9361 {
9362 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_kp_u__2};
9363 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
9364 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
9365 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 80, __pyx_L1_error)
9366 __Pyx_GOTREF(__pyx_t_1);
9367 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
9368 }
9369 if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) {
9370 __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2);
9371 __pyx_t_5 = 0;
9372 __pyx_t_6 = NULL;
9373 } else {
9374 __pyx_t_5 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 80, __pyx_L1_error)
9375 __Pyx_GOTREF(__pyx_t_2);
9376 __pyx_t_6 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 80, __pyx_L1_error)
9377 }
9378 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
9379 for (;;) {
9380 if (likely(!__pyx_t_6)) {
9381 if (likely(PyList_CheckExact(__pyx_t_2))) {
9382 {
9383 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2);
9384 #if !CYTHON_ASSUME_SAFE_MACROS
9385 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 80, __pyx_L1_error)
9386 #endif
9387 if (__pyx_t_5 >= __pyx_temp) break;
9388 }
9389 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
9390 __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely((0 < 0))) __PYX_ERR(0, 80, __pyx_L1_error)
9391 #else
9392 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 80, __pyx_L1_error)
9393 __Pyx_GOTREF(__pyx_t_1);
9394 #endif
9395 } else {
9396 {
9397 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_2);
9398 #if !CYTHON_ASSUME_SAFE_MACROS
9399 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 80, __pyx_L1_error)
9400 #endif
9401 if (__pyx_t_5 >= __pyx_temp) break;
9402 }
9403 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
9404 __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely((0 < 0))) __PYX_ERR(0, 80, __pyx_L1_error)
9405 #else
9406 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 80, __pyx_L1_error)
9407 __Pyx_GOTREF(__pyx_t_1);
9408 #endif
9409 }
9410 } else {
9411 __pyx_t_1 = __pyx_t_6(__pyx_t_2);
9412 if (unlikely(!__pyx_t_1)) {
9413 PyObject* exc_type = PyErr_Occurred();
9414 if (exc_type) {
9415 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
9416 else __PYX_ERR(0, 80, __pyx_L1_error)
9417 }
9418 break;
9419 }
9420 __Pyx_GOTREF(__pyx_t_1);
9421 }
9422 __Pyx_XDECREF_SET(__pyx_v_r, __pyx_t_1);
9423 __pyx_t_1 = 0;
9424
9425 /* "pysam/libcvcf.pyx":81
9426 * result = []
9427 * for r in string.split(','):
9428 * elts = r.split(':') # <<<<<<<<<<<<<<
9429 * chrom, start, end = elts[0], 0, 3000000000
9430 * if len(elts)==1: pass
9431 */
9432 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_r, __pyx_n_s_split); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 81, __pyx_L1_error)
9433 __Pyx_GOTREF(__pyx_t_3);
9434 __pyx_t_7 = NULL;
9435 __pyx_t_4 = 0;
9436 #if CYTHON_UNPACK_METHODS
9437 if (likely(PyMethod_Check(__pyx_t_3))) {
9438 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_3);
9439 if (likely(__pyx_t_7)) {
9440 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
9441 __Pyx_INCREF(__pyx_t_7);
9442 __Pyx_INCREF(function);
9443 __Pyx_DECREF_SET(__pyx_t_3, function);
9444 __pyx_t_4 = 1;
9445 }
9446 }
9447 #endif
9448 {
9449 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_kp_u__3};
9450 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
9451 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
9452 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 81, __pyx_L1_error)
9453 __Pyx_GOTREF(__pyx_t_1);
9454 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
9455 }
9456 __Pyx_XDECREF_SET(__pyx_v_elts, __pyx_t_1);
9457 __pyx_t_1 = 0;
9458
9459 /* "pysam/libcvcf.pyx":82
9460 * for r in string.split(','):
9461 * elts = r.split(':')
9462 * chrom, start, end = elts[0], 0, 3000000000 # <<<<<<<<<<<<<<
9463 * if len(elts)==1: pass
9464 * elif len(elts)==2:
9465 */
9466 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_elts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 82, __pyx_L1_error)
9467 __Pyx_GOTREF(__pyx_t_1);
9468 __pyx_t_3 = __pyx_int_0;
9469 __Pyx_INCREF(__pyx_t_3);
9470 __pyx_t_7 = __pyx_int_3000000000;
9471 __Pyx_INCREF(__pyx_t_7);
9472 __Pyx_XDECREF_SET(__pyx_v_chrom, __pyx_t_1);
9473 __pyx_t_1 = 0;
9474 __Pyx_XDECREF_SET(__pyx_v_start, __pyx_t_3);
9475 __pyx_t_3 = 0;
9476 __Pyx_XDECREF_SET(__pyx_v_end, __pyx_t_7);
9477 __pyx_t_7 = 0;
9478
9479 /* "pysam/libcvcf.pyx":83
9480 * elts = r.split(':')
9481 * chrom, start, end = elts[0], 0, 3000000000
9482 * if len(elts)==1: pass # <<<<<<<<<<<<<<
9483 * elif len(elts)==2:
9484 * if len(elts[1])>0:
9485 */
9486 __pyx_t_8 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_8 == ((Py_ssize_t)-1))) __PYX_ERR(0, 83, __pyx_L1_error)
9487 __pyx_t_9 = (__pyx_t_8 == 1);
9488 if (__pyx_t_9) {
9489 goto __pyx_L5;
9490 }
9491
9492 /* "pysam/libcvcf.pyx":84
9493 * chrom, start, end = elts[0], 0, 3000000000
9494 * if len(elts)==1: pass
9495 * elif len(elts)==2: # <<<<<<<<<<<<<<
9496 * if len(elts[1])>0:
9497 * ielts = elts[1].split('-')
9498 */
9499 __pyx_t_8 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_8 == ((Py_ssize_t)-1))) __PYX_ERR(0, 84, __pyx_L1_error)
9500 __pyx_t_9 = (__pyx_t_8 == 2);
9501 if (likely(__pyx_t_9)) {
9502
9503 /* "pysam/libcvcf.pyx":85
9504 * if len(elts)==1: pass
9505 * elif len(elts)==2:
9506 * if len(elts[1])>0: # <<<<<<<<<<<<<<
9507 * ielts = elts[1].split('-')
9508 * if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
9509 */
9510 __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_elts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 85, __pyx_L1_error)
9511 __Pyx_GOTREF(__pyx_t_7);
9512 __pyx_t_8 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_8 == ((Py_ssize_t)-1))) __PYX_ERR(0, 85, __pyx_L1_error)
9513 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
9514 __pyx_t_9 = (__pyx_t_8 > 0);
9515 if (__pyx_t_9) {
9516
9517 /* "pysam/libcvcf.pyx":86
9518 * elif len(elts)==2:
9519 * if len(elts[1])>0:
9520 * ielts = elts[1].split('-') # <<<<<<<<<<<<<<
9521 * if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
9522 * try: start, end = int(ielts[0])-1, int(ielts[1])
9523 */
9524 __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_elts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 86, __pyx_L1_error)
9525 __Pyx_GOTREF(__pyx_t_3);
9526 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_split); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 86, __pyx_L1_error)
9527 __Pyx_GOTREF(__pyx_t_1);
9528 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
9529 __pyx_t_3 = NULL;
9530 __pyx_t_4 = 0;
9531 #if CYTHON_UNPACK_METHODS
9532 if (likely(PyMethod_Check(__pyx_t_1))) {
9533 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_1);
9534 if (likely(__pyx_t_3)) {
9535 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
9536 __Pyx_INCREF(__pyx_t_3);
9537 __Pyx_INCREF(function);
9538 __Pyx_DECREF_SET(__pyx_t_1, function);
9539 __pyx_t_4 = 1;
9540 }
9541 }
9542 #endif
9543 {
9544 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_kp_u__4};
9545 __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
9546 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
9547 if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 86, __pyx_L1_error)
9548 __Pyx_GOTREF(__pyx_t_7);
9549 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
9550 }
9551 __Pyx_XDECREF_SET(__pyx_v_ielts, __pyx_t_7);
9552 __pyx_t_7 = 0;
9553
9554 /* "pysam/libcvcf.pyx":87
9555 * if len(elts[1])>0:
9556 * ielts = elts[1].split('-')
9557 * if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r) # <<<<<<<<<<<<<<
9558 * try: start, end = int(ielts[0])-1, int(ielts[1])
9559 * except: raise ValueError("Don't understand region string '%s'" % r)
9560 */
9561 __pyx_t_8 = PyObject_Length(__pyx_v_ielts); if (unlikely(__pyx_t_8 == ((Py_ssize_t)-1))) __PYX_ERR(0, 87, __pyx_L1_error)
9562 __pyx_t_9 = (__pyx_t_8 != 2);
9563 if (__pyx_t_9) {
9564 __pyx_t_7 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_Don_t_understand_region_string_s, __pyx_v_r); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 87, __pyx_L1_error)
9565 __Pyx_GOTREF(__pyx_t_7);
9566 __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 87, __pyx_L1_error)
9567 __Pyx_GOTREF(__pyx_t_1);
9568 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
9569 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
9570 }
9571
9572 /* "pysam/libcvcf.pyx":88
9573 * ielts = elts[1].split('-')
9574 * if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
9575 * try: start, end = int(ielts[0])-1, int(ielts[1]) # <<<<<<<<<<<<<<
9576 * except: raise ValueError("Don't understand region string '%s'" % r)
9577 * else:
9578 */
9579 {
9580 __Pyx_PyThreadState_declare
9581 __Pyx_PyThreadState_assign
9582 __Pyx_ExceptionSave(&__pyx_t_10, &__pyx_t_11, &__pyx_t_12);
9583 __Pyx_XGOTREF(__pyx_t_10);
9584 __Pyx_XGOTREF(__pyx_t_11);
9585 __Pyx_XGOTREF(__pyx_t_12);
9586 /*try:*/ {
9587 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_ielts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 88, __pyx_L8_error)
9588 __Pyx_GOTREF(__pyx_t_1);
9589 __pyx_t_7 = __Pyx_PyNumber_Int(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 88, __pyx_L8_error)
9590 __Pyx_GOTREF(__pyx_t_7);
9591 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
9592 __pyx_t_1 = __Pyx_PyInt_SubtractObjC(__pyx_t_7, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 88, __pyx_L8_error)
9593 __Pyx_GOTREF(__pyx_t_1);
9594 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
9595 __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_ielts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 88, __pyx_L8_error)
9596 __Pyx_GOTREF(__pyx_t_7);
9597 __pyx_t_3 = __Pyx_PyNumber_Int(__pyx_t_7); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 88, __pyx_L8_error)
9598 __Pyx_GOTREF(__pyx_t_3);
9599 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
9600 __Pyx_DECREF_SET(__pyx_v_start, __pyx_t_1);
9601 __pyx_t_1 = 0;
9602 __Pyx_DECREF_SET(__pyx_v_end, __pyx_t_3);
9603 __pyx_t_3 = 0;
9604 }
9605 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
9606 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
9607 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
9608 goto __pyx_L15_try_end;
9609 __pyx_L8_error:;
9610 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
9611 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
9612 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
9613
9614 /* "pysam/libcvcf.pyx":89
9615 * if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
9616 * try: start, end = int(ielts[0])-1, int(ielts[1])
9617 * except: raise ValueError("Don't understand region string '%s'" % r) # <<<<<<<<<<<<<<
9618 * else:
9619 * raise ValueError("Don't understand region string '%s'" % r)
9620 */
9621 /*except:*/ {
9622 __Pyx_AddTraceback("pysam.libcvcf.parse_regions", __pyx_clineno, __pyx_lineno, __pyx_filename);
9623 if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_1, &__pyx_t_7) < 0) __PYX_ERR(0, 89, __pyx_L10_except_error)
9624 __Pyx_XGOTREF(__pyx_t_3);
9625 __Pyx_XGOTREF(__pyx_t_1);
9626 __Pyx_XGOTREF(__pyx_t_7);
9627 __pyx_t_13 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_Don_t_understand_region_string_s, __pyx_v_r); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 89, __pyx_L10_except_error)
9628 __Pyx_GOTREF(__pyx_t_13);
9629 __pyx_t_14 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_13); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 89, __pyx_L10_except_error)
9630 __Pyx_GOTREF(__pyx_t_14);
9631 __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
9632 __Pyx_Raise(__pyx_t_14, 0, 0, 0);
9633 __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
9634 __PYX_ERR(0, 89, __pyx_L10_except_error)
9635 }
9636
9637 /* "pysam/libcvcf.pyx":88
9638 * ielts = elts[1].split('-')
9639 * if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
9640 * try: start, end = int(ielts[0])-1, int(ielts[1]) # <<<<<<<<<<<<<<
9641 * except: raise ValueError("Don't understand region string '%s'" % r)
9642 * else:
9643 */
9644 __pyx_L10_except_error:;
9645 __Pyx_XGIVEREF(__pyx_t_10);
9646 __Pyx_XGIVEREF(__pyx_t_11);
9647 __Pyx_XGIVEREF(__pyx_t_12);
9648 __Pyx_ExceptionReset(__pyx_t_10, __pyx_t_11, __pyx_t_12);
9649 goto __pyx_L1_error;
9650 __pyx_L15_try_end:;
9651 }
9652
9653 /* "pysam/libcvcf.pyx":85
9654 * if len(elts)==1: pass
9655 * elif len(elts)==2:
9656 * if len(elts[1])>0: # <<<<<<<<<<<<<<
9657 * ielts = elts[1].split('-')
9658 * if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
9659 */
9660 }
9661
9662 /* "pysam/libcvcf.pyx":84
9663 * chrom, start, end = elts[0], 0, 3000000000
9664 * if len(elts)==1: pass
9665 * elif len(elts)==2: # <<<<<<<<<<<<<<
9666 * if len(elts[1])>0:
9667 * ielts = elts[1].split('-')
9668 */
9669 goto __pyx_L5;
9670 }
9671
9672 /* "pysam/libcvcf.pyx":91
9673 * except: raise ValueError("Don't understand region string '%s'" % r)
9674 * else:
9675 * raise ValueError("Don't understand region string '%s'" % r) # <<<<<<<<<<<<<<
9676 * result.append( (chrom,start,end) )
9677 * return result
9678 */
9679 /*else*/ {
9680 __pyx_t_7 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_Don_t_understand_region_string_s, __pyx_v_r); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 91, __pyx_L1_error)
9681 __Pyx_GOTREF(__pyx_t_7);
9682 __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 91, __pyx_L1_error)
9683 __Pyx_GOTREF(__pyx_t_1);
9684 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
9685 __Pyx_Raise(__pyx_t_1, 0, 0, 0);
9686 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
9687 __PYX_ERR(0, 91, __pyx_L1_error)
9688 }
9689 __pyx_L5:;
9690
9691 /* "pysam/libcvcf.pyx":92
9692 * else:
9693 * raise ValueError("Don't understand region string '%s'" % r)
9694 * result.append( (chrom,start,end) ) # <<<<<<<<<<<<<<
9695 * return result
9696 *
9697 */
9698 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 92, __pyx_L1_error)
9699 __Pyx_GOTREF(__pyx_t_1);
9700 __Pyx_INCREF(__pyx_v_chrom);
9701 __Pyx_GIVEREF(__pyx_v_chrom);
9702 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_chrom)) __PYX_ERR(0, 92, __pyx_L1_error);
9703 __Pyx_INCREF(__pyx_v_start);
9704 __Pyx_GIVEREF(__pyx_v_start);
9705 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_start)) __PYX_ERR(0, 92, __pyx_L1_error);
9706 __Pyx_INCREF(__pyx_v_end);
9707 __Pyx_GIVEREF(__pyx_v_end);
9708 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_end)) __PYX_ERR(0, 92, __pyx_L1_error);
9709 __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_result, __pyx_t_1); if (unlikely(__pyx_t_15 == ((int)-1))) __PYX_ERR(0, 92, __pyx_L1_error)
9710 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
9711
9712 /* "pysam/libcvcf.pyx":80
9713 * def parse_regions( string ):
9714 * result = []
9715 * for r in string.split(','): # <<<<<<<<<<<<<<
9716 * elts = r.split(':')
9717 * chrom, start, end = elts[0], 0, 3000000000
9718 */
9719 }
9720 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
9721
9722 /* "pysam/libcvcf.pyx":93
9723 * raise ValueError("Don't understand region string '%s'" % r)
9724 * result.append( (chrom,start,end) )
9725 * return result # <<<<<<<<<<<<<<
9726 *
9727 *
9728 */
9729 __Pyx_XDECREF(__pyx_r);
9730 __Pyx_INCREF(__pyx_v_result);
9731 __pyx_r = __pyx_v_result;
9732 goto __pyx_L0;
9733
9734 /* "pysam/libcvcf.pyx":78
9735 *
9736 * # Utility function. Parses a region string
9737 * def parse_regions( string ): # <<<<<<<<<<<<<<
9738 * result = []
9739 * for r in string.split(','):
9740 */
9741
9742 /* function exit code */
9743 __pyx_L1_error:;
9744 __Pyx_XDECREF(__pyx_t_1);
9745 __Pyx_XDECREF(__pyx_t_2);
9746 __Pyx_XDECREF(__pyx_t_3);
9747 __Pyx_XDECREF(__pyx_t_7);
9748 __Pyx_XDECREF(__pyx_t_13);
9749 __Pyx_XDECREF(__pyx_t_14);
9750 __Pyx_AddTraceback("pysam.libcvcf.parse_regions", __pyx_clineno, __pyx_lineno, __pyx_filename);
9751 __pyx_r = NULL;
9752 __pyx_L0:;
9753 __Pyx_XDECREF(__pyx_v_result);
9754 __Pyx_XDECREF(__pyx_v_r);
9755 __Pyx_XDECREF(__pyx_v_elts);
9756 __Pyx_XDECREF(__pyx_v_chrom);
9757 __Pyx_XDECREF(__pyx_v_start);
9758 __Pyx_XDECREF(__pyx_v_end);
9759 __Pyx_XDECREF(__pyx_v_ielts);
9760 __Pyx_XGIVEREF(__pyx_r);
9761 __Pyx_RefNannyFinishContext();
9762 return __pyx_r;
9763 }
9764
9765 /* "pysam/libcvcf.pyx":114
9766 * cdef uint32_t pos
9767 *
9768 * def __init__(self, vcf): # <<<<<<<<<<<<<<
9769 * self.vcf = vcf
9770 * self.encoding = vcf.encoding
9771 */
9772
9773 /* Python wrapper */
9774 static int __pyx_pw_5pysam_7libcvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
9775 static int __pyx_pw_5pysam_7libcvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
9776 PyObject *__pyx_v_vcf = 0;
9777 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
9778 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
9779 PyObject* values[1] = {0};
9780 int __pyx_lineno = 0;
9781 const char *__pyx_filename = NULL;
9782 int __pyx_clineno = 0;
9783 int __pyx_r;
9784 __Pyx_RefNannyDeclarations
9785 __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
9786 #if CYTHON_ASSUME_SAFE_MACROS
9787 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
9788 #else
9789 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1;
9790 #endif
9791 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
9792 {
9793 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_vcf,0};
9794 if (__pyx_kwds) {
9795 Py_ssize_t kw_args;
9796 switch (__pyx_nargs) {
9797 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
9798 CYTHON_FALLTHROUGH;
9799 case 0: break;
9800 default: goto __pyx_L5_argtuple_error;
9801 }
9802 kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds);
9803 switch (__pyx_nargs) {
9804 case 0:
9805 if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_vcf)) != 0)) {
9806 (void)__Pyx_Arg_NewRef_VARARGS(values[0]);
9807 kw_args--;
9808 }
9809 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 114, __pyx_L3_error)
9810 else goto __pyx_L5_argtuple_error;
9811 }
9812 if (unlikely(kw_args > 0)) {
9813 const Py_ssize_t kwd_pos_args = __pyx_nargs;
9814 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 114, __pyx_L3_error)
9815 }
9816 } else if (unlikely(__pyx_nargs != 1)) {
9817 goto __pyx_L5_argtuple_error;
9818 } else {
9819 values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
9820 }
9821 __pyx_v_vcf = values[0];
9822 }
9823 goto __pyx_L6_skip;
9824 __pyx_L5_argtuple_error:;
9825 __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 114, __pyx_L3_error)
9826 __pyx_L6_skip:;
9827 goto __pyx_L4_argument_unpacking_done;
9828 __pyx_L3_error:;
9829 {
9830 Py_ssize_t __pyx_temp;
9831 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
9832 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
9833 }
9834 }
9835 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
9836 __Pyx_RefNannyFinishContext();
9837 return -1;
9838 __pyx_L4_argument_unpacking_done:;
9839 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord___init__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self), __pyx_v_vcf);
9840
9841 /* function exit code */
9842 {
9843 Py_ssize_t __pyx_temp;
9844 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
9845 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
9846 }
9847 }
9848 __Pyx_RefNannyFinishContext();
9849 return __pyx_r;
9850 }
9851
9852 static int __pyx_pf_5pysam_7libcvcf_9VCFRecord___init__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf) {
9853 int __pyx_r;
9854 __Pyx_RefNannyDeclarations
9855 PyObject *__pyx_t_1 = NULL;
9856 int __pyx_lineno = 0;
9857 const char *__pyx_filename = NULL;
9858 int __pyx_clineno = 0;
9859 __Pyx_RefNannySetupContext("__init__", 1);
9860
9861 /* "pysam/libcvcf.pyx":115
9862 *
9863 * def __init__(self, vcf):
9864 * self.vcf = vcf # <<<<<<<<<<<<<<
9865 * self.encoding = vcf.encoding
9866 *
9867 */
9868 __Pyx_INCREF(__pyx_v_vcf);
9869 __Pyx_GIVEREF(__pyx_v_vcf);
9870 __Pyx_GOTREF(__pyx_v_self->vcf);
9871 __Pyx_DECREF(__pyx_v_self->vcf);
9872 __pyx_v_self->vcf = __pyx_v_vcf;
9873
9874 /* "pysam/libcvcf.pyx":116
9875 * def __init__(self, vcf):
9876 * self.vcf = vcf
9877 * self.encoding = vcf.encoding # <<<<<<<<<<<<<<
9878 *
9879 * # if len(data) != len(self.vcf._samples):
9880 */
9881 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_vcf, __pyx_n_s_encoding); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 116, __pyx_L1_error)
9882 __Pyx_GOTREF(__pyx_t_1);
9883 __Pyx_GIVEREF(__pyx_t_1);
9884 __Pyx_GOTREF(__pyx_v_self->__pyx_base.encoding);
9885 __Pyx_DECREF(__pyx_v_self->__pyx_base.encoding);
9886 __pyx_v_self->__pyx_base.encoding = __pyx_t_1;
9887 __pyx_t_1 = 0;
9888
9889 /* "pysam/libcvcf.pyx":114
9890 * cdef uint32_t pos
9891 *
9892 * def __init__(self, vcf): # <<<<<<<<<<<<<<
9893 * self.vcf = vcf
9894 * self.encoding = vcf.encoding
9895 */
9896
9897 /* function exit code */
9898 __pyx_r = 0;
9899 goto __pyx_L0;
9900 __pyx_L1_error:;
9901 __Pyx_XDECREF(__pyx_t_1);
9902 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
9903 __pyx_r = -1;
9904 __pyx_L0:;
9905 __Pyx_RefNannyFinishContext();
9906 return __pyx_r;
9907 }
9908
9909 /* "pysam/libcvcf.pyx":127
9910 * # len(data)))
9911 *
9912 * def __cinit__(self, vcf): # <<<<<<<<<<<<<<
9913 * # start indexed access at genotypes
9914 * self.offset = 9
9915 */
9916
9917 /* Python wrapper */
9918 static int __pyx_pw_5pysam_7libcvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
9919 static int __pyx_pw_5pysam_7libcvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
9920 PyObject *__pyx_v_vcf = 0;
9921 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
9922 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
9923 PyObject* values[1] = {0};
9924 int __pyx_lineno = 0;
9925 const char *__pyx_filename = NULL;
9926 int __pyx_clineno = 0;
9927 int __pyx_r;
9928 __Pyx_RefNannyDeclarations
9929 __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
9930 #if CYTHON_ASSUME_SAFE_MACROS
9931 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
9932 #else
9933 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1;
9934 #endif
9935 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
9936 {
9937 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_vcf,0};
9938 if (__pyx_kwds) {
9939 Py_ssize_t kw_args;
9940 switch (__pyx_nargs) {
9941 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
9942 CYTHON_FALLTHROUGH;
9943 case 0: break;
9944 default: goto __pyx_L5_argtuple_error;
9945 }
9946 kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds);
9947 switch (__pyx_nargs) {
9948 case 0:
9949 if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_vcf)) != 0)) {
9950 (void)__Pyx_Arg_NewRef_VARARGS(values[0]);
9951 kw_args--;
9952 }
9953 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 127, __pyx_L3_error)
9954 else goto __pyx_L5_argtuple_error;
9955 }
9956 if (unlikely(kw_args > 0)) {
9957 const Py_ssize_t kwd_pos_args = __pyx_nargs;
9958 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__cinit__") < 0)) __PYX_ERR(0, 127, __pyx_L3_error)
9959 }
9960 } else if (unlikely(__pyx_nargs != 1)) {
9961 goto __pyx_L5_argtuple_error;
9962 } else {
9963 values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
9964 }
9965 __pyx_v_vcf = values[0];
9966 }
9967 goto __pyx_L6_skip;
9968 __pyx_L5_argtuple_error:;
9969 __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 127, __pyx_L3_error)
9970 __pyx_L6_skip:;
9971 goto __pyx_L4_argument_unpacking_done;
9972 __pyx_L3_error:;
9973 {
9974 Py_ssize_t __pyx_temp;
9975 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
9976 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
9977 }
9978 }
9979 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
9980 __Pyx_RefNannyFinishContext();
9981 return -1;
9982 __pyx_L4_argument_unpacking_done:;
9983 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_2__cinit__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self), __pyx_v_vcf);
9984
9985 /* function exit code */
9986 {
9987 Py_ssize_t __pyx_temp;
9988 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
9989 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
9990 }
9991 }
9992 __Pyx_RefNannyFinishContext();
9993 return __pyx_r;
9994 }
9995
9996 static int __pyx_pf_5pysam_7libcvcf_9VCFRecord_2__cinit__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf) {
9997 int __pyx_r;
9998 __Pyx_RefNannyDeclarations
9999 PyObject *__pyx_t_1 = NULL;
10000 int __pyx_lineno = 0;
10001 const char *__pyx_filename = NULL;
10002 int __pyx_clineno = 0;
10003 __Pyx_RefNannySetupContext("__cinit__", 1);
10004
10005 /* "pysam/libcvcf.pyx":129
10006 * def __cinit__(self, vcf):
10007 * # start indexed access at genotypes
10008 * self.offset = 9 # <<<<<<<<<<<<<<
10009 *
10010 * self.vcf = vcf
10011 */
10012 __pyx_v_self->__pyx_base.offset = 9;
10013
10014 /* "pysam/libcvcf.pyx":131
10015 * self.offset = 9
10016 *
10017 * self.vcf = vcf # <<<<<<<<<<<<<<
10018 * self.encoding = vcf.encoding
10019 *
10020 */
10021 __Pyx_INCREF(__pyx_v_vcf);
10022 __Pyx_GIVEREF(__pyx_v_vcf);
10023 __Pyx_GOTREF(__pyx_v_self->vcf);
10024 __Pyx_DECREF(__pyx_v_self->vcf);
10025 __pyx_v_self->vcf = __pyx_v_vcf;
10026
10027 /* "pysam/libcvcf.pyx":132
10028 *
10029 * self.vcf = vcf
10030 * self.encoding = vcf.encoding # <<<<<<<<<<<<<<
10031 *
10032 * def error(self, line, error, opt=None):
10033 */
10034 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_vcf, __pyx_n_s_encoding); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 132, __pyx_L1_error)
10035 __Pyx_GOTREF(__pyx_t_1);
10036 __Pyx_GIVEREF(__pyx_t_1);
10037 __Pyx_GOTREF(__pyx_v_self->__pyx_base.encoding);
10038 __Pyx_DECREF(__pyx_v_self->__pyx_base.encoding);
10039 __pyx_v_self->__pyx_base.encoding = __pyx_t_1;
10040 __pyx_t_1 = 0;
10041
10042 /* "pysam/libcvcf.pyx":127
10043 * # len(data)))
10044 *
10045 * def __cinit__(self, vcf): # <<<<<<<<<<<<<<
10046 * # start indexed access at genotypes
10047 * self.offset = 9
10048 */
10049
10050 /* function exit code */
10051 __pyx_r = 0;
10052 goto __pyx_L0;
10053 __pyx_L1_error:;
10054 __Pyx_XDECREF(__pyx_t_1);
10055 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
10056 __pyx_r = -1;
10057 __pyx_L0:;
10058 __Pyx_RefNannyFinishContext();
10059 return __pyx_r;
10060 }
10061
10062 /* "pysam/libcvcf.pyx":134
10063 * self.encoding = vcf.encoding
10064 *
10065 * def error(self, line, error, opt=None): # <<<<<<<<<<<<<<
10066 * '''raise error.'''
10067 * # pass to vcf file for error handling
10068 */
10069
10070 /* Python wrapper */
10071 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_5error(PyObject *__pyx_v_self,
10072 #if CYTHON_METH_FASTCALL
10073 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
10074 #else
10075 PyObject *__pyx_args, PyObject *__pyx_kwds
10076 #endif
10077 ); /*proto*/
10078 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_9VCFRecord_4error, "VCFRecord.error(self, line, error, opt=None)\nraise error.");
10079 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_9VCFRecord_5error = {"error", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_9VCFRecord_5error, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_9VCFRecord_4error};
10080 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_5error(PyObject *__pyx_v_self,
10081 #if CYTHON_METH_FASTCALL
10082 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
10083 #else
10084 PyObject *__pyx_args, PyObject *__pyx_kwds
10085 #endif
10086 ) {
10087 PyObject *__pyx_v_line = 0;
10088 PyObject *__pyx_v_error = 0;
10089 PyObject *__pyx_v_opt = 0;
10090 #if !CYTHON_METH_FASTCALL
10091 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
10092 #endif
10093 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
10094 PyObject* values[3] = {0,0,0};
10095 int __pyx_lineno = 0;
10096 const char *__pyx_filename = NULL;
10097 int __pyx_clineno = 0;
10098 PyObject *__pyx_r = 0;
10099 __Pyx_RefNannyDeclarations
10100 __Pyx_RefNannySetupContext("error (wrapper)", 0);
10101 #if !CYTHON_METH_FASTCALL
10102 #if CYTHON_ASSUME_SAFE_MACROS
10103 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
10104 #else
10105 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
10106 #endif
10107 #endif
10108 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
10109 {
10110 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_line,&__pyx_n_s_error,&__pyx_n_s_opt,0};
10111 values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
10112 if (__pyx_kwds) {
10113 Py_ssize_t kw_args;
10114 switch (__pyx_nargs) {
10115 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
10116 CYTHON_FALLTHROUGH;
10117 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
10118 CYTHON_FALLTHROUGH;
10119 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
10120 CYTHON_FALLTHROUGH;
10121 case 0: break;
10122 default: goto __pyx_L5_argtuple_error;
10123 }
10124 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
10125 switch (__pyx_nargs) {
10126 case 0:
10127 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_line)) != 0)) {
10128 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
10129 kw_args--;
10130 }
10131 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 134, __pyx_L3_error)
10132 else goto __pyx_L5_argtuple_error;
10133 CYTHON_FALLTHROUGH;
10134 case 1:
10135 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_error)) != 0)) {
10136 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
10137 kw_args--;
10138 }
10139 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 134, __pyx_L3_error)
10140 else {
10141 __Pyx_RaiseArgtupleInvalid("error", 0, 2, 3, 1); __PYX_ERR(0, 134, __pyx_L3_error)
10142 }
10143 CYTHON_FALLTHROUGH;
10144 case 2:
10145 if (kw_args > 0) {
10146 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_opt);
10147 if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
10148 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 134, __pyx_L3_error)
10149 }
10150 }
10151 if (unlikely(kw_args > 0)) {
10152 const Py_ssize_t kwd_pos_args = __pyx_nargs;
10153 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "error") < 0)) __PYX_ERR(0, 134, __pyx_L3_error)
10154 }
10155 } else {
10156 switch (__pyx_nargs) {
10157 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
10158 CYTHON_FALLTHROUGH;
10159 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
10160 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
10161 break;
10162 default: goto __pyx_L5_argtuple_error;
10163 }
10164 }
10165 __pyx_v_line = values[0];
10166 __pyx_v_error = values[1];
10167 __pyx_v_opt = values[2];
10168 }
10169 goto __pyx_L6_skip;
10170 __pyx_L5_argtuple_error:;
10171 __Pyx_RaiseArgtupleInvalid("error", 0, 2, 3, __pyx_nargs); __PYX_ERR(0, 134, __pyx_L3_error)
10172 __pyx_L6_skip:;
10173 goto __pyx_L4_argument_unpacking_done;
10174 __pyx_L3_error:;
10175 {
10176 Py_ssize_t __pyx_temp;
10177 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
10178 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
10179 }
10180 }
10181 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.error", __pyx_clineno, __pyx_lineno, __pyx_filename);
10182 __Pyx_RefNannyFinishContext();
10183 return NULL;
10184 __pyx_L4_argument_unpacking_done:;
10185 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_4error(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self), __pyx_v_line, __pyx_v_error, __pyx_v_opt);
10186
10187 /* function exit code */
10188 {
10189 Py_ssize_t __pyx_temp;
10190 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
10191 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
10192 }
10193 }
10194 __Pyx_RefNannyFinishContext();
10195 return __pyx_r;
10196 }
10197
10198 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_4error(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt) {
10199 PyObject *__pyx_r = NULL;
10200 __Pyx_RefNannyDeclarations
10201 PyObject *__pyx_t_1 = NULL;
10202 PyObject *__pyx_t_2 = NULL;
10203 PyObject *__pyx_t_3 = NULL;
10204 unsigned int __pyx_t_4;
10205 int __pyx_lineno = 0;
10206 const char *__pyx_filename = NULL;
10207 int __pyx_clineno = 0;
10208 __Pyx_RefNannySetupContext("error", 1);
10209
10210 /* "pysam/libcvcf.pyx":137
10211 * '''raise error.'''
10212 * # pass to vcf file for error handling
10213 * return self.vcf.error(line, error, opt) # <<<<<<<<<<<<<<
10214 *
10215 * cdef update(self, char * buffer, size_t nbytes):
10216 */
10217 __Pyx_XDECREF(__pyx_r);
10218 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_error); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 137, __pyx_L1_error)
10219 __Pyx_GOTREF(__pyx_t_2);
10220 __pyx_t_3 = NULL;
10221 __pyx_t_4 = 0;
10222 #if CYTHON_UNPACK_METHODS
10223 if (likely(PyMethod_Check(__pyx_t_2))) {
10224 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
10225 if (likely(__pyx_t_3)) {
10226 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
10227 __Pyx_INCREF(__pyx_t_3);
10228 __Pyx_INCREF(function);
10229 __Pyx_DECREF_SET(__pyx_t_2, function);
10230 __pyx_t_4 = 1;
10231 }
10232 }
10233 #endif
10234 {
10235 PyObject *__pyx_callargs[4] = {__pyx_t_3, __pyx_v_line, __pyx_v_error, __pyx_v_opt};
10236 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
10237 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
10238 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 137, __pyx_L1_error)
10239 __Pyx_GOTREF(__pyx_t_1);
10240 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
10241 }
10242 __pyx_r = __pyx_t_1;
10243 __pyx_t_1 = 0;
10244 goto __pyx_L0;
10245
10246 /* "pysam/libcvcf.pyx":134
10247 * self.encoding = vcf.encoding
10248 *
10249 * def error(self, line, error, opt=None): # <<<<<<<<<<<<<<
10250 * '''raise error.'''
10251 * # pass to vcf file for error handling
10252 */
10253
10254 /* function exit code */
10255 __pyx_L1_error:;
10256 __Pyx_XDECREF(__pyx_t_1);
10257 __Pyx_XDECREF(__pyx_t_2);
10258 __Pyx_XDECREF(__pyx_t_3);
10259 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.error", __pyx_clineno, __pyx_lineno, __pyx_filename);
10260 __pyx_r = NULL;
10261 __pyx_L0:;
10262 __Pyx_XGIVEREF(__pyx_r);
10263 __Pyx_RefNannyFinishContext();
10264 return __pyx_r;
10265 }
10266
10267 /* "pysam/libcvcf.pyx":139
10268 * return self.vcf.error(line, error, opt)
10269 *
10270 * cdef update(self, char * buffer, size_t nbytes): # <<<<<<<<<<<<<<
10271 * '''update internal data.
10272 *
10273 */
10274
10275 static PyObject *__pyx_f_5pysam_7libcvcf_9VCFRecord_update(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
10276 PyObject *__pyx_r = NULL;
10277 __Pyx_RefNannyDeclarations
10278 PyObject *__pyx_t_1 = NULL;
10279 int __pyx_lineno = 0;
10280 const char *__pyx_filename = NULL;
10281 int __pyx_clineno = 0;
10282 __Pyx_RefNannySetupContext("update", 1);
10283
10284 /* "pysam/libcvcf.pyx":144
10285 * nbytes does not include the terminal '\0'.
10286 * '''
10287 * libctabixproxies.TupleProxy.update(self, buffer, nbytes) # <<<<<<<<<<<<<<
10288 *
10289 * self.contig = self.fields[0]
10290 */
10291 __pyx_t_1 = __pyx_vtabptr_5pysam_16libctabixproxies_TupleProxy->update(((struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *)__pyx_v_self), __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 144, __pyx_L1_error)
10292 __Pyx_GOTREF(__pyx_t_1);
10293 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
10294
10295 /* "pysam/libcvcf.pyx":146
10296 * libctabixproxies.TupleProxy.update(self, buffer, nbytes)
10297 *
10298 * self.contig = self.fields[0] # <<<<<<<<<<<<<<
10299 * # vcf counts from 1 - correct here
10300 * self.pos = atoi(self.fields[1]) - 1
10301 */
10302 __pyx_v_self->contig = (__pyx_v_self->__pyx_base.fields[0]);
10303
10304 /* "pysam/libcvcf.pyx":148
10305 * self.contig = self.fields[0]
10306 * # vcf counts from 1 - correct here
10307 * self.pos = atoi(self.fields[1]) - 1 # <<<<<<<<<<<<<<
10308 *
10309 * def __len__(self):
10310 */
10311 __pyx_v_self->pos = (atoi((__pyx_v_self->__pyx_base.fields[1])) - 1);
10312
10313 /* "pysam/libcvcf.pyx":139
10314 * return self.vcf.error(line, error, opt)
10315 *
10316 * cdef update(self, char * buffer, size_t nbytes): # <<<<<<<<<<<<<<
10317 * '''update internal data.
10318 *
10319 */
10320
10321 /* function exit code */
10322 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
10323 goto __pyx_L0;
10324 __pyx_L1_error:;
10325 __Pyx_XDECREF(__pyx_t_1);
10326 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.update", __pyx_clineno, __pyx_lineno, __pyx_filename);
10327 __pyx_r = 0;
10328 __pyx_L0:;
10329 __Pyx_XGIVEREF(__pyx_r);
10330 __Pyx_RefNannyFinishContext();
10331 return __pyx_r;
10332 }
10333
10334 /* "pysam/libcvcf.pyx":150
10335 * self.pos = atoi(self.fields[1]) - 1
10336 *
10337 * def __len__(self): # <<<<<<<<<<<<<<
10338 * return max(0, self.nfields - 9)
10339 *
10340 */
10341
10342 /* Python wrapper */
10343 static Py_ssize_t __pyx_pw_5pysam_7libcvcf_9VCFRecord_7__len__(PyObject *__pyx_v_self); /*proto*/
10344 static Py_ssize_t __pyx_pw_5pysam_7libcvcf_9VCFRecord_7__len__(PyObject *__pyx_v_self) {
10345 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
10346 Py_ssize_t __pyx_r;
10347 __Pyx_RefNannyDeclarations
10348 __Pyx_RefNannySetupContext("__len__ (wrapper)", 0);
10349 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
10350 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_6__len__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self));
10351
10352 /* function exit code */
10353 __Pyx_RefNannyFinishContext();
10354 return __pyx_r;
10355 }
10356
10357 static Py_ssize_t __pyx_pf_5pysam_7libcvcf_9VCFRecord_6__len__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self) {
10358 Py_ssize_t __pyx_r;
10359 long __pyx_t_1;
10360 long __pyx_t_2;
10361 long __pyx_t_3;
10362 int __pyx_t_4;
10363
10364 /* "pysam/libcvcf.pyx":151
10365 *
10366 * def __len__(self):
10367 * return max(0, self.nfields - 9) # <<<<<<<<<<<<<<
10368 *
10369 * property contig:
10370 */
10371 __pyx_t_1 = (__pyx_v_self->__pyx_base.nfields - 9);
10372 __pyx_t_2 = 0;
10373 __pyx_t_4 = (__pyx_t_1 > __pyx_t_2);
10374 if (__pyx_t_4) {
10375 __pyx_t_3 = __pyx_t_1;
10376 } else {
10377 __pyx_t_3 = __pyx_t_2;
10378 }
10379 __pyx_r = __pyx_t_3;
10380 goto __pyx_L0;
10381
10382 /* "pysam/libcvcf.pyx":150
10383 * self.pos = atoi(self.fields[1]) - 1
10384 *
10385 * def __len__(self): # <<<<<<<<<<<<<<
10386 * return max(0, self.nfields - 9)
10387 *
10388 */
10389
10390 /* function exit code */
10391 __pyx_L0:;
10392 return __pyx_r;
10393 }
10394
10395 /* "pysam/libcvcf.pyx":154
10396 *
10397 * property contig:
10398 * def __get__(self): return self.contig # <<<<<<<<<<<<<<
10399 *
10400 * property pos:
10401 */
10402
10403 /* Python wrapper */
10404 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_6contig_1__get__(PyObject *__pyx_v_self); /*proto*/
10405 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_6contig_1__get__(PyObject *__pyx_v_self) {
10406 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
10407 PyObject *__pyx_r = 0;
10408 __Pyx_RefNannyDeclarations
10409 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
10410 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
10411 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_6contig___get__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self));
10412
10413 /* function exit code */
10414 __Pyx_RefNannyFinishContext();
10415 return __pyx_r;
10416 }
10417
10418 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_6contig___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self) {
10419 PyObject *__pyx_r = NULL;
10420 __Pyx_RefNannyDeclarations
10421 PyObject *__pyx_t_1 = NULL;
10422 int __pyx_lineno = 0;
10423 const char *__pyx_filename = NULL;
10424 int __pyx_clineno = 0;
10425 __Pyx_RefNannySetupContext("__get__", 1);
10426 __Pyx_XDECREF(__pyx_r);
10427 __pyx_t_1 = __Pyx_PyBytes_FromString(__pyx_v_self->contig); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 154, __pyx_L1_error)
10428 __Pyx_GOTREF(__pyx_t_1);
10429 __pyx_r = __pyx_t_1;
10430 __pyx_t_1 = 0;
10431 goto __pyx_L0;
10432
10433 /* function exit code */
10434 __pyx_L1_error:;
10435 __Pyx_XDECREF(__pyx_t_1);
10436 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.contig.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
10437 __pyx_r = NULL;
10438 __pyx_L0:;
10439 __Pyx_XGIVEREF(__pyx_r);
10440 __Pyx_RefNannyFinishContext();
10441 return __pyx_r;
10442 }
10443
10444 /* "pysam/libcvcf.pyx":157
10445 *
10446 * property pos:
10447 * def __get__(self): return self.pos # <<<<<<<<<<<<<<
10448 *
10449 * property id:
10450 */
10451
10452 /* Python wrapper */
10453 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
10454 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_3pos_1__get__(PyObject *__pyx_v_self) {
10455 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
10456 PyObject *__pyx_r = 0;
10457 __Pyx_RefNannyDeclarations
10458 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
10459 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
10460 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_3pos___get__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self));
10461
10462 /* function exit code */
10463 __Pyx_RefNannyFinishContext();
10464 return __pyx_r;
10465 }
10466
10467 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_3pos___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self) {
10468 PyObject *__pyx_r = NULL;
10469 __Pyx_RefNannyDeclarations
10470 PyObject *__pyx_t_1 = NULL;
10471 int __pyx_lineno = 0;
10472 const char *__pyx_filename = NULL;
10473 int __pyx_clineno = 0;
10474 __Pyx_RefNannySetupContext("__get__", 1);
10475 __Pyx_XDECREF(__pyx_r);
10476 __pyx_t_1 = __Pyx_PyInt_From_uint32_t(__pyx_v_self->pos); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 157, __pyx_L1_error)
10477 __Pyx_GOTREF(__pyx_t_1);
10478 __pyx_r = __pyx_t_1;
10479 __pyx_t_1 = 0;
10480 goto __pyx_L0;
10481
10482 /* function exit code */
10483 __pyx_L1_error:;
10484 __Pyx_XDECREF(__pyx_t_1);
10485 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
10486 __pyx_r = NULL;
10487 __pyx_L0:;
10488 __Pyx_XGIVEREF(__pyx_r);
10489 __Pyx_RefNannyFinishContext();
10490 return __pyx_r;
10491 }
10492
10493 /* "pysam/libcvcf.pyx":160
10494 *
10495 * property id:
10496 * def __get__(self): return self.fields[2] # <<<<<<<<<<<<<<
10497 *
10498 * property ref:
10499 */
10500
10501 /* Python wrapper */
10502 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_2id_1__get__(PyObject *__pyx_v_self); /*proto*/
10503 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_2id_1__get__(PyObject *__pyx_v_self) {
10504 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
10505 PyObject *__pyx_r = 0;
10506 __Pyx_RefNannyDeclarations
10507 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
10508 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
10509 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_2id___get__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self));
10510
10511 /* function exit code */
10512 __Pyx_RefNannyFinishContext();
10513 return __pyx_r;
10514 }
10515
10516 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_2id___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self) {
10517 PyObject *__pyx_r = NULL;
10518 __Pyx_RefNannyDeclarations
10519 PyObject *__pyx_t_1 = NULL;
10520 int __pyx_lineno = 0;
10521 const char *__pyx_filename = NULL;
10522 int __pyx_clineno = 0;
10523 __Pyx_RefNannySetupContext("__get__", 1);
10524 __Pyx_XDECREF(__pyx_r);
10525 __pyx_t_1 = __Pyx_PyBytes_FromString((__pyx_v_self->__pyx_base.fields[2])); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 160, __pyx_L1_error)
10526 __Pyx_GOTREF(__pyx_t_1);
10527 __pyx_r = __pyx_t_1;
10528 __pyx_t_1 = 0;
10529 goto __pyx_L0;
10530
10531 /* function exit code */
10532 __pyx_L1_error:;
10533 __Pyx_XDECREF(__pyx_t_1);
10534 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.id.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
10535 __pyx_r = NULL;
10536 __pyx_L0:;
10537 __Pyx_XGIVEREF(__pyx_r);
10538 __Pyx_RefNannyFinishContext();
10539 return __pyx_r;
10540 }
10541
10542 /* "pysam/libcvcf.pyx":163
10543 *
10544 * property ref:
10545 * def __get__(self): # <<<<<<<<<<<<<<
10546 * return self.fields[3]
10547 *
10548 */
10549
10550 /* Python wrapper */
10551 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_3ref_1__get__(PyObject *__pyx_v_self); /*proto*/
10552 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_3ref_1__get__(PyObject *__pyx_v_self) {
10553 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
10554 PyObject *__pyx_r = 0;
10555 __Pyx_RefNannyDeclarations
10556 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
10557 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
10558 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_3ref___get__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self));
10559
10560 /* function exit code */
10561 __Pyx_RefNannyFinishContext();
10562 return __pyx_r;
10563 }
10564
10565 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_3ref___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self) {
10566 PyObject *__pyx_r = NULL;
10567 __Pyx_RefNannyDeclarations
10568 PyObject *__pyx_t_1 = NULL;
10569 int __pyx_lineno = 0;
10570 const char *__pyx_filename = NULL;
10571 int __pyx_clineno = 0;
10572 __Pyx_RefNannySetupContext("__get__", 1);
10573
10574 /* "pysam/libcvcf.pyx":164
10575 * property ref:
10576 * def __get__(self):
10577 * return self.fields[3] # <<<<<<<<<<<<<<
10578 *
10579 * property alt:
10580 */
10581 __Pyx_XDECREF(__pyx_r);
10582 __pyx_t_1 = __Pyx_PyBytes_FromString((__pyx_v_self->__pyx_base.fields[3])); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 164, __pyx_L1_error)
10583 __Pyx_GOTREF(__pyx_t_1);
10584 __pyx_r = __pyx_t_1;
10585 __pyx_t_1 = 0;
10586 goto __pyx_L0;
10587
10588 /* "pysam/libcvcf.pyx":163
10589 *
10590 * property ref:
10591 * def __get__(self): # <<<<<<<<<<<<<<
10592 * return self.fields[3]
10593 *
10594 */
10595
10596 /* function exit code */
10597 __pyx_L1_error:;
10598 __Pyx_XDECREF(__pyx_t_1);
10599 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.ref.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
10600 __pyx_r = NULL;
10601 __pyx_L0:;
10602 __Pyx_XGIVEREF(__pyx_r);
10603 __Pyx_RefNannyFinishContext();
10604 return __pyx_r;
10605 }
10606
10607 /* "pysam/libcvcf.pyx":167
10608 *
10609 * property alt:
10610 * def __get__(self): # <<<<<<<<<<<<<<
10611 * # convert v3.3 to v4.0 alleles below
10612 * alt = self.fields[4]
10613 */
10614
10615 /* Python wrapper */
10616 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_3alt_1__get__(PyObject *__pyx_v_self); /*proto*/
10617 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_3alt_1__get__(PyObject *__pyx_v_self) {
10618 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
10619 PyObject *__pyx_r = 0;
10620 __Pyx_RefNannyDeclarations
10621 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
10622 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
10623 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_3alt___get__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self));
10624
10625 /* function exit code */
10626 __Pyx_RefNannyFinishContext();
10627 return __pyx_r;
10628 }
10629
10630 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_3alt___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self) {
10631 PyObject *__pyx_v_alt = NULL;
10632 PyObject *__pyx_r = NULL;
10633 __Pyx_RefNannyDeclarations
10634 PyObject *__pyx_t_1 = NULL;
10635 int __pyx_t_2;
10636 PyObject *__pyx_t_3 = NULL;
10637 PyObject *__pyx_t_4 = NULL;
10638 PyObject *__pyx_t_5 = NULL;
10639 unsigned int __pyx_t_6;
10640 int __pyx_lineno = 0;
10641 const char *__pyx_filename = NULL;
10642 int __pyx_clineno = 0;
10643 __Pyx_RefNannySetupContext("__get__", 1);
10644
10645 /* "pysam/libcvcf.pyx":169
10646 * def __get__(self):
10647 * # convert v3.3 to v4.0 alleles below
10648 * alt = self.fields[4] # <<<<<<<<<<<<<<
10649 * if alt == ".": alt = []
10650 * else: alt = alt.upper().split(',')
10651 */
10652 __pyx_t_1 = __Pyx_PyBytes_FromString((__pyx_v_self->__pyx_base.fields[4])); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 169, __pyx_L1_error)
10653 __Pyx_GOTREF(__pyx_t_1);
10654 __pyx_v_alt = __pyx_t_1;
10655 __pyx_t_1 = 0;
10656
10657 /* "pysam/libcvcf.pyx":170
10658 * # convert v3.3 to v4.0 alleles below
10659 * alt = self.fields[4]
10660 * if alt == ".": alt = [] # <<<<<<<<<<<<<<
10661 * else: alt = alt.upper().split(',')
10662 * return alt
10663 */
10664 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_v_alt, __pyx_kp_u__5, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 170, __pyx_L1_error)
10665 if (__pyx_t_2) {
10666 __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 170, __pyx_L1_error)
10667 __Pyx_GOTREF(__pyx_t_1);
10668 __Pyx_DECREF_SET(__pyx_v_alt, __pyx_t_1);
10669 __pyx_t_1 = 0;
10670 goto __pyx_L3;
10671 }
10672
10673 /* "pysam/libcvcf.pyx":171
10674 * alt = self.fields[4]
10675 * if alt == ".": alt = []
10676 * else: alt = alt.upper().split(',') # <<<<<<<<<<<<<<
10677 * return alt
10678 *
10679 */
10680 /*else*/ {
10681 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_alt, __pyx_n_s_upper); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 171, __pyx_L1_error)
10682 __Pyx_GOTREF(__pyx_t_4);
10683 __pyx_t_5 = NULL;
10684 __pyx_t_6 = 0;
10685 #if CYTHON_UNPACK_METHODS
10686 if (likely(PyMethod_Check(__pyx_t_4))) {
10687 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_4);
10688 if (likely(__pyx_t_5)) {
10689 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
10690 __Pyx_INCREF(__pyx_t_5);
10691 __Pyx_INCREF(function);
10692 __Pyx_DECREF_SET(__pyx_t_4, function);
10693 __pyx_t_6 = 1;
10694 }
10695 }
10696 #endif
10697 {
10698 PyObject *__pyx_callargs[2] = {__pyx_t_5, NULL};
10699 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_6, 0+__pyx_t_6);
10700 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
10701 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 171, __pyx_L1_error)
10702 __Pyx_GOTREF(__pyx_t_3);
10703 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
10704 }
10705 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_split); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 171, __pyx_L1_error)
10706 __Pyx_GOTREF(__pyx_t_4);
10707 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
10708 __pyx_t_3 = NULL;
10709 __pyx_t_6 = 0;
10710 #if CYTHON_UNPACK_METHODS
10711 if (likely(PyMethod_Check(__pyx_t_4))) {
10712 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_4);
10713 if (likely(__pyx_t_3)) {
10714 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
10715 __Pyx_INCREF(__pyx_t_3);
10716 __Pyx_INCREF(function);
10717 __Pyx_DECREF_SET(__pyx_t_4, function);
10718 __pyx_t_6 = 1;
10719 }
10720 }
10721 #endif
10722 {
10723 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_kp_u__2};
10724 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_6, 1+__pyx_t_6);
10725 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
10726 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 171, __pyx_L1_error)
10727 __Pyx_GOTREF(__pyx_t_1);
10728 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
10729 }
10730 __Pyx_DECREF_SET(__pyx_v_alt, __pyx_t_1);
10731 __pyx_t_1 = 0;
10732 }
10733 __pyx_L3:;
10734
10735 /* "pysam/libcvcf.pyx":172
10736 * if alt == ".": alt = []
10737 * else: alt = alt.upper().split(',')
10738 * return alt # <<<<<<<<<<<<<<
10739 *
10740 * property qual:
10741 */
10742 __Pyx_XDECREF(__pyx_r);
10743 __Pyx_INCREF(__pyx_v_alt);
10744 __pyx_r = __pyx_v_alt;
10745 goto __pyx_L0;
10746
10747 /* "pysam/libcvcf.pyx":167
10748 *
10749 * property alt:
10750 * def __get__(self): # <<<<<<<<<<<<<<
10751 * # convert v3.3 to v4.0 alleles below
10752 * alt = self.fields[4]
10753 */
10754
10755 /* function exit code */
10756 __pyx_L1_error:;
10757 __Pyx_XDECREF(__pyx_t_1);
10758 __Pyx_XDECREF(__pyx_t_3);
10759 __Pyx_XDECREF(__pyx_t_4);
10760 __Pyx_XDECREF(__pyx_t_5);
10761 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.alt.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
10762 __pyx_r = NULL;
10763 __pyx_L0:;
10764 __Pyx_XDECREF(__pyx_v_alt);
10765 __Pyx_XGIVEREF(__pyx_r);
10766 __Pyx_RefNannyFinishContext();
10767 return __pyx_r;
10768 }
10769
10770 /* "pysam/libcvcf.pyx":175
10771 *
10772 * property qual:
10773 * def __get__(self): # <<<<<<<<<<<<<<
10774 * qual = self.fields[5]
10775 * if qual == b".": qual = -1
10776 */
10777
10778 /* Python wrapper */
10779 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_4qual_1__get__(PyObject *__pyx_v_self); /*proto*/
10780 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_4qual_1__get__(PyObject *__pyx_v_self) {
10781 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
10782 PyObject *__pyx_r = 0;
10783 __Pyx_RefNannyDeclarations
10784 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
10785 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
10786 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_4qual___get__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self));
10787
10788 /* function exit code */
10789 __Pyx_RefNannyFinishContext();
10790 return __pyx_r;
10791 }
10792
10793 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_4qual___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self) {
10794 PyObject *__pyx_v_qual = NULL;
10795 PyObject *__pyx_r = NULL;
10796 __Pyx_RefNannyDeclarations
10797 PyObject *__pyx_t_1 = NULL;
10798 int __pyx_t_2;
10799 PyObject *__pyx_t_3 = NULL;
10800 PyObject *__pyx_t_4 = NULL;
10801 PyObject *__pyx_t_5 = NULL;
10802 PyObject *__pyx_t_6 = NULL;
10803 PyObject *__pyx_t_7 = NULL;
10804 PyObject *__pyx_t_8 = NULL;
10805 PyObject *__pyx_t_9 = NULL;
10806 PyObject *__pyx_t_10 = NULL;
10807 PyObject *__pyx_t_11 = NULL;
10808 PyObject *__pyx_t_12 = NULL;
10809 unsigned int __pyx_t_13;
10810 int __pyx_lineno = 0;
10811 const char *__pyx_filename = NULL;
10812 int __pyx_clineno = 0;
10813 __Pyx_RefNannySetupContext("__get__", 1);
10814
10815 /* "pysam/libcvcf.pyx":176
10816 * property qual:
10817 * def __get__(self):
10818 * qual = self.fields[5] # <<<<<<<<<<<<<<
10819 * if qual == b".": qual = -1
10820 * else:
10821 */
10822 __pyx_t_1 = __Pyx_PyBytes_FromString((__pyx_v_self->__pyx_base.fields[5])); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 176, __pyx_L1_error)
10823 __Pyx_GOTREF(__pyx_t_1);
10824 __pyx_v_qual = __pyx_t_1;
10825 __pyx_t_1 = 0;
10826
10827 /* "pysam/libcvcf.pyx":177
10828 * def __get__(self):
10829 * qual = self.fields[5]
10830 * if qual == b".": qual = -1 # <<<<<<<<<<<<<<
10831 * else:
10832 * try: qual = float(qual)
10833 */
10834 __pyx_t_2 = (__Pyx_PyBytes_Equals(__pyx_v_qual, __pyx_kp_b__5, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 177, __pyx_L1_error)
10835 if (__pyx_t_2) {
10836 __Pyx_INCREF(__pyx_int_neg_1);
10837 __Pyx_DECREF_SET(__pyx_v_qual, __pyx_int_neg_1);
10838 goto __pyx_L3;
10839 }
10840
10841 /* "pysam/libcvcf.pyx":179
10842 * if qual == b".": qual = -1
10843 * else:
10844 * try: qual = float(qual) # <<<<<<<<<<<<<<
10845 * except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL)
10846 * return qual
10847 */
10848 /*else*/ {
10849 {
10850 __Pyx_PyThreadState_declare
10851 __Pyx_PyThreadState_assign
10852 __Pyx_ExceptionSave(&__pyx_t_3, &__pyx_t_4, &__pyx_t_5);
10853 __Pyx_XGOTREF(__pyx_t_3);
10854 __Pyx_XGOTREF(__pyx_t_4);
10855 __Pyx_XGOTREF(__pyx_t_5);
10856 /*try:*/ {
10857 __pyx_t_1 = __Pyx_PyNumber_Float(__pyx_v_qual); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 179, __pyx_L4_error)
10858 __Pyx_GOTREF(__pyx_t_1);
10859 __Pyx_DECREF_SET(__pyx_v_qual, __pyx_t_1);
10860 __pyx_t_1 = 0;
10861 }
10862 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
10863 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
10864 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
10865 goto __pyx_L9_try_end;
10866 __pyx_L4_error:;
10867 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
10868
10869 /* "pysam/libcvcf.pyx":180
10870 * else:
10871 * try: qual = float(qual)
10872 * except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL) # <<<<<<<<<<<<<<
10873 * return qual
10874 *
10875 */
10876 /*except:*/ {
10877 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.qual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
10878 if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(0, 180, __pyx_L6_except_error)
10879 __Pyx_XGOTREF(__pyx_t_1);
10880 __Pyx_XGOTREF(__pyx_t_6);
10881 __Pyx_XGOTREF(__pyx_t_7);
10882 __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_error); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 180, __pyx_L6_except_error)
10883 __Pyx_GOTREF(__pyx_t_9);
10884 __pyx_t_10 = __Pyx_PyObject_Unicode(((PyObject *)__pyx_v_self)); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 180, __pyx_L6_except_error)
10885 __Pyx_GOTREF(__pyx_t_10);
10886 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_QUAL_NOT_NUMERICAL); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 180, __pyx_L6_except_error)
10887 __Pyx_GOTREF(__pyx_t_11);
10888 __pyx_t_12 = NULL;
10889 __pyx_t_13 = 0;
10890 #if CYTHON_UNPACK_METHODS
10891 if (likely(PyMethod_Check(__pyx_t_9))) {
10892 __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_9);
10893 if (likely(__pyx_t_12)) {
10894 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_9);
10895 __Pyx_INCREF(__pyx_t_12);
10896 __Pyx_INCREF(function);
10897 __Pyx_DECREF_SET(__pyx_t_9, function);
10898 __pyx_t_13 = 1;
10899 }
10900 }
10901 #endif
10902 {
10903 PyObject *__pyx_callargs[3] = {__pyx_t_12, __pyx_t_10, __pyx_t_11};
10904 __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_13, 2+__pyx_t_13);
10905 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
10906 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
10907 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
10908 if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 180, __pyx_L6_except_error)
10909 __Pyx_GOTREF(__pyx_t_8);
10910 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
10911 }
10912 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
10913 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
10914 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
10915 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
10916 goto __pyx_L5_exception_handled;
10917 }
10918
10919 /* "pysam/libcvcf.pyx":179
10920 * if qual == b".": qual = -1
10921 * else:
10922 * try: qual = float(qual) # <<<<<<<<<<<<<<
10923 * except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL)
10924 * return qual
10925 */
10926 __pyx_L6_except_error:;
10927 __Pyx_XGIVEREF(__pyx_t_3);
10928 __Pyx_XGIVEREF(__pyx_t_4);
10929 __Pyx_XGIVEREF(__pyx_t_5);
10930 __Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
10931 goto __pyx_L1_error;
10932 __pyx_L5_exception_handled:;
10933 __Pyx_XGIVEREF(__pyx_t_3);
10934 __Pyx_XGIVEREF(__pyx_t_4);
10935 __Pyx_XGIVEREF(__pyx_t_5);
10936 __Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
10937 __pyx_L9_try_end:;
10938 }
10939 }
10940 __pyx_L3:;
10941
10942 /* "pysam/libcvcf.pyx":181
10943 * try: qual = float(qual)
10944 * except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL)
10945 * return qual # <<<<<<<<<<<<<<
10946 *
10947 * property filter:
10948 */
10949 __Pyx_XDECREF(__pyx_r);
10950 __Pyx_INCREF(__pyx_v_qual);
10951 __pyx_r = __pyx_v_qual;
10952 goto __pyx_L0;
10953
10954 /* "pysam/libcvcf.pyx":175
10955 *
10956 * property qual:
10957 * def __get__(self): # <<<<<<<<<<<<<<
10958 * qual = self.fields[5]
10959 * if qual == b".": qual = -1
10960 */
10961
10962 /* function exit code */
10963 __pyx_L1_error:;
10964 __Pyx_XDECREF(__pyx_t_1);
10965 __Pyx_XDECREF(__pyx_t_6);
10966 __Pyx_XDECREF(__pyx_t_7);
10967 __Pyx_XDECREF(__pyx_t_8);
10968 __Pyx_XDECREF(__pyx_t_9);
10969 __Pyx_XDECREF(__pyx_t_10);
10970 __Pyx_XDECREF(__pyx_t_11);
10971 __Pyx_XDECREF(__pyx_t_12);
10972 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.qual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
10973 __pyx_r = NULL;
10974 __pyx_L0:;
10975 __Pyx_XDECREF(__pyx_v_qual);
10976 __Pyx_XGIVEREF(__pyx_r);
10977 __Pyx_RefNannyFinishContext();
10978 return __pyx_r;
10979 }
10980
10981 /* "pysam/libcvcf.pyx":184
10982 *
10983 * property filter:
10984 * def __get__(self): # <<<<<<<<<<<<<<
10985 * f = self.fields[6]
10986 * # postpone checking that filters exist. Encode missing filter or no filtering as empty list
10987 */
10988
10989 /* Python wrapper */
10990 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_6filter_1__get__(PyObject *__pyx_v_self); /*proto*/
10991 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_6filter_1__get__(PyObject *__pyx_v_self) {
10992 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
10993 PyObject *__pyx_r = 0;
10994 __Pyx_RefNannyDeclarations
10995 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
10996 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
10997 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_6filter___get__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self));
10998
10999 /* function exit code */
11000 __Pyx_RefNannyFinishContext();
11001 return __pyx_r;
11002 }
11003
11004 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_6filter___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self) {
11005 char *__pyx_v_f;
11006 PyObject *__pyx_r = NULL;
11007 __Pyx_RefNannyDeclarations
11008 int __pyx_t_1;
11009 PyObject *__pyx_t_2 = NULL;
11010 int __pyx_t_3;
11011 PyObject *__pyx_t_4 = NULL;
11012 PyObject *__pyx_t_5 = NULL;
11013 unsigned int __pyx_t_6;
11014 int __pyx_lineno = 0;
11015 const char *__pyx_filename = NULL;
11016 int __pyx_clineno = 0;
11017 __Pyx_RefNannySetupContext("__get__", 1);
11018
11019 /* "pysam/libcvcf.pyx":185
11020 * property filter:
11021 * def __get__(self):
11022 * f = self.fields[6] # <<<<<<<<<<<<<<
11023 * # postpone checking that filters exist. Encode missing filter or no filtering as empty list
11024 * if f == b"." or f == b"PASS" or f == b"0": return []
11025 */
11026 __pyx_v_f = (__pyx_v_self->__pyx_base.fields[6]);
11027
11028 /* "pysam/libcvcf.pyx":187
11029 * f = self.fields[6]
11030 * # postpone checking that filters exist. Encode missing filter or no filtering as empty list
11031 * if f == b"." or f == b"PASS" or f == b"0": return [] # <<<<<<<<<<<<<<
11032 * else: return f.split(';')
11033 *
11034 */
11035 __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 187, __pyx_L1_error)
11036 __Pyx_GOTREF(__pyx_t_2);
11037 __pyx_t_3 = (__Pyx_PyBytes_Equals(__pyx_t_2, __pyx_kp_b__5, Py_EQ)); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 187, __pyx_L1_error)
11038 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
11039 if (!__pyx_t_3) {
11040 } else {
11041 __pyx_t_1 = __pyx_t_3;
11042 goto __pyx_L4_bool_binop_done;
11043 }
11044 __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 187, __pyx_L1_error)
11045 __Pyx_GOTREF(__pyx_t_2);
11046 __pyx_t_3 = (__Pyx_PyBytes_Equals(__pyx_t_2, __pyx_n_b_PASS, Py_EQ)); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 187, __pyx_L1_error)
11047 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
11048 if (!__pyx_t_3) {
11049 } else {
11050 __pyx_t_1 = __pyx_t_3;
11051 goto __pyx_L4_bool_binop_done;
11052 }
11053 __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 187, __pyx_L1_error)
11054 __Pyx_GOTREF(__pyx_t_2);
11055 __pyx_t_3 = (__Pyx_PyBytes_Equals(__pyx_t_2, __pyx_kp_b_0, Py_EQ)); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 187, __pyx_L1_error)
11056 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
11057 __pyx_t_1 = __pyx_t_3;
11058 __pyx_L4_bool_binop_done:;
11059 if (__pyx_t_1) {
11060 __Pyx_XDECREF(__pyx_r);
11061 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 187, __pyx_L1_error)
11062 __Pyx_GOTREF(__pyx_t_2);
11063 __pyx_r = __pyx_t_2;
11064 __pyx_t_2 = 0;
11065 goto __pyx_L0;
11066 }
11067
11068 /* "pysam/libcvcf.pyx":188
11069 * # postpone checking that filters exist. Encode missing filter or no filtering as empty list
11070 * if f == b"." or f == b"PASS" or f == b"0": return []
11071 * else: return f.split(';') # <<<<<<<<<<<<<<
11072 *
11073 * property info:
11074 */
11075 /*else*/ {
11076 __Pyx_XDECREF(__pyx_r);
11077 __pyx_t_4 = __Pyx_PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 188, __pyx_L1_error)
11078 __Pyx_GOTREF(__pyx_t_4);
11079 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_split); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 188, __pyx_L1_error)
11080 __Pyx_GOTREF(__pyx_t_5);
11081 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
11082 __pyx_t_4 = NULL;
11083 __pyx_t_6 = 0;
11084 #if CYTHON_UNPACK_METHODS
11085 if (likely(PyMethod_Check(__pyx_t_5))) {
11086 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_5);
11087 if (likely(__pyx_t_4)) {
11088 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
11089 __Pyx_INCREF(__pyx_t_4);
11090 __Pyx_INCREF(function);
11091 __Pyx_DECREF_SET(__pyx_t_5, function);
11092 __pyx_t_6 = 1;
11093 }
11094 }
11095 #endif
11096 {
11097 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_kp_u__6};
11098 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_6, 1+__pyx_t_6);
11099 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
11100 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 188, __pyx_L1_error)
11101 __Pyx_GOTREF(__pyx_t_2);
11102 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
11103 }
11104 __pyx_r = __pyx_t_2;
11105 __pyx_t_2 = 0;
11106 goto __pyx_L0;
11107 }
11108
11109 /* "pysam/libcvcf.pyx":184
11110 *
11111 * property filter:
11112 * def __get__(self): # <<<<<<<<<<<<<<
11113 * f = self.fields[6]
11114 * # postpone checking that filters exist. Encode missing filter or no filtering as empty list
11115 */
11116
11117 /* function exit code */
11118 __pyx_L1_error:;
11119 __Pyx_XDECREF(__pyx_t_2);
11120 __Pyx_XDECREF(__pyx_t_4);
11121 __Pyx_XDECREF(__pyx_t_5);
11122 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.filter.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
11123 __pyx_r = NULL;
11124 __pyx_L0:;
11125 __Pyx_XGIVEREF(__pyx_r);
11126 __Pyx_RefNannyFinishContext();
11127 return __pyx_r;
11128 }
11129
11130 /* "pysam/libcvcf.pyx":191
11131 *
11132 * property info:
11133 * def __get__(self): # <<<<<<<<<<<<<<
11134 * col = self.fields[7]
11135 * # dictionary of keys, and list of values
11136 */
11137
11138 /* Python wrapper */
11139 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_4info_1__get__(PyObject *__pyx_v_self); /*proto*/
11140 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_4info_1__get__(PyObject *__pyx_v_self) {
11141 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
11142 PyObject *__pyx_r = 0;
11143 __Pyx_RefNannyDeclarations
11144 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
11145 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
11146 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_4info___get__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self));
11147
11148 /* function exit code */
11149 __Pyx_RefNannyFinishContext();
11150 return __pyx_r;
11151 }
11152
11153 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_4info___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self) {
11154 char *__pyx_v_col;
11155 PyObject *__pyx_v_info = NULL;
11156 PyObject *__pyx_v_blurp = NULL;
11157 PyObject *__pyx_v_elts = NULL;
11158 PyObject *__pyx_v_v = NULL;
11159 PyObject *__pyx_r = NULL;
11160 __Pyx_RefNannyDeclarations
11161 PyObject *__pyx_t_1 = NULL;
11162 int __pyx_t_2;
11163 PyObject *__pyx_t_3 = NULL;
11164 PyObject *__pyx_t_4 = NULL;
11165 unsigned int __pyx_t_5;
11166 Py_ssize_t __pyx_t_6;
11167 PyObject *(*__pyx_t_7)(PyObject *);
11168 PyObject *__pyx_t_8 = NULL;
11169 Py_ssize_t __pyx_t_9;
11170 PyObject *__pyx_t_10 = NULL;
11171 PyObject *__pyx_t_11 = NULL;
11172 PyObject *__pyx_t_12 = NULL;
11173 int __pyx_lineno = 0;
11174 const char *__pyx_filename = NULL;
11175 int __pyx_clineno = 0;
11176 __Pyx_RefNannySetupContext("__get__", 1);
11177
11178 /* "pysam/libcvcf.pyx":192
11179 * property info:
11180 * def __get__(self):
11181 * col = self.fields[7] # <<<<<<<<<<<<<<
11182 * # dictionary of keys, and list of values
11183 * info = {}
11184 */
11185 __pyx_v_col = (__pyx_v_self->__pyx_base.fields[7]);
11186
11187 /* "pysam/libcvcf.pyx":194
11188 * col = self.fields[7]
11189 * # dictionary of keys, and list of values
11190 * info = {} # <<<<<<<<<<<<<<
11191 * if col != b".":
11192 * for blurp in col.split(';'):
11193 */
11194 __pyx_t_1 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 194, __pyx_L1_error)
11195 __Pyx_GOTREF(__pyx_t_1);
11196 __pyx_v_info = ((PyObject*)__pyx_t_1);
11197 __pyx_t_1 = 0;
11198
11199 /* "pysam/libcvcf.pyx":195
11200 * # dictionary of keys, and list of values
11201 * info = {}
11202 * if col != b".": # <<<<<<<<<<<<<<
11203 * for blurp in col.split(';'):
11204 * elts = blurp.split('=')
11205 */
11206 __pyx_t_1 = __Pyx_PyBytes_FromString(__pyx_v_col); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 195, __pyx_L1_error)
11207 __Pyx_GOTREF(__pyx_t_1);
11208 __pyx_t_2 = (__Pyx_PyBytes_Equals(__pyx_t_1, __pyx_kp_b__5, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 195, __pyx_L1_error)
11209 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
11210 if (__pyx_t_2) {
11211
11212 /* "pysam/libcvcf.pyx":196
11213 * info = {}
11214 * if col != b".":
11215 * for blurp in col.split(';'): # <<<<<<<<<<<<<<
11216 * elts = blurp.split('=')
11217 * if len(elts) == 1: v = None
11218 */
11219 __pyx_t_3 = __Pyx_PyBytes_FromString(__pyx_v_col); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 196, __pyx_L1_error)
11220 __Pyx_GOTREF(__pyx_t_3);
11221 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_split); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 196, __pyx_L1_error)
11222 __Pyx_GOTREF(__pyx_t_4);
11223 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
11224 __pyx_t_3 = NULL;
11225 __pyx_t_5 = 0;
11226 #if CYTHON_UNPACK_METHODS
11227 if (likely(PyMethod_Check(__pyx_t_4))) {
11228 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_4);
11229 if (likely(__pyx_t_3)) {
11230 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
11231 __Pyx_INCREF(__pyx_t_3);
11232 __Pyx_INCREF(function);
11233 __Pyx_DECREF_SET(__pyx_t_4, function);
11234 __pyx_t_5 = 1;
11235 }
11236 }
11237 #endif
11238 {
11239 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_kp_u__6};
11240 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
11241 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
11242 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 196, __pyx_L1_error)
11243 __Pyx_GOTREF(__pyx_t_1);
11244 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
11245 }
11246 if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) {
11247 __pyx_t_4 = __pyx_t_1; __Pyx_INCREF(__pyx_t_4);
11248 __pyx_t_6 = 0;
11249 __pyx_t_7 = NULL;
11250 } else {
11251 __pyx_t_6 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 196, __pyx_L1_error)
11252 __Pyx_GOTREF(__pyx_t_4);
11253 __pyx_t_7 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_4); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 196, __pyx_L1_error)
11254 }
11255 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
11256 for (;;) {
11257 if (likely(!__pyx_t_7)) {
11258 if (likely(PyList_CheckExact(__pyx_t_4))) {
11259 {
11260 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_4);
11261 #if !CYTHON_ASSUME_SAFE_MACROS
11262 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 196, __pyx_L1_error)
11263 #endif
11264 if (__pyx_t_6 >= __pyx_temp) break;
11265 }
11266 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
11267 __pyx_t_1 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 196, __pyx_L1_error)
11268 #else
11269 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_4, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 196, __pyx_L1_error)
11270 __Pyx_GOTREF(__pyx_t_1);
11271 #endif
11272 } else {
11273 {
11274 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_4);
11275 #if !CYTHON_ASSUME_SAFE_MACROS
11276 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 196, __pyx_L1_error)
11277 #endif
11278 if (__pyx_t_6 >= __pyx_temp) break;
11279 }
11280 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
11281 __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 196, __pyx_L1_error)
11282 #else
11283 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_4, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 196, __pyx_L1_error)
11284 __Pyx_GOTREF(__pyx_t_1);
11285 #endif
11286 }
11287 } else {
11288 __pyx_t_1 = __pyx_t_7(__pyx_t_4);
11289 if (unlikely(!__pyx_t_1)) {
11290 PyObject* exc_type = PyErr_Occurred();
11291 if (exc_type) {
11292 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
11293 else __PYX_ERR(0, 196, __pyx_L1_error)
11294 }
11295 break;
11296 }
11297 __Pyx_GOTREF(__pyx_t_1);
11298 }
11299 __Pyx_XDECREF_SET(__pyx_v_blurp, __pyx_t_1);
11300 __pyx_t_1 = 0;
11301
11302 /* "pysam/libcvcf.pyx":197
11303 * if col != b".":
11304 * for blurp in col.split(';'):
11305 * elts = blurp.split('=') # <<<<<<<<<<<<<<
11306 * if len(elts) == 1: v = None
11307 * elif len(elts) == 2: v = elts[1]
11308 */
11309 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_blurp, __pyx_n_s_split); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 197, __pyx_L1_error)
11310 __Pyx_GOTREF(__pyx_t_3);
11311 __pyx_t_8 = NULL;
11312 __pyx_t_5 = 0;
11313 #if CYTHON_UNPACK_METHODS
11314 if (likely(PyMethod_Check(__pyx_t_3))) {
11315 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_3);
11316 if (likely(__pyx_t_8)) {
11317 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
11318 __Pyx_INCREF(__pyx_t_8);
11319 __Pyx_INCREF(function);
11320 __Pyx_DECREF_SET(__pyx_t_3, function);
11321 __pyx_t_5 = 1;
11322 }
11323 }
11324 #endif
11325 {
11326 PyObject *__pyx_callargs[2] = {__pyx_t_8, __pyx_kp_u__7};
11327 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
11328 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
11329 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 197, __pyx_L1_error)
11330 __Pyx_GOTREF(__pyx_t_1);
11331 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
11332 }
11333 __Pyx_XDECREF_SET(__pyx_v_elts, __pyx_t_1);
11334 __pyx_t_1 = 0;
11335
11336 /* "pysam/libcvcf.pyx":198
11337 * for blurp in col.split(';'):
11338 * elts = blurp.split('=')
11339 * if len(elts) == 1: v = None # <<<<<<<<<<<<<<
11340 * elif len(elts) == 2: v = elts[1]
11341 * else: self.vcf.error(str(self),self.ERROR_INFO_STRING)
11342 */
11343 __pyx_t_9 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 198, __pyx_L1_error)
11344 __pyx_t_2 = (__pyx_t_9 == 1);
11345 if (__pyx_t_2) {
11346 __Pyx_INCREF(Py_None);
11347 __Pyx_XDECREF_SET(__pyx_v_v, Py_None);
11348 goto __pyx_L6;
11349 }
11350
11351 /* "pysam/libcvcf.pyx":199
11352 * elts = blurp.split('=')
11353 * if len(elts) == 1: v = None
11354 * elif len(elts) == 2: v = elts[1] # <<<<<<<<<<<<<<
11355 * else: self.vcf.error(str(self),self.ERROR_INFO_STRING)
11356 * info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self.vcf))
11357 */
11358 __pyx_t_9 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 199, __pyx_L1_error)
11359 __pyx_t_2 = (__pyx_t_9 == 2);
11360 if (__pyx_t_2) {
11361 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_elts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 199, __pyx_L1_error)
11362 __Pyx_GOTREF(__pyx_t_1);
11363 __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_1);
11364 __pyx_t_1 = 0;
11365 goto __pyx_L6;
11366 }
11367
11368 /* "pysam/libcvcf.pyx":200
11369 * if len(elts) == 1: v = None
11370 * elif len(elts) == 2: v = elts[1]
11371 * else: self.vcf.error(str(self),self.ERROR_INFO_STRING) # <<<<<<<<<<<<<<
11372 * info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self.vcf))
11373 * return info
11374 */
11375 /*else*/ {
11376 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 200, __pyx_L1_error)
11377 __Pyx_GOTREF(__pyx_t_3);
11378 __pyx_t_8 = __Pyx_PyObject_Unicode(((PyObject *)__pyx_v_self)); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 200, __pyx_L1_error)
11379 __Pyx_GOTREF(__pyx_t_8);
11380 __pyx_t_10 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_ERROR_INFO_STRING); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 200, __pyx_L1_error)
11381 __Pyx_GOTREF(__pyx_t_10);
11382 __pyx_t_11 = NULL;
11383 __pyx_t_5 = 0;
11384 #if CYTHON_UNPACK_METHODS
11385 if (likely(PyMethod_Check(__pyx_t_3))) {
11386 __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_3);
11387 if (likely(__pyx_t_11)) {
11388 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
11389 __Pyx_INCREF(__pyx_t_11);
11390 __Pyx_INCREF(function);
11391 __Pyx_DECREF_SET(__pyx_t_3, function);
11392 __pyx_t_5 = 1;
11393 }
11394 }
11395 #endif
11396 {
11397 PyObject *__pyx_callargs[3] = {__pyx_t_11, __pyx_t_8, __pyx_t_10};
11398 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
11399 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
11400 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
11401 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
11402 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 200, __pyx_L1_error)
11403 __Pyx_GOTREF(__pyx_t_1);
11404 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
11405 }
11406 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
11407 }
11408 __pyx_L6:;
11409
11410 /* "pysam/libcvcf.pyx":201
11411 * elif len(elts) == 2: v = elts[1]
11412 * else: self.vcf.error(str(self),self.ERROR_INFO_STRING)
11413 * info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self.vcf)) # <<<<<<<<<<<<<<
11414 * return info
11415 *
11416 */
11417 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_parse_formatdata); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 201, __pyx_L1_error)
11418 __Pyx_GOTREF(__pyx_t_3);
11419 __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_elts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 201, __pyx_L1_error)
11420 __Pyx_GOTREF(__pyx_t_10);
11421 if (unlikely(!__pyx_v_v)) { __Pyx_RaiseUnboundLocalError("v"); __PYX_ERR(0, 201, __pyx_L1_error) }
11422 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_info); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 201, __pyx_L1_error)
11423 __Pyx_GOTREF(__pyx_t_8);
11424 __pyx_t_11 = __Pyx_PyObject_Unicode(__pyx_v_self->vcf); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 201, __pyx_L1_error)
11425 __Pyx_GOTREF(__pyx_t_11);
11426 __pyx_t_12 = NULL;
11427 __pyx_t_5 = 0;
11428 #if CYTHON_UNPACK_METHODS
11429 if (likely(PyMethod_Check(__pyx_t_3))) {
11430 __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_3);
11431 if (likely(__pyx_t_12)) {
11432 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
11433 __Pyx_INCREF(__pyx_t_12);
11434 __Pyx_INCREF(function);
11435 __Pyx_DECREF_SET(__pyx_t_3, function);
11436 __pyx_t_5 = 1;
11437 }
11438 }
11439 #endif
11440 {
11441 PyObject *__pyx_callargs[5] = {__pyx_t_12, __pyx_t_10, __pyx_v_v, __pyx_t_8, __pyx_t_11};
11442 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 4+__pyx_t_5);
11443 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
11444 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
11445 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
11446 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
11447 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 201, __pyx_L1_error)
11448 __Pyx_GOTREF(__pyx_t_1);
11449 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
11450 }
11451 __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_elts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 201, __pyx_L1_error)
11452 __Pyx_GOTREF(__pyx_t_3);
11453 if (unlikely((PyDict_SetItem(__pyx_v_info, __pyx_t_3, __pyx_t_1) < 0))) __PYX_ERR(0, 201, __pyx_L1_error)
11454 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
11455 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
11456
11457 /* "pysam/libcvcf.pyx":196
11458 * info = {}
11459 * if col != b".":
11460 * for blurp in col.split(';'): # <<<<<<<<<<<<<<
11461 * elts = blurp.split('=')
11462 * if len(elts) == 1: v = None
11463 */
11464 }
11465 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
11466
11467 /* "pysam/libcvcf.pyx":195
11468 * # dictionary of keys, and list of values
11469 * info = {}
11470 * if col != b".": # <<<<<<<<<<<<<<
11471 * for blurp in col.split(';'):
11472 * elts = blurp.split('=')
11473 */
11474 }
11475
11476 /* "pysam/libcvcf.pyx":202
11477 * else: self.vcf.error(str(self),self.ERROR_INFO_STRING)
11478 * info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self.vcf))
11479 * return info # <<<<<<<<<<<<<<
11480 *
11481 * property format:
11482 */
11483 __Pyx_XDECREF(__pyx_r);
11484 __Pyx_INCREF(__pyx_v_info);
11485 __pyx_r = __pyx_v_info;
11486 goto __pyx_L0;
11487
11488 /* "pysam/libcvcf.pyx":191
11489 *
11490 * property info:
11491 * def __get__(self): # <<<<<<<<<<<<<<
11492 * col = self.fields[7]
11493 * # dictionary of keys, and list of values
11494 */
11495
11496 /* function exit code */
11497 __pyx_L1_error:;
11498 __Pyx_XDECREF(__pyx_t_1);
11499 __Pyx_XDECREF(__pyx_t_3);
11500 __Pyx_XDECREF(__pyx_t_4);
11501 __Pyx_XDECREF(__pyx_t_8);
11502 __Pyx_XDECREF(__pyx_t_10);
11503 __Pyx_XDECREF(__pyx_t_11);
11504 __Pyx_XDECREF(__pyx_t_12);
11505 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.info.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
11506 __pyx_r = NULL;
11507 __pyx_L0:;
11508 __Pyx_XDECREF(__pyx_v_info);
11509 __Pyx_XDECREF(__pyx_v_blurp);
11510 __Pyx_XDECREF(__pyx_v_elts);
11511 __Pyx_XDECREF(__pyx_v_v);
11512 __Pyx_XGIVEREF(__pyx_r);
11513 __Pyx_RefNannyFinishContext();
11514 return __pyx_r;
11515 }
11516
11517 /* "pysam/libcvcf.pyx":205
11518 *
11519 * property format:
11520 * def __get__(self): # <<<<<<<<<<<<<<
11521 * return self.fields[8].split(':')
11522 *
11523 */
11524
11525 /* Python wrapper */
11526 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_6format_1__get__(PyObject *__pyx_v_self); /*proto*/
11527 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_6format_1__get__(PyObject *__pyx_v_self) {
11528 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
11529 PyObject *__pyx_r = 0;
11530 __Pyx_RefNannyDeclarations
11531 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
11532 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
11533 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_6format___get__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self));
11534
11535 /* function exit code */
11536 __Pyx_RefNannyFinishContext();
11537 return __pyx_r;
11538 }
11539
11540 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_6format___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self) {
11541 PyObject *__pyx_r = NULL;
11542 __Pyx_RefNannyDeclarations
11543 PyObject *__pyx_t_1 = NULL;
11544 PyObject *__pyx_t_2 = NULL;
11545 PyObject *__pyx_t_3 = NULL;
11546 unsigned int __pyx_t_4;
11547 int __pyx_lineno = 0;
11548 const char *__pyx_filename = NULL;
11549 int __pyx_clineno = 0;
11550 __Pyx_RefNannySetupContext("__get__", 1);
11551
11552 /* "pysam/libcvcf.pyx":206
11553 * property format:
11554 * def __get__(self):
11555 * return self.fields[8].split(':') # <<<<<<<<<<<<<<
11556 *
11557 * property samples:
11558 */
11559 __Pyx_XDECREF(__pyx_r);
11560 __pyx_t_2 = __Pyx_PyBytes_FromString((__pyx_v_self->__pyx_base.fields[8])); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 206, __pyx_L1_error)
11561 __Pyx_GOTREF(__pyx_t_2);
11562 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_split); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 206, __pyx_L1_error)
11563 __Pyx_GOTREF(__pyx_t_3);
11564 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
11565 __pyx_t_2 = NULL;
11566 __pyx_t_4 = 0;
11567 #if CYTHON_UNPACK_METHODS
11568 if (likely(PyMethod_Check(__pyx_t_3))) {
11569 __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_3);
11570 if (likely(__pyx_t_2)) {
11571 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
11572 __Pyx_INCREF(__pyx_t_2);
11573 __Pyx_INCREF(function);
11574 __Pyx_DECREF_SET(__pyx_t_3, function);
11575 __pyx_t_4 = 1;
11576 }
11577 }
11578 #endif
11579 {
11580 PyObject *__pyx_callargs[2] = {__pyx_t_2, __pyx_kp_u__3};
11581 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
11582 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
11583 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 206, __pyx_L1_error)
11584 __Pyx_GOTREF(__pyx_t_1);
11585 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
11586 }
11587 __pyx_r = __pyx_t_1;
11588 __pyx_t_1 = 0;
11589 goto __pyx_L0;
11590
11591 /* "pysam/libcvcf.pyx":205
11592 *
11593 * property format:
11594 * def __get__(self): # <<<<<<<<<<<<<<
11595 * return self.fields[8].split(':')
11596 *
11597 */
11598
11599 /* function exit code */
11600 __pyx_L1_error:;
11601 __Pyx_XDECREF(__pyx_t_1);
11602 __Pyx_XDECREF(__pyx_t_2);
11603 __Pyx_XDECREF(__pyx_t_3);
11604 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.format.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
11605 __pyx_r = NULL;
11606 __pyx_L0:;
11607 __Pyx_XGIVEREF(__pyx_r);
11608 __Pyx_RefNannyFinishContext();
11609 return __pyx_r;
11610 }
11611
11612 /* "pysam/libcvcf.pyx":209
11613 *
11614 * property samples:
11615 * def __get__(self): # <<<<<<<<<<<<<<
11616 * return self.vcf._samples
11617 *
11618 */
11619
11620 /* Python wrapper */
11621 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_7samples_1__get__(PyObject *__pyx_v_self); /*proto*/
11622 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_7samples_1__get__(PyObject *__pyx_v_self) {
11623 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
11624 PyObject *__pyx_r = 0;
11625 __Pyx_RefNannyDeclarations
11626 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
11627 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
11628 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_7samples___get__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self));
11629
11630 /* function exit code */
11631 __Pyx_RefNannyFinishContext();
11632 return __pyx_r;
11633 }
11634
11635 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_7samples___get__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self) {
11636 PyObject *__pyx_r = NULL;
11637 __Pyx_RefNannyDeclarations
11638 PyObject *__pyx_t_1 = NULL;
11639 int __pyx_lineno = 0;
11640 const char *__pyx_filename = NULL;
11641 int __pyx_clineno = 0;
11642 __Pyx_RefNannySetupContext("__get__", 1);
11643
11644 /* "pysam/libcvcf.pyx":210
11645 * property samples:
11646 * def __get__(self):
11647 * return self.vcf._samples # <<<<<<<<<<<<<<
11648 *
11649 * def __getitem__(self, key):
11650 */
11651 __Pyx_XDECREF(__pyx_r);
11652 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_samples); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 210, __pyx_L1_error)
11653 __Pyx_GOTREF(__pyx_t_1);
11654 __pyx_r = __pyx_t_1;
11655 __pyx_t_1 = 0;
11656 goto __pyx_L0;
11657
11658 /* "pysam/libcvcf.pyx":209
11659 *
11660 * property samples:
11661 * def __get__(self): # <<<<<<<<<<<<<<
11662 * return self.vcf._samples
11663 *
11664 */
11665
11666 /* function exit code */
11667 __pyx_L1_error:;
11668 __Pyx_XDECREF(__pyx_t_1);
11669 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.samples.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
11670 __pyx_r = NULL;
11671 __pyx_L0:;
11672 __Pyx_XGIVEREF(__pyx_r);
11673 __Pyx_RefNannyFinishContext();
11674 return __pyx_r;
11675 }
11676
11677 /* "pysam/libcvcf.pyx":212
11678 * return self.vcf._samples
11679 *
11680 * def __getitem__(self, key): # <<<<<<<<<<<<<<
11681 *
11682 * # parse sample columns
11683 */
11684
11685 /* Python wrapper */
11686 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_9__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key); /*proto*/
11687 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_9__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) {
11688 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
11689 PyObject *__pyx_r = 0;
11690 __Pyx_RefNannyDeclarations
11691 __Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0);
11692 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
11693 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_8__getitem__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self), ((PyObject *)__pyx_v_key));
11694
11695 /* function exit code */
11696 __Pyx_RefNannyFinishContext();
11697 return __pyx_r;
11698 }
11699
11700 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_8__getitem__(struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_key) {
11701 PyObject *__pyx_v_values = NULL;
11702 PyObject *__pyx_v_alt = NULL;
11703 PyObject *__pyx_v_format = NULL;
11704 PyObject *__pyx_v_result = NULL;
11705 Py_ssize_t __pyx_v_idx;
11706 PyObject *__pyx_v_expected = NULL;
11707 PyObject *__pyx_v_value = NULL;
11708 PyObject *__pyx_r = NULL;
11709 __Pyx_RefNannyDeclarations
11710 PyObject *__pyx_t_1 = NULL;
11711 PyObject *__pyx_t_2 = NULL;
11712 PyObject *__pyx_t_3 = NULL;
11713 Py_ssize_t __pyx_t_4;
11714 unsigned int __pyx_t_5;
11715 Py_ssize_t __pyx_t_6;
11716 int __pyx_t_7;
11717 PyObject *__pyx_t_8 = NULL;
11718 PyObject *__pyx_t_9 = NULL;
11719 Py_UCS4 __pyx_t_10;
11720 PyObject *__pyx_t_11 = NULL;
11721 Py_ssize_t __pyx_t_12;
11722 Py_ssize_t __pyx_t_13;
11723 int __pyx_t_14;
11724 PyObject *__pyx_t_15 = NULL;
11725 int __pyx_lineno = 0;
11726 const char *__pyx_filename = NULL;
11727 int __pyx_clineno = 0;
11728 __Pyx_RefNannySetupContext("__getitem__", 1);
11729
11730 /* "pysam/libcvcf.pyx":215
11731 *
11732 * # parse sample columns
11733 * values = self.fields[self.vcf._sample2column[key]].split(':') # <<<<<<<<<<<<<<
11734 * alt = self.alt
11735 * format = self.format
11736 */
11737 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_sample2column); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 215, __pyx_L1_error)
11738 __Pyx_GOTREF(__pyx_t_2);
11739 __pyx_t_3 = __Pyx_PyObject_GetItem(__pyx_t_2, __pyx_v_key); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 215, __pyx_L1_error)
11740 __Pyx_GOTREF(__pyx_t_3);
11741 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
11742 __pyx_t_4 = __Pyx_PyIndex_AsSsize_t(__pyx_t_3); if (unlikely((__pyx_t_4 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 215, __pyx_L1_error)
11743 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
11744 __pyx_t_3 = __Pyx_PyBytes_FromString((__pyx_v_self->__pyx_base.fields[__pyx_t_4])); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 215, __pyx_L1_error)
11745 __Pyx_GOTREF(__pyx_t_3);
11746 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_split); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 215, __pyx_L1_error)
11747 __Pyx_GOTREF(__pyx_t_2);
11748 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
11749 __pyx_t_3 = NULL;
11750 __pyx_t_5 = 0;
11751 #if CYTHON_UNPACK_METHODS
11752 if (likely(PyMethod_Check(__pyx_t_2))) {
11753 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
11754 if (likely(__pyx_t_3)) {
11755 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
11756 __Pyx_INCREF(__pyx_t_3);
11757 __Pyx_INCREF(function);
11758 __Pyx_DECREF_SET(__pyx_t_2, function);
11759 __pyx_t_5 = 1;
11760 }
11761 }
11762 #endif
11763 {
11764 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_kp_u__3};
11765 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
11766 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
11767 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 215, __pyx_L1_error)
11768 __Pyx_GOTREF(__pyx_t_1);
11769 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
11770 }
11771 __pyx_v_values = __pyx_t_1;
11772 __pyx_t_1 = 0;
11773
11774 /* "pysam/libcvcf.pyx":216
11775 * # parse sample columns
11776 * values = self.fields[self.vcf._sample2column[key]].split(':')
11777 * alt = self.alt # <<<<<<<<<<<<<<
11778 * format = self.format
11779 *
11780 */
11781 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_alt); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 216, __pyx_L1_error)
11782 __Pyx_GOTREF(__pyx_t_1);
11783 __pyx_v_alt = __pyx_t_1;
11784 __pyx_t_1 = 0;
11785
11786 /* "pysam/libcvcf.pyx":217
11787 * values = self.fields[self.vcf._sample2column[key]].split(':')
11788 * alt = self.alt
11789 * format = self.format # <<<<<<<<<<<<<<
11790 *
11791 * if len(values) > len(format):
11792 */
11793 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_format); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 217, __pyx_L1_error)
11794 __Pyx_GOTREF(__pyx_t_1);
11795 __pyx_v_format = __pyx_t_1;
11796 __pyx_t_1 = 0;
11797
11798 /* "pysam/libcvcf.pyx":219
11799 * format = self.format
11800 *
11801 * if len(values) > len(format): # <<<<<<<<<<<<<<
11802 * self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\
11803 * (len(values),key,len(format)))
11804 */
11805 __pyx_t_4 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_4 == ((Py_ssize_t)-1))) __PYX_ERR(0, 219, __pyx_L1_error)
11806 __pyx_t_6 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 219, __pyx_L1_error)
11807 __pyx_t_7 = (__pyx_t_4 > __pyx_t_6);
11808 if (__pyx_t_7) {
11809
11810 /* "pysam/libcvcf.pyx":220
11811 *
11812 * if len(values) > len(format):
11813 * self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\ # <<<<<<<<<<<<<<
11814 * (len(values),key,len(format)))
11815 *
11816 */
11817 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_error); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 220, __pyx_L1_error)
11818 __Pyx_GOTREF(__pyx_t_2);
11819 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_line); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 220, __pyx_L1_error)
11820 __Pyx_GOTREF(__pyx_t_3);
11821 __pyx_t_8 = __Pyx_PyObject_Unicode(__pyx_t_3); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 220, __pyx_L1_error)
11822 __Pyx_GOTREF(__pyx_t_8);
11823 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
11824 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_BAD_NUMBER_OF_VALUES); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 220, __pyx_L1_error)
11825 __Pyx_GOTREF(__pyx_t_3);
11826 __pyx_t_9 = PyTuple_New(7); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 220, __pyx_L1_error)
11827 __Pyx_GOTREF(__pyx_t_9);
11828 __pyx_t_6 = 0;
11829 __pyx_t_10 = 127;
11830 __Pyx_INCREF(__pyx_kp_u_found);
11831 __pyx_t_6 += 7;
11832 __Pyx_GIVEREF(__pyx_kp_u_found);
11833 PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_kp_u_found);
11834
11835 /* "pysam/libcvcf.pyx":221
11836 * if len(values) > len(format):
11837 * self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\
11838 * (len(values),key,len(format))) # <<<<<<<<<<<<<<
11839 *
11840 * result = {}
11841 */
11842 __pyx_t_4 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_4 == ((Py_ssize_t)-1))) __PYX_ERR(0, 221, __pyx_L1_error)
11843 __pyx_t_11 = __Pyx_PyUnicode_From_Py_ssize_t(__pyx_t_4, 0, ' ', 'd'); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 221, __pyx_L1_error)
11844 __Pyx_GOTREF(__pyx_t_11);
11845 __pyx_t_6 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_11);
11846 __Pyx_GIVEREF(__pyx_t_11);
11847 PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_11);
11848 __pyx_t_11 = 0;
11849 __Pyx_INCREF(__pyx_kp_u_values_in_element);
11850 __pyx_t_6 += 19;
11851 __Pyx_GIVEREF(__pyx_kp_u_values_in_element);
11852 PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_kp_u_values_in_element);
11853 __pyx_t_11 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_key), __pyx_empty_unicode); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 221, __pyx_L1_error)
11854 __Pyx_GOTREF(__pyx_t_11);
11855 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_11) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_11) : __pyx_t_10;
11856 __pyx_t_6 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_11);
11857 __Pyx_GIVEREF(__pyx_t_11);
11858 PyTuple_SET_ITEM(__pyx_t_9, 3, __pyx_t_11);
11859 __pyx_t_11 = 0;
11860 __Pyx_INCREF(__pyx_kp_u_expected);
11861 __pyx_t_6 += 11;
11862 __Pyx_GIVEREF(__pyx_kp_u_expected);
11863 PyTuple_SET_ITEM(__pyx_t_9, 4, __pyx_kp_u_expected);
11864 __pyx_t_4 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_4 == ((Py_ssize_t)-1))) __PYX_ERR(0, 221, __pyx_L1_error)
11865 __pyx_t_11 = __Pyx_PyUnicode_From_Py_ssize_t(__pyx_t_4, 0, ' ', 'd'); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 221, __pyx_L1_error)
11866 __Pyx_GOTREF(__pyx_t_11);
11867 __pyx_t_6 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_11);
11868 __Pyx_GIVEREF(__pyx_t_11);
11869 PyTuple_SET_ITEM(__pyx_t_9, 5, __pyx_t_11);
11870 __pyx_t_11 = 0;
11871 __Pyx_INCREF(__pyx_kp_u__8);
11872 __pyx_t_6 += 1;
11873 __Pyx_GIVEREF(__pyx_kp_u__8);
11874 PyTuple_SET_ITEM(__pyx_t_9, 6, __pyx_kp_u__8);
11875
11876 /* "pysam/libcvcf.pyx":220
11877 *
11878 * if len(values) > len(format):
11879 * self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\ # <<<<<<<<<<<<<<
11880 * (len(values),key,len(format)))
11881 *
11882 */
11883 __pyx_t_11 = __Pyx_PyUnicode_Join(__pyx_t_9, 7, __pyx_t_6, __pyx_t_10); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 220, __pyx_L1_error)
11884 __Pyx_GOTREF(__pyx_t_11);
11885 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
11886 __pyx_t_9 = NULL;
11887 __pyx_t_5 = 0;
11888 #if CYTHON_UNPACK_METHODS
11889 if (likely(PyMethod_Check(__pyx_t_2))) {
11890 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_2);
11891 if (likely(__pyx_t_9)) {
11892 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
11893 __Pyx_INCREF(__pyx_t_9);
11894 __Pyx_INCREF(function);
11895 __Pyx_DECREF_SET(__pyx_t_2, function);
11896 __pyx_t_5 = 1;
11897 }
11898 }
11899 #endif
11900 {
11901 PyObject *__pyx_callargs[4] = {__pyx_t_9, __pyx_t_8, __pyx_t_3, __pyx_t_11};
11902 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_5, 3+__pyx_t_5);
11903 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
11904 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
11905 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
11906 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
11907 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 220, __pyx_L1_error)
11908 __Pyx_GOTREF(__pyx_t_1);
11909 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
11910 }
11911 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
11912
11913 /* "pysam/libcvcf.pyx":219
11914 * format = self.format
11915 *
11916 * if len(values) > len(format): # <<<<<<<<<<<<<<
11917 * self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\
11918 * (len(values),key,len(format)))
11919 */
11920 }
11921
11922 /* "pysam/libcvcf.pyx":223
11923 * (len(values),key,len(format)))
11924 *
11925 * result = {} # <<<<<<<<<<<<<<
11926 * for idx in range(len(format)):
11927 * expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
11928 */
11929 __pyx_t_1 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 223, __pyx_L1_error)
11930 __Pyx_GOTREF(__pyx_t_1);
11931 __pyx_v_result = ((PyObject*)__pyx_t_1);
11932 __pyx_t_1 = 0;
11933
11934 /* "pysam/libcvcf.pyx":224
11935 *
11936 * result = {}
11937 * for idx in range(len(format)): # <<<<<<<<<<<<<<
11938 * expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
11939 * if idx < len(values): value = values[idx]
11940 */
11941 __pyx_t_6 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 224, __pyx_L1_error)
11942 __pyx_t_4 = __pyx_t_6;
11943 for (__pyx_t_12 = 0; __pyx_t_12 < __pyx_t_4; __pyx_t_12+=1) {
11944 __pyx_v_idx = __pyx_t_12;
11945
11946 /* "pysam/libcvcf.pyx":225
11947 * result = {}
11948 * for idx in range(len(format)):
11949 * expected = self.vcf.get_expected(format[idx], self.vcf._format, alt) # <<<<<<<<<<<<<<
11950 * if idx < len(values): value = values[idx]
11951 * else:
11952 */
11953 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_get_expected); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 225, __pyx_L1_error)
11954 __Pyx_GOTREF(__pyx_t_2);
11955 __pyx_t_11 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 225, __pyx_L1_error)
11956 __Pyx_GOTREF(__pyx_t_11);
11957 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_format_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 225, __pyx_L1_error)
11958 __Pyx_GOTREF(__pyx_t_3);
11959 __pyx_t_8 = NULL;
11960 __pyx_t_5 = 0;
11961 #if CYTHON_UNPACK_METHODS
11962 if (likely(PyMethod_Check(__pyx_t_2))) {
11963 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_2);
11964 if (likely(__pyx_t_8)) {
11965 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
11966 __Pyx_INCREF(__pyx_t_8);
11967 __Pyx_INCREF(function);
11968 __Pyx_DECREF_SET(__pyx_t_2, function);
11969 __pyx_t_5 = 1;
11970 }
11971 }
11972 #endif
11973 {
11974 PyObject *__pyx_callargs[4] = {__pyx_t_8, __pyx_t_11, __pyx_t_3, __pyx_v_alt};
11975 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_5, 3+__pyx_t_5);
11976 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
11977 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
11978 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
11979 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 225, __pyx_L1_error)
11980 __Pyx_GOTREF(__pyx_t_1);
11981 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
11982 }
11983 __Pyx_XDECREF_SET(__pyx_v_expected, __pyx_t_1);
11984 __pyx_t_1 = 0;
11985
11986 /* "pysam/libcvcf.pyx":226
11987 * for idx in range(len(format)):
11988 * expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
11989 * if idx < len(values): value = values[idx] # <<<<<<<<<<<<<<
11990 * else:
11991 * if expected == -1: value = "."
11992 */
11993 __pyx_t_13 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_13 == ((Py_ssize_t)-1))) __PYX_ERR(0, 226, __pyx_L1_error)
11994 __pyx_t_7 = (__pyx_v_idx < __pyx_t_13);
11995 if (__pyx_t_7) {
11996 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_values, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 226, __pyx_L1_error)
11997 __Pyx_GOTREF(__pyx_t_1);
11998 __Pyx_XDECREF_SET(__pyx_v_value, __pyx_t_1);
11999 __pyx_t_1 = 0;
12000 goto __pyx_L6;
12001 }
12002
12003 /* "pysam/libcvcf.pyx":228
12004 * if idx < len(values): value = values[idx]
12005 * else:
12006 * if expected == -1: value = "." # <<<<<<<<<<<<<<
12007 * else: value = ",".join(["."]*expected)
12008 *
12009 */
12010 /*else*/ {
12011 __pyx_t_7 = (__Pyx_PyInt_BoolEqObjC(__pyx_v_expected, __pyx_int_neg_1, -1L, 0)); if (unlikely((__pyx_t_7 < 0))) __PYX_ERR(0, 228, __pyx_L1_error)
12012 if (__pyx_t_7) {
12013 __Pyx_INCREF(__pyx_kp_u__5);
12014 __Pyx_XDECREF_SET(__pyx_v_value, __pyx_kp_u__5);
12015 goto __pyx_L7;
12016 }
12017
12018 /* "pysam/libcvcf.pyx":229
12019 * else:
12020 * if expected == -1: value = "."
12021 * else: value = ",".join(["."]*expected) # <<<<<<<<<<<<<<
12022 *
12023 * result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data))
12024 */
12025 /*else*/ {
12026 __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 229, __pyx_L1_error)
12027 __Pyx_GOTREF(__pyx_t_1);
12028 __Pyx_INCREF(__pyx_kp_u__5);
12029 __Pyx_GIVEREF(__pyx_kp_u__5);
12030 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_kp_u__5)) __PYX_ERR(0, 229, __pyx_L1_error);
12031 { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_1, __pyx_v_expected); if (unlikely(!__pyx_temp)) __PYX_ERR(0, 229, __pyx_L1_error)
12032 __Pyx_GOTREF(__pyx_temp);
12033 __Pyx_DECREF(__pyx_t_1);
12034 __pyx_t_1 = __pyx_temp;
12035 }
12036 __pyx_t_2 = PyUnicode_Join(__pyx_kp_u__2, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 229, __pyx_L1_error)
12037 __Pyx_GOTREF(__pyx_t_2);
12038 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
12039 __Pyx_XDECREF_SET(__pyx_v_value, __pyx_t_2);
12040 __pyx_t_2 = 0;
12041 }
12042 __pyx_L7:;
12043 }
12044 __pyx_L6:;
12045
12046 /* "pysam/libcvcf.pyx":231
12047 * else: value = ",".join(["."]*expected)
12048 *
12049 * result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data)) # <<<<<<<<<<<<<<
12050 * if expected != -1 and len(result[format[idx]]) != expected:
12051 * self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
12052 */
12053 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_parse_formatdata); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 231, __pyx_L1_error)
12054 __Pyx_GOTREF(__pyx_t_1);
12055 __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 231, __pyx_L1_error)
12056 __Pyx_GOTREF(__pyx_t_3);
12057 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_format_2); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 231, __pyx_L1_error)
12058 __Pyx_GOTREF(__pyx_t_11);
12059 __pyx_t_8 = __Pyx_PyBytes_FromString(__pyx_v_self->__pyx_base.data); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 231, __pyx_L1_error)
12060 __Pyx_GOTREF(__pyx_t_8);
12061 __pyx_t_9 = __Pyx_PyObject_Unicode(__pyx_t_8); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 231, __pyx_L1_error)
12062 __Pyx_GOTREF(__pyx_t_9);
12063 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
12064 __pyx_t_8 = NULL;
12065 __pyx_t_5 = 0;
12066 #if CYTHON_UNPACK_METHODS
12067 if (likely(PyMethod_Check(__pyx_t_1))) {
12068 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_1);
12069 if (likely(__pyx_t_8)) {
12070 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
12071 __Pyx_INCREF(__pyx_t_8);
12072 __Pyx_INCREF(function);
12073 __Pyx_DECREF_SET(__pyx_t_1, function);
12074 __pyx_t_5 = 1;
12075 }
12076 }
12077 #endif
12078 {
12079 PyObject *__pyx_callargs[5] = {__pyx_t_8, __pyx_t_3, __pyx_v_value, __pyx_t_11, __pyx_t_9};
12080 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_5, 4+__pyx_t_5);
12081 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
12082 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
12083 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
12084 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
12085 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 231, __pyx_L1_error)
12086 __Pyx_GOTREF(__pyx_t_2);
12087 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
12088 }
12089 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 231, __pyx_L1_error)
12090 __Pyx_GOTREF(__pyx_t_1);
12091 if (unlikely((PyDict_SetItem(__pyx_v_result, __pyx_t_1, __pyx_t_2) < 0))) __PYX_ERR(0, 231, __pyx_L1_error)
12092 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
12093 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
12094
12095 /* "pysam/libcvcf.pyx":232
12096 *
12097 * result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data))
12098 * if expected != -1 and len(result[format[idx]]) != expected: # <<<<<<<<<<<<<<
12099 * self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
12100 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
12101 */
12102 __pyx_t_14 = (__Pyx_PyInt_BoolNeObjC(__pyx_v_expected, __pyx_int_neg_1, -1L, 0)); if (unlikely((__pyx_t_14 < 0))) __PYX_ERR(0, 232, __pyx_L1_error)
12103 if (__pyx_t_14) {
12104 } else {
12105 __pyx_t_7 = __pyx_t_14;
12106 goto __pyx_L9_bool_binop_done;
12107 }
12108 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 232, __pyx_L1_error)
12109 __Pyx_GOTREF(__pyx_t_2);
12110 __pyx_t_1 = __Pyx_PyDict_GetItem(__pyx_v_result, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 232, __pyx_L1_error)
12111 __Pyx_GOTREF(__pyx_t_1);
12112 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
12113 __pyx_t_13 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_13 == ((Py_ssize_t)-1))) __PYX_ERR(0, 232, __pyx_L1_error)
12114 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
12115 __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_13); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 232, __pyx_L1_error)
12116 __Pyx_GOTREF(__pyx_t_1);
12117 __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_v_expected, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 232, __pyx_L1_error)
12118 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
12119 __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_14 < 0))) __PYX_ERR(0, 232, __pyx_L1_error)
12120 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
12121 __pyx_t_7 = __pyx_t_14;
12122 __pyx_L9_bool_binop_done:;
12123 if (__pyx_t_7) {
12124
12125 /* "pysam/libcvcf.pyx":233
12126 * result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data))
12127 * if expected != -1 and len(result[format[idx]]) != expected:
12128 * self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS, # <<<<<<<<<<<<<<
12129 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
12130 * if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
12131 */
12132 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->vcf, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 233, __pyx_L1_error)
12133 __Pyx_GOTREF(__pyx_t_1);
12134 __pyx_t_9 = __Pyx_PyBytes_FromString(__pyx_v_self->__pyx_base.data); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 233, __pyx_L1_error)
12135 __Pyx_GOTREF(__pyx_t_9);
12136 __pyx_t_11 = __Pyx_PyObject_Unicode(__pyx_t_9); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 233, __pyx_L1_error)
12137 __Pyx_GOTREF(__pyx_t_11);
12138 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
12139 __pyx_t_9 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_BAD_NUMBER_OF_PARAMETERS); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 233, __pyx_L1_error)
12140 __Pyx_GOTREF(__pyx_t_9);
12141
12142 /* "pysam/libcvcf.pyx":234
12143 * if expected != -1 and len(result[format[idx]]) != expected:
12144 * self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
12145 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]])) # <<<<<<<<<<<<<<
12146 * if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
12147 * result[format[idx]] = result[format[idx]][:expected]
12148 */
12149 __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 234, __pyx_L1_error)
12150 __Pyx_GOTREF(__pyx_t_3);
12151 __pyx_t_13 = 0;
12152 __pyx_t_10 = 127;
12153 __Pyx_INCREF(__pyx_kp_u_id);
12154 __pyx_t_13 += 3;
12155 __Pyx_GIVEREF(__pyx_kp_u_id);
12156 PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_kp_u_id);
12157 __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 234, __pyx_L1_error)
12158 __Pyx_GOTREF(__pyx_t_8);
12159 __pyx_t_15 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_8), __pyx_empty_unicode); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 234, __pyx_L1_error)
12160 __Pyx_GOTREF(__pyx_t_15);
12161 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
12162 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_15) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_15) : __pyx_t_10;
12163 __pyx_t_13 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_15);
12164 __Pyx_GIVEREF(__pyx_t_15);
12165 PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_15);
12166 __pyx_t_15 = 0;
12167 __Pyx_INCREF(__pyx_kp_u_expected_2);
12168 __pyx_t_13 += 11;
12169 __Pyx_GIVEREF(__pyx_kp_u_expected_2);
12170 PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_kp_u_expected_2);
12171 __pyx_t_15 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_expected), __pyx_empty_unicode); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 234, __pyx_L1_error)
12172 __Pyx_GOTREF(__pyx_t_15);
12173 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_15) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_15) : __pyx_t_10;
12174 __pyx_t_13 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_15);
12175 __Pyx_GIVEREF(__pyx_t_15);
12176 PyTuple_SET_ITEM(__pyx_t_3, 3, __pyx_t_15);
12177 __pyx_t_15 = 0;
12178 __Pyx_INCREF(__pyx_kp_u_parameters_got);
12179 __pyx_t_13 += 17;
12180 __Pyx_GIVEREF(__pyx_kp_u_parameters_got);
12181 PyTuple_SET_ITEM(__pyx_t_3, 4, __pyx_kp_u_parameters_got);
12182 __pyx_t_15 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 234, __pyx_L1_error)
12183 __Pyx_GOTREF(__pyx_t_15);
12184 __pyx_t_8 = __Pyx_PyDict_GetItem(__pyx_v_result, __pyx_t_15); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 234, __pyx_L1_error)
12185 __Pyx_GOTREF(__pyx_t_8);
12186 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
12187 __pyx_t_15 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_8), __pyx_empty_unicode); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 234, __pyx_L1_error)
12188 __Pyx_GOTREF(__pyx_t_15);
12189 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
12190 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_15) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_15) : __pyx_t_10;
12191 __pyx_t_13 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_15);
12192 __Pyx_GIVEREF(__pyx_t_15);
12193 PyTuple_SET_ITEM(__pyx_t_3, 5, __pyx_t_15);
12194 __pyx_t_15 = 0;
12195 __pyx_t_15 = __Pyx_PyUnicode_Join(__pyx_t_3, 6, __pyx_t_13, __pyx_t_10); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 234, __pyx_L1_error)
12196 __Pyx_GOTREF(__pyx_t_15);
12197 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
12198 __pyx_t_3 = NULL;
12199 __pyx_t_5 = 0;
12200 #if CYTHON_UNPACK_METHODS
12201 if (likely(PyMethod_Check(__pyx_t_1))) {
12202 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_1);
12203 if (likely(__pyx_t_3)) {
12204 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
12205 __Pyx_INCREF(__pyx_t_3);
12206 __Pyx_INCREF(function);
12207 __Pyx_DECREF_SET(__pyx_t_1, function);
12208 __pyx_t_5 = 1;
12209 }
12210 }
12211 #endif
12212 {
12213 PyObject *__pyx_callargs[4] = {__pyx_t_3, __pyx_t_11, __pyx_t_9, __pyx_t_15};
12214 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_5, 3+__pyx_t_5);
12215 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
12216 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
12217 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
12218 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
12219 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 233, __pyx_L1_error)
12220 __Pyx_GOTREF(__pyx_t_2);
12221 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
12222 }
12223 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
12224
12225 /* "pysam/libcvcf.pyx":235
12226 * self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
12227 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
12228 * if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]])) # <<<<<<<<<<<<<<
12229 * result[format[idx]] = result[format[idx]][:expected]
12230 *
12231 */
12232 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 235, __pyx_L1_error)
12233 __Pyx_GOTREF(__pyx_t_2);
12234 __pyx_t_1 = __Pyx_PyDict_GetItem(__pyx_v_result, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 235, __pyx_L1_error)
12235 __Pyx_GOTREF(__pyx_t_1);
12236 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
12237 __pyx_t_13 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_13 == ((Py_ssize_t)-1))) __PYX_ERR(0, 235, __pyx_L1_error)
12238 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
12239 __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_13); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 235, __pyx_L1_error)
12240 __Pyx_GOTREF(__pyx_t_1);
12241 __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_v_expected, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 235, __pyx_L1_error)
12242 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
12243 __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_7 < 0))) __PYX_ERR(0, 235, __pyx_L1_error)
12244 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
12245 if (__pyx_t_7) {
12246 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 235, __pyx_L1_error)
12247 __Pyx_GOTREF(__pyx_t_2);
12248 __pyx_t_1 = __Pyx_PyDict_GetItem(__pyx_v_result, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 235, __pyx_L1_error)
12249 __Pyx_GOTREF(__pyx_t_1);
12250 __pyx_t_15 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 235, __pyx_L1_error)
12251 __Pyx_GOTREF(__pyx_t_15);
12252 __pyx_t_9 = __Pyx_PyDict_GetItem(__pyx_v_result, __pyx_t_15); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 235, __pyx_L1_error)
12253 __Pyx_GOTREF(__pyx_t_9);
12254 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
12255 __pyx_t_15 = __Pyx_GetItemInt(__pyx_t_9, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 235, __pyx_L1_error)
12256 __Pyx_GOTREF(__pyx_t_15);
12257 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
12258 __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 235, __pyx_L1_error)
12259 __Pyx_GOTREF(__pyx_t_9);
12260 __pyx_t_11 = __Pyx_PyDict_GetItem(__pyx_v_result, __pyx_t_9); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 235, __pyx_L1_error)
12261 __Pyx_GOTREF(__pyx_t_11);
12262 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
12263 __pyx_t_13 = PyObject_Length(__pyx_t_11); if (unlikely(__pyx_t_13 == ((Py_ssize_t)-1))) __PYX_ERR(0, 235, __pyx_L1_error)
12264 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
12265 __pyx_t_11 = PyInt_FromSsize_t(__pyx_t_13); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 235, __pyx_L1_error)
12266 __Pyx_GOTREF(__pyx_t_11);
12267 __pyx_t_9 = PyNumber_Subtract(__pyx_v_expected, __pyx_t_11); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 235, __pyx_L1_error)
12268 __Pyx_GOTREF(__pyx_t_9);
12269 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
12270 __pyx_t_11 = PyList_New(1); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 235, __pyx_L1_error)
12271 __Pyx_GOTREF(__pyx_t_11);
12272 __Pyx_GIVEREF(__pyx_t_15);
12273 if (__Pyx_PyList_SET_ITEM(__pyx_t_11, 0, __pyx_t_15)) __PYX_ERR(0, 235, __pyx_L1_error);
12274 { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_11, __pyx_t_9); if (unlikely(!__pyx_temp)) __PYX_ERR(0, 235, __pyx_L1_error)
12275 __Pyx_GOTREF(__pyx_temp);
12276 __Pyx_DECREF(__pyx_t_11);
12277 __pyx_t_11 = __pyx_temp;
12278 }
12279 __pyx_t_15 = 0;
12280 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
12281 __pyx_t_9 = PyNumber_InPlaceAdd(__pyx_t_1, __pyx_t_11); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 235, __pyx_L1_error)
12282 __Pyx_GOTREF(__pyx_t_9);
12283 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
12284 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
12285 if (unlikely((PyDict_SetItem(__pyx_v_result, __pyx_t_2, __pyx_t_9) < 0))) __PYX_ERR(0, 235, __pyx_L1_error)
12286 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
12287 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
12288 }
12289
12290 /* "pysam/libcvcf.pyx":236
12291 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
12292 * if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
12293 * result[format[idx]] = result[format[idx]][:expected] # <<<<<<<<<<<<<<
12294 *
12295 * return result
12296 */
12297 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 236, __pyx_L1_error)
12298 __Pyx_GOTREF(__pyx_t_2);
12299 __pyx_t_9 = __Pyx_PyDict_GetItem(__pyx_v_result, __pyx_t_2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 236, __pyx_L1_error)
12300 __Pyx_GOTREF(__pyx_t_9);
12301 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
12302 __pyx_t_2 = __Pyx_PyObject_GetSlice(__pyx_t_9, 0, 0, NULL, &__pyx_v_expected, NULL, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 236, __pyx_L1_error)
12303 __Pyx_GOTREF(__pyx_t_2);
12304 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
12305 __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 236, __pyx_L1_error)
12306 __Pyx_GOTREF(__pyx_t_9);
12307 if (unlikely((PyDict_SetItem(__pyx_v_result, __pyx_t_9, __pyx_t_2) < 0))) __PYX_ERR(0, 236, __pyx_L1_error)
12308 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
12309 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
12310
12311 /* "pysam/libcvcf.pyx":232
12312 *
12313 * result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data))
12314 * if expected != -1 and len(result[format[idx]]) != expected: # <<<<<<<<<<<<<<
12315 * self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
12316 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
12317 */
12318 }
12319 }
12320
12321 /* "pysam/libcvcf.pyx":238
12322 * result[format[idx]] = result[format[idx]][:expected]
12323 *
12324 * return result # <<<<<<<<<<<<<<
12325 *
12326 *
12327 */
12328 __Pyx_XDECREF(__pyx_r);
12329 __Pyx_INCREF(__pyx_v_result);
12330 __pyx_r = __pyx_v_result;
12331 goto __pyx_L0;
12332
12333 /* "pysam/libcvcf.pyx":212
12334 * return self.vcf._samples
12335 *
12336 * def __getitem__(self, key): # <<<<<<<<<<<<<<
12337 *
12338 * # parse sample columns
12339 */
12340
12341 /* function exit code */
12342 __pyx_L1_error:;
12343 __Pyx_XDECREF(__pyx_t_1);
12344 __Pyx_XDECREF(__pyx_t_2);
12345 __Pyx_XDECREF(__pyx_t_3);
12346 __Pyx_XDECREF(__pyx_t_8);
12347 __Pyx_XDECREF(__pyx_t_9);
12348 __Pyx_XDECREF(__pyx_t_11);
12349 __Pyx_XDECREF(__pyx_t_15);
12350 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename);
12351 __pyx_r = NULL;
12352 __pyx_L0:;
12353 __Pyx_XDECREF(__pyx_v_values);
12354 __Pyx_XDECREF(__pyx_v_alt);
12355 __Pyx_XDECREF(__pyx_v_format);
12356 __Pyx_XDECREF(__pyx_v_result);
12357 __Pyx_XDECREF(__pyx_v_expected);
12358 __Pyx_XDECREF(__pyx_v_value);
12359 __Pyx_XGIVEREF(__pyx_r);
12360 __Pyx_RefNannyFinishContext();
12361 return __pyx_r;
12362 }
12363
12364 /* "(tree fragment)":1
12365 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
12366 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
12367 * def __setstate_cython__(self, __pyx_state):
12368 */
12369
12370 /* Python wrapper */
12371 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_11__reduce_cython__(PyObject *__pyx_v_self,
12372 #if CYTHON_METH_FASTCALL
12373 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
12374 #else
12375 PyObject *__pyx_args, PyObject *__pyx_kwds
12376 #endif
12377 ); /*proto*/
12378 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_9VCFRecord_10__reduce_cython__, "VCFRecord.__reduce_cython__(self)");
12379 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_9VCFRecord_11__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_9VCFRecord_11__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_9VCFRecord_10__reduce_cython__};
12380 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_11__reduce_cython__(PyObject *__pyx_v_self,
12381 #if CYTHON_METH_FASTCALL
12382 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
12383 #else
12384 PyObject *__pyx_args, PyObject *__pyx_kwds
12385 #endif
12386 ) {
12387 #if !CYTHON_METH_FASTCALL
12388 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
12389 #endif
12390 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
12391 PyObject *__pyx_r = 0;
12392 __Pyx_RefNannyDeclarations
12393 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
12394 #if !CYTHON_METH_FASTCALL
12395 #if CYTHON_ASSUME_SAFE_MACROS
12396 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
12397 #else
12398 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
12399 #endif
12400 #endif
12401 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
12402 if (unlikely(__pyx_nargs > 0)) {
12403 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
12404 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
12405 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_10__reduce_cython__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self));
12406
12407 /* function exit code */
12408 __Pyx_RefNannyFinishContext();
12409 return __pyx_r;
12410 }
12411
12412 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_10__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self) {
12413 PyObject *__pyx_r = NULL;
12414 __Pyx_RefNannyDeclarations
12415 int __pyx_lineno = 0;
12416 const char *__pyx_filename = NULL;
12417 int __pyx_clineno = 0;
12418 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
12419
12420 /* "(tree fragment)":2
12421 * def __reduce_cython__(self):
12422 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<<
12423 * def __setstate_cython__(self, __pyx_state):
12424 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
12425 */
12426 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0);
12427 __PYX_ERR(1, 2, __pyx_L1_error)
12428
12429 /* "(tree fragment)":1
12430 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
12431 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
12432 * def __setstate_cython__(self, __pyx_state):
12433 */
12434
12435 /* function exit code */
12436 __pyx_L1_error:;
12437 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
12438 __pyx_r = NULL;
12439 __Pyx_XGIVEREF(__pyx_r);
12440 __Pyx_RefNannyFinishContext();
12441 return __pyx_r;
12442 }
12443
12444 /* "(tree fragment)":3
12445 * def __reduce_cython__(self):
12446 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
12447 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
12448 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
12449 */
12450
12451 /* Python wrapper */
12452 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_13__setstate_cython__(PyObject *__pyx_v_self,
12453 #if CYTHON_METH_FASTCALL
12454 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
12455 #else
12456 PyObject *__pyx_args, PyObject *__pyx_kwds
12457 #endif
12458 ); /*proto*/
12459 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_9VCFRecord_12__setstate_cython__, "VCFRecord.__setstate_cython__(self, __pyx_state)");
12460 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_9VCFRecord_13__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_9VCFRecord_13__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_9VCFRecord_12__setstate_cython__};
12461 static PyObject *__pyx_pw_5pysam_7libcvcf_9VCFRecord_13__setstate_cython__(PyObject *__pyx_v_self,
12462 #if CYTHON_METH_FASTCALL
12463 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
12464 #else
12465 PyObject *__pyx_args, PyObject *__pyx_kwds
12466 #endif
12467 ) {
12468 CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0;
12469 #if !CYTHON_METH_FASTCALL
12470 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
12471 #endif
12472 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
12473 PyObject* values[1] = {0};
12474 int __pyx_lineno = 0;
12475 const char *__pyx_filename = NULL;
12476 int __pyx_clineno = 0;
12477 PyObject *__pyx_r = 0;
12478 __Pyx_RefNannyDeclarations
12479 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
12480 #if !CYTHON_METH_FASTCALL
12481 #if CYTHON_ASSUME_SAFE_MACROS
12482 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
12483 #else
12484 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
12485 #endif
12486 #endif
12487 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
12488 {
12489 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
12490 if (__pyx_kwds) {
12491 Py_ssize_t kw_args;
12492 switch (__pyx_nargs) {
12493 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
12494 CYTHON_FALLTHROUGH;
12495 case 0: break;
12496 default: goto __pyx_L5_argtuple_error;
12497 }
12498 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
12499 switch (__pyx_nargs) {
12500 case 0:
12501 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
12502 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
12503 kw_args--;
12504 }
12505 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error)
12506 else goto __pyx_L5_argtuple_error;
12507 }
12508 if (unlikely(kw_args > 0)) {
12509 const Py_ssize_t kwd_pos_args = __pyx_nargs;
12510 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error)
12511 }
12512 } else if (unlikely(__pyx_nargs != 1)) {
12513 goto __pyx_L5_argtuple_error;
12514 } else {
12515 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
12516 }
12517 __pyx_v___pyx_state = values[0];
12518 }
12519 goto __pyx_L6_skip;
12520 __pyx_L5_argtuple_error:;
12521 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error)
12522 __pyx_L6_skip:;
12523 goto __pyx_L4_argument_unpacking_done;
12524 __pyx_L3_error:;
12525 {
12526 Py_ssize_t __pyx_temp;
12527 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
12528 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
12529 }
12530 }
12531 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
12532 __Pyx_RefNannyFinishContext();
12533 return NULL;
12534 __pyx_L4_argument_unpacking_done:;
12535 __pyx_r = __pyx_pf_5pysam_7libcvcf_9VCFRecord_12__setstate_cython__(((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_v_self), __pyx_v___pyx_state);
12536
12537 /* function exit code */
12538 {
12539 Py_ssize_t __pyx_temp;
12540 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
12541 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
12542 }
12543 }
12544 __Pyx_RefNannyFinishContext();
12545 return __pyx_r;
12546 }
12547
12548 static PyObject *__pyx_pf_5pysam_7libcvcf_9VCFRecord_12__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
12549 PyObject *__pyx_r = NULL;
12550 __Pyx_RefNannyDeclarations
12551 int __pyx_lineno = 0;
12552 const char *__pyx_filename = NULL;
12553 int __pyx_clineno = 0;
12554 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
12555
12556 /* "(tree fragment)":4
12557 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
12558 * def __setstate_cython__(self, __pyx_state):
12559 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<<
12560 */
12561 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0);
12562 __PYX_ERR(1, 4, __pyx_L1_error)
12563
12564 /* "(tree fragment)":3
12565 * def __reduce_cython__(self):
12566 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
12567 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
12568 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
12569 */
12570
12571 /* function exit code */
12572 __pyx_L1_error:;
12573 __Pyx_AddTraceback("pysam.libcvcf.VCFRecord.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
12574 __pyx_r = NULL;
12575 __Pyx_XGIVEREF(__pyx_r);
12576 __Pyx_RefNannyFinishContext();
12577 return __pyx_r;
12578 }
12579
12580 /* "pysam/libcvcf.pyx":244
12581 * '''converts a :term:`tabix row` into a VCF record.'''
12582 * cdef vcffile
12583 * def __init__(self, vcffile): # <<<<<<<<<<<<<<
12584 * self.vcffile = vcffile
12585 *
12586 */
12587
12588 /* Python wrapper */
12589 static int __pyx_pw_5pysam_7libcvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
12590 static int __pyx_pw_5pysam_7libcvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
12591 PyObject *__pyx_v_vcffile = 0;
12592 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
12593 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
12594 PyObject* values[1] = {0};
12595 int __pyx_lineno = 0;
12596 const char *__pyx_filename = NULL;
12597 int __pyx_clineno = 0;
12598 int __pyx_r;
12599 __Pyx_RefNannyDeclarations
12600 __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
12601 #if CYTHON_ASSUME_SAFE_MACROS
12602 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
12603 #else
12604 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1;
12605 #endif
12606 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
12607 {
12608 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_vcffile,0};
12609 if (__pyx_kwds) {
12610 Py_ssize_t kw_args;
12611 switch (__pyx_nargs) {
12612 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
12613 CYTHON_FALLTHROUGH;
12614 case 0: break;
12615 default: goto __pyx_L5_argtuple_error;
12616 }
12617 kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds);
12618 switch (__pyx_nargs) {
12619 case 0:
12620 if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_vcffile)) != 0)) {
12621 (void)__Pyx_Arg_NewRef_VARARGS(values[0]);
12622 kw_args--;
12623 }
12624 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 244, __pyx_L3_error)
12625 else goto __pyx_L5_argtuple_error;
12626 }
12627 if (unlikely(kw_args > 0)) {
12628 const Py_ssize_t kwd_pos_args = __pyx_nargs;
12629 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 244, __pyx_L3_error)
12630 }
12631 } else if (unlikely(__pyx_nargs != 1)) {
12632 goto __pyx_L5_argtuple_error;
12633 } else {
12634 values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
12635 }
12636 __pyx_v_vcffile = values[0];
12637 }
12638 goto __pyx_L6_skip;
12639 __pyx_L5_argtuple_error:;
12640 __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 244, __pyx_L3_error)
12641 __pyx_L6_skip:;
12642 goto __pyx_L4_argument_unpacking_done;
12643 __pyx_L3_error:;
12644 {
12645 Py_ssize_t __pyx_temp;
12646 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
12647 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
12648 }
12649 }
12650 __Pyx_AddTraceback("pysam.libcvcf.asVCFRecord.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
12651 __Pyx_RefNannyFinishContext();
12652 return -1;
12653 __pyx_L4_argument_unpacking_done:;
12654 __pyx_r = __pyx_pf_5pysam_7libcvcf_11asVCFRecord___init__(((struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *)__pyx_v_self), __pyx_v_vcffile);
12655
12656 /* function exit code */
12657 {
12658 Py_ssize_t __pyx_temp;
12659 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
12660 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
12661 }
12662 }
12663 __Pyx_RefNannyFinishContext();
12664 return __pyx_r;
12665 }
12666
12667 static int __pyx_pf_5pysam_7libcvcf_11asVCFRecord___init__(struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v_vcffile) {
12668 int __pyx_r;
12669 __Pyx_RefNannyDeclarations
12670 __Pyx_RefNannySetupContext("__init__", 1);
12671
12672 /* "pysam/libcvcf.pyx":245
12673 * cdef vcffile
12674 * def __init__(self, vcffile):
12675 * self.vcffile = vcffile # <<<<<<<<<<<<<<
12676 *
12677 * cdef parse(self, char * buffer, int len):
12678 */
12679 __Pyx_INCREF(__pyx_v_vcffile);
12680 __Pyx_GIVEREF(__pyx_v_vcffile);
12681 __Pyx_GOTREF(__pyx_v_self->vcffile);
12682 __Pyx_DECREF(__pyx_v_self->vcffile);
12683 __pyx_v_self->vcffile = __pyx_v_vcffile;
12684
12685 /* "pysam/libcvcf.pyx":244
12686 * '''converts a :term:`tabix row` into a VCF record.'''
12687 * cdef vcffile
12688 * def __init__(self, vcffile): # <<<<<<<<<<<<<<
12689 * self.vcffile = vcffile
12690 *
12691 */
12692
12693 /* function exit code */
12694 __pyx_r = 0;
12695 __Pyx_RefNannyFinishContext();
12696 return __pyx_r;
12697 }
12698
12699 /* "pysam/libcvcf.pyx":247
12700 * self.vcffile = vcffile
12701 *
12702 * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<<
12703 * cdef VCFRecord r
12704 * r = VCFRecord(self.vcffile)
12705 */
12706
12707 static PyObject *__pyx_f_5pysam_7libcvcf_11asVCFRecord_parse(struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) {
12708 struct __pyx_obj_5pysam_7libcvcf_VCFRecord *__pyx_v_r = 0;
12709 PyObject *__pyx_r = NULL;
12710 __Pyx_RefNannyDeclarations
12711 PyObject *__pyx_t_1 = NULL;
12712 int __pyx_lineno = 0;
12713 const char *__pyx_filename = NULL;
12714 int __pyx_clineno = 0;
12715 __Pyx_RefNannySetupContext("parse", 1);
12716
12717 /* "pysam/libcvcf.pyx":249
12718 * cdef parse(self, char * buffer, int len):
12719 * cdef VCFRecord r
12720 * r = VCFRecord(self.vcffile) # <<<<<<<<<<<<<<
12721 * r.copy(buffer, len)
12722 * return r
12723 */
12724 __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_7libcvcf_VCFRecord), __pyx_v_self->vcffile); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 249, __pyx_L1_error)
12725 __Pyx_GOTREF(__pyx_t_1);
12726 __pyx_v_r = ((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)__pyx_t_1);
12727 __pyx_t_1 = 0;
12728
12729 /* "pysam/libcvcf.pyx":250
12730 * cdef VCFRecord r
12731 * r = VCFRecord(self.vcffile)
12732 * r.copy(buffer, len) # <<<<<<<<<<<<<<
12733 * return r
12734 *
12735 */
12736 __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_7libcvcf_VCFRecord *)__pyx_v_r->__pyx_base.__pyx_vtab)->__pyx_base.copy(((struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 250, __pyx_L1_error)
12737 __Pyx_GOTREF(__pyx_t_1);
12738 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
12739
12740 /* "pysam/libcvcf.pyx":251
12741 * r = VCFRecord(self.vcffile)
12742 * r.copy(buffer, len)
12743 * return r # <<<<<<<<<<<<<<
12744 *
12745 * class VCF(object):
12746 */
12747 __Pyx_XDECREF(__pyx_r);
12748 __Pyx_INCREF((PyObject *)__pyx_v_r);
12749 __pyx_r = ((PyObject *)__pyx_v_r);
12750 goto __pyx_L0;
12751
12752 /* "pysam/libcvcf.pyx":247
12753 * self.vcffile = vcffile
12754 *
12755 * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<<
12756 * cdef VCFRecord r
12757 * r = VCFRecord(self.vcffile)
12758 */
12759
12760 /* function exit code */
12761 __pyx_L1_error:;
12762 __Pyx_XDECREF(__pyx_t_1);
12763 __Pyx_AddTraceback("pysam.libcvcf.asVCFRecord.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
12764 __pyx_r = 0;
12765 __pyx_L0:;
12766 __Pyx_XDECREF((PyObject *)__pyx_v_r);
12767 __Pyx_XGIVEREF(__pyx_r);
12768 __Pyx_RefNannyFinishContext();
12769 return __pyx_r;
12770 }
12771
12772 /* "(tree fragment)":1
12773 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
12774 * cdef tuple state
12775 * cdef object _dict
12776 */
12777
12778 /* Python wrapper */
12779 static PyObject *__pyx_pw_5pysam_7libcvcf_11asVCFRecord_3__reduce_cython__(PyObject *__pyx_v_self,
12780 #if CYTHON_METH_FASTCALL
12781 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
12782 #else
12783 PyObject *__pyx_args, PyObject *__pyx_kwds
12784 #endif
12785 ); /*proto*/
12786 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_11asVCFRecord_2__reduce_cython__, "asVCFRecord.__reduce_cython__(self)");
12787 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_11asVCFRecord_3__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_11asVCFRecord_3__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_11asVCFRecord_2__reduce_cython__};
12788 static PyObject *__pyx_pw_5pysam_7libcvcf_11asVCFRecord_3__reduce_cython__(PyObject *__pyx_v_self,
12789 #if CYTHON_METH_FASTCALL
12790 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
12791 #else
12792 PyObject *__pyx_args, PyObject *__pyx_kwds
12793 #endif
12794 ) {
12795 #if !CYTHON_METH_FASTCALL
12796 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
12797 #endif
12798 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
12799 PyObject *__pyx_r = 0;
12800 __Pyx_RefNannyDeclarations
12801 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
12802 #if !CYTHON_METH_FASTCALL
12803 #if CYTHON_ASSUME_SAFE_MACROS
12804 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
12805 #else
12806 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
12807 #endif
12808 #endif
12809 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
12810 if (unlikely(__pyx_nargs > 0)) {
12811 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
12812 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
12813 __pyx_r = __pyx_pf_5pysam_7libcvcf_11asVCFRecord_2__reduce_cython__(((struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *)__pyx_v_self));
12814
12815 /* function exit code */
12816 __Pyx_RefNannyFinishContext();
12817 return __pyx_r;
12818 }
12819
12820 static PyObject *__pyx_pf_5pysam_7libcvcf_11asVCFRecord_2__reduce_cython__(struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *__pyx_v_self) {
12821 PyObject *__pyx_v_state = 0;
12822 PyObject *__pyx_v__dict = 0;
12823 int __pyx_v_use_setstate;
12824 PyObject *__pyx_r = NULL;
12825 __Pyx_RefNannyDeclarations
12826 PyObject *__pyx_t_1 = NULL;
12827 int __pyx_t_2;
12828 PyObject *__pyx_t_3 = NULL;
12829 int __pyx_t_4;
12830 PyObject *__pyx_t_5 = NULL;
12831 int __pyx_lineno = 0;
12832 const char *__pyx_filename = NULL;
12833 int __pyx_clineno = 0;
12834 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
12835
12836 /* "(tree fragment)":5
12837 * cdef object _dict
12838 * cdef bint use_setstate
12839 * state = (self.encoding, self.vcffile) # <<<<<<<<<<<<<<
12840 * _dict = getattr(self, '__dict__', None)
12841 * if _dict is not None:
12842 */
12843 __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
12844 __Pyx_GOTREF(__pyx_t_1);
12845 __Pyx_INCREF(__pyx_v_self->__pyx_base.encoding);
12846 __Pyx_GIVEREF(__pyx_v_self->__pyx_base.encoding);
12847 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.encoding)) __PYX_ERR(1, 5, __pyx_L1_error);
12848 __Pyx_INCREF(__pyx_v_self->vcffile);
12849 __Pyx_GIVEREF(__pyx_v_self->vcffile);
12850 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_self->vcffile)) __PYX_ERR(1, 5, __pyx_L1_error);
12851 __pyx_v_state = ((PyObject*)__pyx_t_1);
12852 __pyx_t_1 = 0;
12853
12854 /* "(tree fragment)":6
12855 * cdef bint use_setstate
12856 * state = (self.encoding, self.vcffile)
12857 * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<<
12858 * if _dict is not None:
12859 * state += (_dict,)
12860 */
12861 __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
12862 __Pyx_GOTREF(__pyx_t_1);
12863 __pyx_v__dict = __pyx_t_1;
12864 __pyx_t_1 = 0;
12865
12866 /* "(tree fragment)":7
12867 * state = (self.encoding, self.vcffile)
12868 * _dict = getattr(self, '__dict__', None)
12869 * if _dict is not None: # <<<<<<<<<<<<<<
12870 * state += (_dict,)
12871 * use_setstate = True
12872 */
12873 __pyx_t_2 = (__pyx_v__dict != Py_None);
12874 if (__pyx_t_2) {
12875
12876 /* "(tree fragment)":8
12877 * _dict = getattr(self, '__dict__', None)
12878 * if _dict is not None:
12879 * state += (_dict,) # <<<<<<<<<<<<<<
12880 * use_setstate = True
12881 * else:
12882 */
12883 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error)
12884 __Pyx_GOTREF(__pyx_t_1);
12885 __Pyx_INCREF(__pyx_v__dict);
12886 __Pyx_GIVEREF(__pyx_v__dict);
12887 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error);
12888 __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error)
12889 __Pyx_GOTREF(__pyx_t_3);
12890 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
12891 __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3));
12892 __pyx_t_3 = 0;
12893
12894 /* "(tree fragment)":9
12895 * if _dict is not None:
12896 * state += (_dict,)
12897 * use_setstate = True # <<<<<<<<<<<<<<
12898 * else:
12899 * use_setstate = self.encoding is not None or self.vcffile is not None
12900 */
12901 __pyx_v_use_setstate = 1;
12902
12903 /* "(tree fragment)":7
12904 * state = (self.encoding, self.vcffile)
12905 * _dict = getattr(self, '__dict__', None)
12906 * if _dict is not None: # <<<<<<<<<<<<<<
12907 * state += (_dict,)
12908 * use_setstate = True
12909 */
12910 goto __pyx_L3;
12911 }
12912
12913 /* "(tree fragment)":11
12914 * use_setstate = True
12915 * else:
12916 * use_setstate = self.encoding is not None or self.vcffile is not None # <<<<<<<<<<<<<<
12917 * if use_setstate:
12918 * return __pyx_unpickle_asVCFRecord, (type(self), 0xe48d6d5, None), state
12919 */
12920 /*else*/ {
12921 __pyx_t_4 = (__pyx_v_self->__pyx_base.encoding != Py_None);
12922 if (!__pyx_t_4) {
12923 } else {
12924 __pyx_t_2 = __pyx_t_4;
12925 goto __pyx_L4_bool_binop_done;
12926 }
12927 __pyx_t_4 = (__pyx_v_self->vcffile != Py_None);
12928 __pyx_t_2 = __pyx_t_4;
12929 __pyx_L4_bool_binop_done:;
12930 __pyx_v_use_setstate = __pyx_t_2;
12931 }
12932 __pyx_L3:;
12933
12934 /* "(tree fragment)":12
12935 * else:
12936 * use_setstate = self.encoding is not None or self.vcffile is not None
12937 * if use_setstate: # <<<<<<<<<<<<<<
12938 * return __pyx_unpickle_asVCFRecord, (type(self), 0xe48d6d5, None), state
12939 * else:
12940 */
12941 if (__pyx_v_use_setstate) {
12942
12943 /* "(tree fragment)":13
12944 * use_setstate = self.encoding is not None or self.vcffile is not None
12945 * if use_setstate:
12946 * return __pyx_unpickle_asVCFRecord, (type(self), 0xe48d6d5, None), state # <<<<<<<<<<<<<<
12947 * else:
12948 * return __pyx_unpickle_asVCFRecord, (type(self), 0xe48d6d5, state)
12949 */
12950 __Pyx_XDECREF(__pyx_r);
12951 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_asVCFRecord); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error)
12952 __Pyx_GOTREF(__pyx_t_3);
12953 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error)
12954 __Pyx_GOTREF(__pyx_t_1);
12955 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
12956 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
12957 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error);
12958 __Pyx_INCREF(__pyx_int_239654613);
12959 __Pyx_GIVEREF(__pyx_int_239654613);
12960 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_239654613)) __PYX_ERR(1, 13, __pyx_L1_error);
12961 __Pyx_INCREF(Py_None);
12962 __Pyx_GIVEREF(Py_None);
12963 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error);
12964 __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 13, __pyx_L1_error)
12965 __Pyx_GOTREF(__pyx_t_5);
12966 __Pyx_GIVEREF(__pyx_t_3);
12967 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error);
12968 __Pyx_GIVEREF(__pyx_t_1);
12969 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error);
12970 __Pyx_INCREF(__pyx_v_state);
12971 __Pyx_GIVEREF(__pyx_v_state);
12972 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error);
12973 __pyx_t_3 = 0;
12974 __pyx_t_1 = 0;
12975 __pyx_r = __pyx_t_5;
12976 __pyx_t_5 = 0;
12977 goto __pyx_L0;
12978
12979 /* "(tree fragment)":12
12980 * else:
12981 * use_setstate = self.encoding is not None or self.vcffile is not None
12982 * if use_setstate: # <<<<<<<<<<<<<<
12983 * return __pyx_unpickle_asVCFRecord, (type(self), 0xe48d6d5, None), state
12984 * else:
12985 */
12986 }
12987
12988 /* "(tree fragment)":15
12989 * return __pyx_unpickle_asVCFRecord, (type(self), 0xe48d6d5, None), state
12990 * else:
12991 * return __pyx_unpickle_asVCFRecord, (type(self), 0xe48d6d5, state) # <<<<<<<<<<<<<<
12992 * def __setstate_cython__(self, __pyx_state):
12993 * __pyx_unpickle_asVCFRecord__set_state(self, __pyx_state)
12994 */
12995 /*else*/ {
12996 __Pyx_XDECREF(__pyx_r);
12997 __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_pyx_unpickle_asVCFRecord); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 15, __pyx_L1_error)
12998 __Pyx_GOTREF(__pyx_t_5);
12999 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error)
13000 __Pyx_GOTREF(__pyx_t_1);
13001 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
13002 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
13003 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error);
13004 __Pyx_INCREF(__pyx_int_239654613);
13005 __Pyx_GIVEREF(__pyx_int_239654613);
13006 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_239654613)) __PYX_ERR(1, 15, __pyx_L1_error);
13007 __Pyx_INCREF(__pyx_v_state);
13008 __Pyx_GIVEREF(__pyx_v_state);
13009 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error);
13010 __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error)
13011 __Pyx_GOTREF(__pyx_t_3);
13012 __Pyx_GIVEREF(__pyx_t_5);
13013 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_5)) __PYX_ERR(1, 15, __pyx_L1_error);
13014 __Pyx_GIVEREF(__pyx_t_1);
13015 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error);
13016 __pyx_t_5 = 0;
13017 __pyx_t_1 = 0;
13018 __pyx_r = __pyx_t_3;
13019 __pyx_t_3 = 0;
13020 goto __pyx_L0;
13021 }
13022
13023 /* "(tree fragment)":1
13024 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
13025 * cdef tuple state
13026 * cdef object _dict
13027 */
13028
13029 /* function exit code */
13030 __pyx_L1_error:;
13031 __Pyx_XDECREF(__pyx_t_1);
13032 __Pyx_XDECREF(__pyx_t_3);
13033 __Pyx_XDECREF(__pyx_t_5);
13034 __Pyx_AddTraceback("pysam.libcvcf.asVCFRecord.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
13035 __pyx_r = NULL;
13036 __pyx_L0:;
13037 __Pyx_XDECREF(__pyx_v_state);
13038 __Pyx_XDECREF(__pyx_v__dict);
13039 __Pyx_XGIVEREF(__pyx_r);
13040 __Pyx_RefNannyFinishContext();
13041 return __pyx_r;
13042 }
13043
13044 /* "(tree fragment)":16
13045 * else:
13046 * return __pyx_unpickle_asVCFRecord, (type(self), 0xe48d6d5, state)
13047 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
13048 * __pyx_unpickle_asVCFRecord__set_state(self, __pyx_state)
13049 */
13050
13051 /* Python wrapper */
13052 static PyObject *__pyx_pw_5pysam_7libcvcf_11asVCFRecord_5__setstate_cython__(PyObject *__pyx_v_self,
13053 #if CYTHON_METH_FASTCALL
13054 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
13055 #else
13056 PyObject *__pyx_args, PyObject *__pyx_kwds
13057 #endif
13058 ); /*proto*/
13059 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_11asVCFRecord_4__setstate_cython__, "asVCFRecord.__setstate_cython__(self, __pyx_state)");
13060 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_11asVCFRecord_5__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_11asVCFRecord_5__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_11asVCFRecord_4__setstate_cython__};
13061 static PyObject *__pyx_pw_5pysam_7libcvcf_11asVCFRecord_5__setstate_cython__(PyObject *__pyx_v_self,
13062 #if CYTHON_METH_FASTCALL
13063 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
13064 #else
13065 PyObject *__pyx_args, PyObject *__pyx_kwds
13066 #endif
13067 ) {
13068 PyObject *__pyx_v___pyx_state = 0;
13069 #if !CYTHON_METH_FASTCALL
13070 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
13071 #endif
13072 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
13073 PyObject* values[1] = {0};
13074 int __pyx_lineno = 0;
13075 const char *__pyx_filename = NULL;
13076 int __pyx_clineno = 0;
13077 PyObject *__pyx_r = 0;
13078 __Pyx_RefNannyDeclarations
13079 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
13080 #if !CYTHON_METH_FASTCALL
13081 #if CYTHON_ASSUME_SAFE_MACROS
13082 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
13083 #else
13084 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
13085 #endif
13086 #endif
13087 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
13088 {
13089 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
13090 if (__pyx_kwds) {
13091 Py_ssize_t kw_args;
13092 switch (__pyx_nargs) {
13093 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
13094 CYTHON_FALLTHROUGH;
13095 case 0: break;
13096 default: goto __pyx_L5_argtuple_error;
13097 }
13098 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
13099 switch (__pyx_nargs) {
13100 case 0:
13101 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
13102 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
13103 kw_args--;
13104 }
13105 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error)
13106 else goto __pyx_L5_argtuple_error;
13107 }
13108 if (unlikely(kw_args > 0)) {
13109 const Py_ssize_t kwd_pos_args = __pyx_nargs;
13110 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error)
13111 }
13112 } else if (unlikely(__pyx_nargs != 1)) {
13113 goto __pyx_L5_argtuple_error;
13114 } else {
13115 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
13116 }
13117 __pyx_v___pyx_state = values[0];
13118 }
13119 goto __pyx_L6_skip;
13120 __pyx_L5_argtuple_error:;
13121 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error)
13122 __pyx_L6_skip:;
13123 goto __pyx_L4_argument_unpacking_done;
13124 __pyx_L3_error:;
13125 {
13126 Py_ssize_t __pyx_temp;
13127 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
13128 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
13129 }
13130 }
13131 __Pyx_AddTraceback("pysam.libcvcf.asVCFRecord.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
13132 __Pyx_RefNannyFinishContext();
13133 return NULL;
13134 __pyx_L4_argument_unpacking_done:;
13135 __pyx_r = __pyx_pf_5pysam_7libcvcf_11asVCFRecord_4__setstate_cython__(((struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *)__pyx_v_self), __pyx_v___pyx_state);
13136
13137 /* function exit code */
13138 {
13139 Py_ssize_t __pyx_temp;
13140 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
13141 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
13142 }
13143 }
13144 __Pyx_RefNannyFinishContext();
13145 return __pyx_r;
13146 }
13147
13148 static PyObject *__pyx_pf_5pysam_7libcvcf_11asVCFRecord_4__setstate_cython__(struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
13149 PyObject *__pyx_r = NULL;
13150 __Pyx_RefNannyDeclarations
13151 PyObject *__pyx_t_1 = NULL;
13152 int __pyx_lineno = 0;
13153 const char *__pyx_filename = NULL;
13154 int __pyx_clineno = 0;
13155 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
13156
13157 /* "(tree fragment)":17
13158 * return __pyx_unpickle_asVCFRecord, (type(self), 0xe48d6d5, state)
13159 * def __setstate_cython__(self, __pyx_state):
13160 * __pyx_unpickle_asVCFRecord__set_state(self, __pyx_state) # <<<<<<<<<<<<<<
13161 */
13162 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error)
13163 __pyx_t_1 = __pyx_f_5pysam_7libcvcf___pyx_unpickle_asVCFRecord__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error)
13164 __Pyx_GOTREF(__pyx_t_1);
13165 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13166
13167 /* "(tree fragment)":16
13168 * else:
13169 * return __pyx_unpickle_asVCFRecord, (type(self), 0xe48d6d5, state)
13170 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
13171 * __pyx_unpickle_asVCFRecord__set_state(self, __pyx_state)
13172 */
13173
13174 /* function exit code */
13175 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
13176 goto __pyx_L0;
13177 __pyx_L1_error:;
13178 __Pyx_XDECREF(__pyx_t_1);
13179 __Pyx_AddTraceback("pysam.libcvcf.asVCFRecord.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
13180 __pyx_r = NULL;
13181 __pyx_L0:;
13182 __Pyx_XGIVEREF(__pyx_r);
13183 __Pyx_RefNannyFinishContext();
13184 return __pyx_r;
13185 }
13186
13187 /* "pysam/libcvcf.pyx":330
13188 * _lines = None
13189 *
13190 * def __init__(self, _copy=None, reference=None, regions=None, # <<<<<<<<<<<<<<
13191 * lines=None, leftalign=False):
13192 * # make error identifiers accessible by name
13193 */
13194
13195 /* Python wrapper */
13196 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_1__init__(PyObject *__pyx_self,
13197 #if CYTHON_METH_FASTCALL
13198 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
13199 #else
13200 PyObject *__pyx_args, PyObject *__pyx_kwds
13201 #endif
13202 ); /*proto*/
13203 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF___init__, "VCF.__init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False)");
13204 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_1__init__ = {"__init__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_1__init__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF___init__};
13205 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_1__init__(PyObject *__pyx_self,
13206 #if CYTHON_METH_FASTCALL
13207 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
13208 #else
13209 PyObject *__pyx_args, PyObject *__pyx_kwds
13210 #endif
13211 ) {
13212 PyObject *__pyx_v_self = 0;
13213 PyObject *__pyx_v__copy = 0;
13214 PyObject *__pyx_v_reference = 0;
13215 PyObject *__pyx_v_regions = 0;
13216 PyObject *__pyx_v_lines = 0;
13217 PyObject *__pyx_v_leftalign = 0;
13218 #if !CYTHON_METH_FASTCALL
13219 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
13220 #endif
13221 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
13222 PyObject* values[6] = {0,0,0,0,0,0};
13223 int __pyx_lineno = 0;
13224 const char *__pyx_filename = NULL;
13225 int __pyx_clineno = 0;
13226 PyObject *__pyx_r = 0;
13227 __Pyx_RefNannyDeclarations
13228 __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
13229 #if !CYTHON_METH_FASTCALL
13230 #if CYTHON_ASSUME_SAFE_MACROS
13231 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
13232 #else
13233 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
13234 #endif
13235 #endif
13236 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
13237 {
13238 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_copy,&__pyx_n_s_reference,&__pyx_n_s_regions,&__pyx_n_s_lines,&__pyx_n_s_leftalign,0};
13239 values[1] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
13240 values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
13241 values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
13242
13243 /* "pysam/libcvcf.pyx":331
13244 *
13245 * def __init__(self, _copy=None, reference=None, regions=None,
13246 * lines=None, leftalign=False): # <<<<<<<<<<<<<<
13247 * # make error identifiers accessible by name
13248 * for id in self._errors.keys():
13249 */
13250 values[4] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
13251 values[5] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False)));
13252 if (__pyx_kwds) {
13253 Py_ssize_t kw_args;
13254 switch (__pyx_nargs) {
13255 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
13256 CYTHON_FALLTHROUGH;
13257 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
13258 CYTHON_FALLTHROUGH;
13259 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
13260 CYTHON_FALLTHROUGH;
13261 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
13262 CYTHON_FALLTHROUGH;
13263 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
13264 CYTHON_FALLTHROUGH;
13265 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
13266 CYTHON_FALLTHROUGH;
13267 case 0: break;
13268 default: goto __pyx_L5_argtuple_error;
13269 }
13270 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
13271 switch (__pyx_nargs) {
13272 case 0:
13273 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
13274 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
13275 kw_args--;
13276 }
13277 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 330, __pyx_L3_error)
13278 else goto __pyx_L5_argtuple_error;
13279 CYTHON_FALLTHROUGH;
13280 case 1:
13281 if (kw_args > 0) {
13282 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_copy);
13283 if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
13284 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 330, __pyx_L3_error)
13285 }
13286 CYTHON_FALLTHROUGH;
13287 case 2:
13288 if (kw_args > 0) {
13289 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_reference);
13290 if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
13291 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 330, __pyx_L3_error)
13292 }
13293 CYTHON_FALLTHROUGH;
13294 case 3:
13295 if (kw_args > 0) {
13296 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_regions);
13297 if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
13298 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 330, __pyx_L3_error)
13299 }
13300 CYTHON_FALLTHROUGH;
13301 case 4:
13302 if (kw_args > 0) {
13303 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_lines);
13304 if (value) { values[4] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
13305 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 330, __pyx_L3_error)
13306 }
13307 CYTHON_FALLTHROUGH;
13308 case 5:
13309 if (kw_args > 0) {
13310 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_leftalign);
13311 if (value) { values[5] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
13312 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 330, __pyx_L3_error)
13313 }
13314 }
13315 if (unlikely(kw_args > 0)) {
13316 const Py_ssize_t kwd_pos_args = __pyx_nargs;
13317 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 330, __pyx_L3_error)
13318 }
13319 } else {
13320 switch (__pyx_nargs) {
13321 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
13322 CYTHON_FALLTHROUGH;
13323 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
13324 CYTHON_FALLTHROUGH;
13325 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
13326 CYTHON_FALLTHROUGH;
13327 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
13328 CYTHON_FALLTHROUGH;
13329 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
13330 CYTHON_FALLTHROUGH;
13331 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
13332 break;
13333 default: goto __pyx_L5_argtuple_error;
13334 }
13335 }
13336 __pyx_v_self = values[0];
13337 __pyx_v__copy = values[1];
13338 __pyx_v_reference = values[2];
13339 __pyx_v_regions = values[3];
13340 __pyx_v_lines = values[4];
13341 __pyx_v_leftalign = values[5];
13342 }
13343 goto __pyx_L6_skip;
13344 __pyx_L5_argtuple_error:;
13345 __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 6, __pyx_nargs); __PYX_ERR(0, 330, __pyx_L3_error)
13346 __pyx_L6_skip:;
13347 goto __pyx_L4_argument_unpacking_done;
13348 __pyx_L3_error:;
13349 {
13350 Py_ssize_t __pyx_temp;
13351 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
13352 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
13353 }
13354 }
13355 __Pyx_AddTraceback("pysam.libcvcf.VCF.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
13356 __Pyx_RefNannyFinishContext();
13357 return NULL;
13358 __pyx_L4_argument_unpacking_done:;
13359 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF___init__(__pyx_self, __pyx_v_self, __pyx_v__copy, __pyx_v_reference, __pyx_v_regions, __pyx_v_lines, __pyx_v_leftalign);
13360
13361 /* "pysam/libcvcf.pyx":330
13362 * _lines = None
13363 *
13364 * def __init__(self, _copy=None, reference=None, regions=None, # <<<<<<<<<<<<<<
13365 * lines=None, leftalign=False):
13366 * # make error identifiers accessible by name
13367 */
13368
13369 /* function exit code */
13370 {
13371 Py_ssize_t __pyx_temp;
13372 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
13373 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
13374 }
13375 }
13376 __Pyx_RefNannyFinishContext();
13377 return __pyx_r;
13378 }
13379
13380 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v__copy, PyObject *__pyx_v_reference, PyObject *__pyx_v_regions, PyObject *__pyx_v_lines, PyObject *__pyx_v_leftalign) {
13381 PyObject *__pyx_v_id = NULL;
13382 PyObject *__pyx_r = NULL;
13383 __Pyx_RefNannyDeclarations
13384 PyObject *__pyx_t_1 = NULL;
13385 Py_ssize_t __pyx_t_2;
13386 Py_ssize_t __pyx_t_3;
13387 int __pyx_t_4;
13388 PyObject *__pyx_t_5 = NULL;
13389 PyObject *__pyx_t_6 = NULL;
13390 int __pyx_t_7;
13391 PyObject *__pyx_t_8 = NULL;
13392 PyObject *__pyx_t_9 = NULL;
13393 unsigned int __pyx_t_10;
13394 int __pyx_t_11;
13395 int __pyx_lineno = 0;
13396 const char *__pyx_filename = NULL;
13397 int __pyx_clineno = 0;
13398 __Pyx_RefNannySetupContext("__init__", 1);
13399
13400 /* "pysam/libcvcf.pyx":333
13401 * lines=None, leftalign=False):
13402 * # make error identifiers accessible by name
13403 * for id in self._errors.keys(): # <<<<<<<<<<<<<<
13404 * self.__dict__[self._errors[id].split(':')[0]] = id
13405 * if _copy != None:
13406 */
13407 __pyx_t_2 = 0;
13408 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_errors); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 333, __pyx_L1_error)
13409 __Pyx_GOTREF(__pyx_t_5);
13410 if (unlikely(__pyx_t_5 == Py_None)) {
13411 PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%.30s'", "keys");
13412 __PYX_ERR(0, 333, __pyx_L1_error)
13413 }
13414 __pyx_t_6 = __Pyx_dict_iterator(__pyx_t_5, 0, __pyx_n_s_keys, (&__pyx_t_3), (&__pyx_t_4)); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 333, __pyx_L1_error)
13415 __Pyx_GOTREF(__pyx_t_6);
13416 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
13417 __Pyx_XDECREF(__pyx_t_1);
13418 __pyx_t_1 = __pyx_t_6;
13419 __pyx_t_6 = 0;
13420 while (1) {
13421 __pyx_t_7 = __Pyx_dict_iter_next(__pyx_t_1, __pyx_t_3, &__pyx_t_2, &__pyx_t_6, NULL, NULL, __pyx_t_4);
13422 if (unlikely(__pyx_t_7 == 0)) break;
13423 if (unlikely(__pyx_t_7 == -1)) __PYX_ERR(0, 333, __pyx_L1_error)
13424 __Pyx_GOTREF(__pyx_t_6);
13425 __Pyx_XDECREF_SET(__pyx_v_id, __pyx_t_6);
13426 __pyx_t_6 = 0;
13427
13428 /* "pysam/libcvcf.pyx":334
13429 * # make error identifiers accessible by name
13430 * for id in self._errors.keys():
13431 * self.__dict__[self._errors[id].split(':')[0]] = id # <<<<<<<<<<<<<<
13432 * if _copy != None:
13433 * self._leftalign = _copy._leftalign
13434 */
13435 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_dict); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 334, __pyx_L1_error)
13436 __Pyx_GOTREF(__pyx_t_6);
13437 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_errors); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 334, __pyx_L1_error)
13438 __Pyx_GOTREF(__pyx_t_8);
13439 __pyx_t_9 = __Pyx_PyObject_GetItem(__pyx_t_8, __pyx_v_id); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 334, __pyx_L1_error)
13440 __Pyx_GOTREF(__pyx_t_9);
13441 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13442 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_9, __pyx_n_s_split); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 334, __pyx_L1_error)
13443 __Pyx_GOTREF(__pyx_t_8);
13444 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
13445 __pyx_t_9 = NULL;
13446 __pyx_t_10 = 0;
13447 #if CYTHON_UNPACK_METHODS
13448 if (likely(PyMethod_Check(__pyx_t_8))) {
13449 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_8);
13450 if (likely(__pyx_t_9)) {
13451 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_8);
13452 __Pyx_INCREF(__pyx_t_9);
13453 __Pyx_INCREF(function);
13454 __Pyx_DECREF_SET(__pyx_t_8, function);
13455 __pyx_t_10 = 1;
13456 }
13457 }
13458 #endif
13459 {
13460 PyObject *__pyx_callargs[2] = {__pyx_t_9, __pyx_kp_u__3};
13461 __pyx_t_5 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10);
13462 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
13463 if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 334, __pyx_L1_error)
13464 __Pyx_GOTREF(__pyx_t_5);
13465 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13466 }
13467 __pyx_t_8 = __Pyx_GetItemInt(__pyx_t_5, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 334, __pyx_L1_error)
13468 __Pyx_GOTREF(__pyx_t_8);
13469 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
13470 if (unlikely((PyObject_SetItem(__pyx_t_6, __pyx_t_8, __pyx_v_id) < 0))) __PYX_ERR(0, 334, __pyx_L1_error)
13471 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
13472 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13473 }
13474 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13475
13476 /* "pysam/libcvcf.pyx":335
13477 * for id in self._errors.keys():
13478 * self.__dict__[self._errors[id].split(':')[0]] = id
13479 * if _copy != None: # <<<<<<<<<<<<<<
13480 * self._leftalign = _copy._leftalign
13481 * self._header = _copy._header[:]
13482 */
13483 __pyx_t_1 = PyObject_RichCompare(__pyx_v__copy, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 335, __pyx_L1_error)
13484 __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_11 < 0))) __PYX_ERR(0, 335, __pyx_L1_error)
13485 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13486 if (__pyx_t_11) {
13487
13488 /* "pysam/libcvcf.pyx":336
13489 * self.__dict__[self._errors[id].split(':')[0]] = id
13490 * if _copy != None:
13491 * self._leftalign = _copy._leftalign # <<<<<<<<<<<<<<
13492 * self._header = _copy._header[:]
13493 * self._version = _copy._version
13494 */
13495 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v__copy, __pyx_n_s_leftalign_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 336, __pyx_L1_error)
13496 __Pyx_GOTREF(__pyx_t_1);
13497 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_leftalign_2, __pyx_t_1) < 0) __PYX_ERR(0, 336, __pyx_L1_error)
13498 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13499
13500 /* "pysam/libcvcf.pyx":337
13501 * if _copy != None:
13502 * self._leftalign = _copy._leftalign
13503 * self._header = _copy._header[:] # <<<<<<<<<<<<<<
13504 * self._version = _copy._version
13505 * self._info = copy.deepcopy(_copy._info)
13506 */
13507 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v__copy, __pyx_n_s_header); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 337, __pyx_L1_error)
13508 __Pyx_GOTREF(__pyx_t_1);
13509 __pyx_t_8 = __Pyx_PyObject_GetSlice(__pyx_t_1, 0, 0, NULL, NULL, &__pyx_slice__9, 0, 0, 1); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 337, __pyx_L1_error)
13510 __Pyx_GOTREF(__pyx_t_8);
13511 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13512 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_header, __pyx_t_8) < 0) __PYX_ERR(0, 337, __pyx_L1_error)
13513 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13514
13515 /* "pysam/libcvcf.pyx":338
13516 * self._leftalign = _copy._leftalign
13517 * self._header = _copy._header[:]
13518 * self._version = _copy._version # <<<<<<<<<<<<<<
13519 * self._info = copy.deepcopy(_copy._info)
13520 * self._filter = copy.deepcopy(_copy._filter)
13521 */
13522 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v__copy, __pyx_n_s_version); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 338, __pyx_L1_error)
13523 __Pyx_GOTREF(__pyx_t_8);
13524 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_version, __pyx_t_8) < 0) __PYX_ERR(0, 338, __pyx_L1_error)
13525 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13526
13527 /* "pysam/libcvcf.pyx":339
13528 * self._header = _copy._header[:]
13529 * self._version = _copy._version
13530 * self._info = copy.deepcopy(_copy._info) # <<<<<<<<<<<<<<
13531 * self._filter = copy.deepcopy(_copy._filter)
13532 * self._format = copy.deepcopy(_copy._format)
13533 */
13534 __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_copy_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 339, __pyx_L1_error)
13535 __Pyx_GOTREF(__pyx_t_1);
13536 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_deepcopy); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 339, __pyx_L1_error)
13537 __Pyx_GOTREF(__pyx_t_6);
13538 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13539 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v__copy, __pyx_n_s_info); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 339, __pyx_L1_error)
13540 __Pyx_GOTREF(__pyx_t_1);
13541 __pyx_t_5 = NULL;
13542 __pyx_t_10 = 0;
13543 #if CYTHON_UNPACK_METHODS
13544 if (unlikely(PyMethod_Check(__pyx_t_6))) {
13545 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_6);
13546 if (likely(__pyx_t_5)) {
13547 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
13548 __Pyx_INCREF(__pyx_t_5);
13549 __Pyx_INCREF(function);
13550 __Pyx_DECREF_SET(__pyx_t_6, function);
13551 __pyx_t_10 = 1;
13552 }
13553 }
13554 #endif
13555 {
13556 PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_t_1};
13557 __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10);
13558 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
13559 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13560 if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 339, __pyx_L1_error)
13561 __Pyx_GOTREF(__pyx_t_8);
13562 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
13563 }
13564 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_info, __pyx_t_8) < 0) __PYX_ERR(0, 339, __pyx_L1_error)
13565 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13566
13567 /* "pysam/libcvcf.pyx":340
13568 * self._version = _copy._version
13569 * self._info = copy.deepcopy(_copy._info)
13570 * self._filter = copy.deepcopy(_copy._filter) # <<<<<<<<<<<<<<
13571 * self._format = copy.deepcopy(_copy._format)
13572 * self._samples = _copy._samples[:]
13573 */
13574 __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_copy_2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 340, __pyx_L1_error)
13575 __Pyx_GOTREF(__pyx_t_6);
13576 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_deepcopy); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 340, __pyx_L1_error)
13577 __Pyx_GOTREF(__pyx_t_1);
13578 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
13579 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v__copy, __pyx_n_s_filter); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 340, __pyx_L1_error)
13580 __Pyx_GOTREF(__pyx_t_6);
13581 __pyx_t_5 = NULL;
13582 __pyx_t_10 = 0;
13583 #if CYTHON_UNPACK_METHODS
13584 if (unlikely(PyMethod_Check(__pyx_t_1))) {
13585 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_1);
13586 if (likely(__pyx_t_5)) {
13587 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
13588 __Pyx_INCREF(__pyx_t_5);
13589 __Pyx_INCREF(function);
13590 __Pyx_DECREF_SET(__pyx_t_1, function);
13591 __pyx_t_10 = 1;
13592 }
13593 }
13594 #endif
13595 {
13596 PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_t_6};
13597 __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10);
13598 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
13599 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
13600 if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 340, __pyx_L1_error)
13601 __Pyx_GOTREF(__pyx_t_8);
13602 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13603 }
13604 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_filter, __pyx_t_8) < 0) __PYX_ERR(0, 340, __pyx_L1_error)
13605 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13606
13607 /* "pysam/libcvcf.pyx":341
13608 * self._info = copy.deepcopy(_copy._info)
13609 * self._filter = copy.deepcopy(_copy._filter)
13610 * self._format = copy.deepcopy(_copy._format) # <<<<<<<<<<<<<<
13611 * self._samples = _copy._samples[:]
13612 * self._sample2column = copy.deepcopy(_copy._sample2column)
13613 */
13614 __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_copy_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 341, __pyx_L1_error)
13615 __Pyx_GOTREF(__pyx_t_1);
13616 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_deepcopy); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 341, __pyx_L1_error)
13617 __Pyx_GOTREF(__pyx_t_6);
13618 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13619 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v__copy, __pyx_n_s_format_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 341, __pyx_L1_error)
13620 __Pyx_GOTREF(__pyx_t_1);
13621 __pyx_t_5 = NULL;
13622 __pyx_t_10 = 0;
13623 #if CYTHON_UNPACK_METHODS
13624 if (unlikely(PyMethod_Check(__pyx_t_6))) {
13625 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_6);
13626 if (likely(__pyx_t_5)) {
13627 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
13628 __Pyx_INCREF(__pyx_t_5);
13629 __Pyx_INCREF(function);
13630 __Pyx_DECREF_SET(__pyx_t_6, function);
13631 __pyx_t_10 = 1;
13632 }
13633 }
13634 #endif
13635 {
13636 PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_t_1};
13637 __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10);
13638 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
13639 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13640 if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 341, __pyx_L1_error)
13641 __Pyx_GOTREF(__pyx_t_8);
13642 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
13643 }
13644 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_format_2, __pyx_t_8) < 0) __PYX_ERR(0, 341, __pyx_L1_error)
13645 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13646
13647 /* "pysam/libcvcf.pyx":342
13648 * self._filter = copy.deepcopy(_copy._filter)
13649 * self._format = copy.deepcopy(_copy._format)
13650 * self._samples = _copy._samples[:] # <<<<<<<<<<<<<<
13651 * self._sample2column = copy.deepcopy(_copy._sample2column)
13652 * self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
13653 */
13654 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v__copy, __pyx_n_s_samples); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 342, __pyx_L1_error)
13655 __Pyx_GOTREF(__pyx_t_8);
13656 __pyx_t_6 = __Pyx_PyObject_GetSlice(__pyx_t_8, 0, 0, NULL, NULL, &__pyx_slice__9, 0, 0, 1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 342, __pyx_L1_error)
13657 __Pyx_GOTREF(__pyx_t_6);
13658 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13659 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_samples, __pyx_t_6) < 0) __PYX_ERR(0, 342, __pyx_L1_error)
13660 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
13661
13662 /* "pysam/libcvcf.pyx":343
13663 * self._format = copy.deepcopy(_copy._format)
13664 * self._samples = _copy._samples[:]
13665 * self._sample2column = copy.deepcopy(_copy._sample2column) # <<<<<<<<<<<<<<
13666 * self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
13667 * self._warn_errors = copy.deepcopy(_copy._warn_errors)
13668 */
13669 __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_copy_2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 343, __pyx_L1_error)
13670 __Pyx_GOTREF(__pyx_t_8);
13671 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_deepcopy); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 343, __pyx_L1_error)
13672 __Pyx_GOTREF(__pyx_t_1);
13673 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13674 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v__copy, __pyx_n_s_sample2column); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 343, __pyx_L1_error)
13675 __Pyx_GOTREF(__pyx_t_8);
13676 __pyx_t_5 = NULL;
13677 __pyx_t_10 = 0;
13678 #if CYTHON_UNPACK_METHODS
13679 if (unlikely(PyMethod_Check(__pyx_t_1))) {
13680 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_1);
13681 if (likely(__pyx_t_5)) {
13682 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
13683 __Pyx_INCREF(__pyx_t_5);
13684 __Pyx_INCREF(function);
13685 __Pyx_DECREF_SET(__pyx_t_1, function);
13686 __pyx_t_10 = 1;
13687 }
13688 }
13689 #endif
13690 {
13691 PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_t_8};
13692 __pyx_t_6 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10);
13693 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
13694 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13695 if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 343, __pyx_L1_error)
13696 __Pyx_GOTREF(__pyx_t_6);
13697 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13698 }
13699 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_sample2column, __pyx_t_6) < 0) __PYX_ERR(0, 343, __pyx_L1_error)
13700 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
13701
13702 /* "pysam/libcvcf.pyx":344
13703 * self._samples = _copy._samples[:]
13704 * self._sample2column = copy.deepcopy(_copy._sample2column)
13705 * self._ignored_errors = copy.deepcopy(_copy._ignored_errors) # <<<<<<<<<<<<<<
13706 * self._warn_errors = copy.deepcopy(_copy._warn_errors)
13707 * self._reference = _copy._reference
13708 */
13709 __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_copy_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 344, __pyx_L1_error)
13710 __Pyx_GOTREF(__pyx_t_1);
13711 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_deepcopy); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 344, __pyx_L1_error)
13712 __Pyx_GOTREF(__pyx_t_8);
13713 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13714 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v__copy, __pyx_n_s_ignored_errors); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 344, __pyx_L1_error)
13715 __Pyx_GOTREF(__pyx_t_1);
13716 __pyx_t_5 = NULL;
13717 __pyx_t_10 = 0;
13718 #if CYTHON_UNPACK_METHODS
13719 if (unlikely(PyMethod_Check(__pyx_t_8))) {
13720 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_8);
13721 if (likely(__pyx_t_5)) {
13722 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_8);
13723 __Pyx_INCREF(__pyx_t_5);
13724 __Pyx_INCREF(function);
13725 __Pyx_DECREF_SET(__pyx_t_8, function);
13726 __pyx_t_10 = 1;
13727 }
13728 }
13729 #endif
13730 {
13731 PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_t_1};
13732 __pyx_t_6 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10);
13733 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
13734 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13735 if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 344, __pyx_L1_error)
13736 __Pyx_GOTREF(__pyx_t_6);
13737 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13738 }
13739 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_ignored_errors, __pyx_t_6) < 0) __PYX_ERR(0, 344, __pyx_L1_error)
13740 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
13741
13742 /* "pysam/libcvcf.pyx":345
13743 * self._sample2column = copy.deepcopy(_copy._sample2column)
13744 * self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
13745 * self._warn_errors = copy.deepcopy(_copy._warn_errors) # <<<<<<<<<<<<<<
13746 * self._reference = _copy._reference
13747 * self._regions = _copy._regions
13748 */
13749 __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_copy_2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 345, __pyx_L1_error)
13750 __Pyx_GOTREF(__pyx_t_8);
13751 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_deepcopy); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 345, __pyx_L1_error)
13752 __Pyx_GOTREF(__pyx_t_1);
13753 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13754 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v__copy, __pyx_n_s_warn_errors); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 345, __pyx_L1_error)
13755 __Pyx_GOTREF(__pyx_t_8);
13756 __pyx_t_5 = NULL;
13757 __pyx_t_10 = 0;
13758 #if CYTHON_UNPACK_METHODS
13759 if (unlikely(PyMethod_Check(__pyx_t_1))) {
13760 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_1);
13761 if (likely(__pyx_t_5)) {
13762 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
13763 __Pyx_INCREF(__pyx_t_5);
13764 __Pyx_INCREF(function);
13765 __Pyx_DECREF_SET(__pyx_t_1, function);
13766 __pyx_t_10 = 1;
13767 }
13768 }
13769 #endif
13770 {
13771 PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_t_8};
13772 __pyx_t_6 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10);
13773 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
13774 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
13775 if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 345, __pyx_L1_error)
13776 __Pyx_GOTREF(__pyx_t_6);
13777 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
13778 }
13779 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_warn_errors, __pyx_t_6) < 0) __PYX_ERR(0, 345, __pyx_L1_error)
13780 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
13781
13782 /* "pysam/libcvcf.pyx":346
13783 * self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
13784 * self._warn_errors = copy.deepcopy(_copy._warn_errors)
13785 * self._reference = _copy._reference # <<<<<<<<<<<<<<
13786 * self._regions = _copy._regions
13787 * if reference: self._reference = reference
13788 */
13789 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v__copy, __pyx_n_s_reference_2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 346, __pyx_L1_error)
13790 __Pyx_GOTREF(__pyx_t_6);
13791 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_reference_2, __pyx_t_6) < 0) __PYX_ERR(0, 346, __pyx_L1_error)
13792 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
13793
13794 /* "pysam/libcvcf.pyx":347
13795 * self._warn_errors = copy.deepcopy(_copy._warn_errors)
13796 * self._reference = _copy._reference
13797 * self._regions = _copy._regions # <<<<<<<<<<<<<<
13798 * if reference: self._reference = reference
13799 * if regions: self._regions = regions
13800 */
13801 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v__copy, __pyx_n_s_regions_2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 347, __pyx_L1_error)
13802 __Pyx_GOTREF(__pyx_t_6);
13803 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_regions_2, __pyx_t_6) < 0) __PYX_ERR(0, 347, __pyx_L1_error)
13804 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
13805
13806 /* "pysam/libcvcf.pyx":335
13807 * for id in self._errors.keys():
13808 * self.__dict__[self._errors[id].split(':')[0]] = id
13809 * if _copy != None: # <<<<<<<<<<<<<<
13810 * self._leftalign = _copy._leftalign
13811 * self._header = _copy._header[:]
13812 */
13813 }
13814
13815 /* "pysam/libcvcf.pyx":348
13816 * self._reference = _copy._reference
13817 * self._regions = _copy._regions
13818 * if reference: self._reference = reference # <<<<<<<<<<<<<<
13819 * if regions: self._regions = regions
13820 * if leftalign: self._leftalign = leftalign
13821 */
13822 __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_reference); if (unlikely((__pyx_t_11 < 0))) __PYX_ERR(0, 348, __pyx_L1_error)
13823 if (__pyx_t_11) {
13824 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_reference_2, __pyx_v_reference) < 0) __PYX_ERR(0, 348, __pyx_L1_error)
13825 }
13826
13827 /* "pysam/libcvcf.pyx":349
13828 * self._regions = _copy._regions
13829 * if reference: self._reference = reference
13830 * if regions: self._regions = regions # <<<<<<<<<<<<<<
13831 * if leftalign: self._leftalign = leftalign
13832 * self._lines = lines
13833 */
13834 __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_regions); if (unlikely((__pyx_t_11 < 0))) __PYX_ERR(0, 349, __pyx_L1_error)
13835 if (__pyx_t_11) {
13836 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_regions_2, __pyx_v_regions) < 0) __PYX_ERR(0, 349, __pyx_L1_error)
13837 }
13838
13839 /* "pysam/libcvcf.pyx":350
13840 * if reference: self._reference = reference
13841 * if regions: self._regions = regions
13842 * if leftalign: self._leftalign = leftalign # <<<<<<<<<<<<<<
13843 * self._lines = lines
13844 * self.encoding = "ascii"
13845 */
13846 __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_leftalign); if (unlikely((__pyx_t_11 < 0))) __PYX_ERR(0, 350, __pyx_L1_error)
13847 if (__pyx_t_11) {
13848 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_leftalign_2, __pyx_v_leftalign) < 0) __PYX_ERR(0, 350, __pyx_L1_error)
13849 }
13850
13851 /* "pysam/libcvcf.pyx":351
13852 * if regions: self._regions = regions
13853 * if leftalign: self._leftalign = leftalign
13854 * self._lines = lines # <<<<<<<<<<<<<<
13855 * self.encoding = "ascii"
13856 * self.tabixfile = None
13857 */
13858 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_lines_2, __pyx_v_lines) < 0) __PYX_ERR(0, 351, __pyx_L1_error)
13859
13860 /* "pysam/libcvcf.pyx":352
13861 * if leftalign: self._leftalign = leftalign
13862 * self._lines = lines
13863 * self.encoding = "ascii" # <<<<<<<<<<<<<<
13864 * self.tabixfile = None
13865 *
13866 */
13867 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_encoding, __pyx_n_u_ascii) < 0) __PYX_ERR(0, 352, __pyx_L1_error)
13868
13869 /* "pysam/libcvcf.pyx":353
13870 * self._lines = lines
13871 * self.encoding = "ascii"
13872 * self.tabixfile = None # <<<<<<<<<<<<<<
13873 *
13874 * def error(self,line,error,opt=None):
13875 */
13876 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_tabixfile, Py_None) < 0) __PYX_ERR(0, 353, __pyx_L1_error)
13877
13878 /* "pysam/libcvcf.pyx":330
13879 * _lines = None
13880 *
13881 * def __init__(self, _copy=None, reference=None, regions=None, # <<<<<<<<<<<<<<
13882 * lines=None, leftalign=False):
13883 * # make error identifiers accessible by name
13884 */
13885
13886 /* function exit code */
13887 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
13888 goto __pyx_L0;
13889 __pyx_L1_error:;
13890 __Pyx_XDECREF(__pyx_t_1);
13891 __Pyx_XDECREF(__pyx_t_5);
13892 __Pyx_XDECREF(__pyx_t_6);
13893 __Pyx_XDECREF(__pyx_t_8);
13894 __Pyx_XDECREF(__pyx_t_9);
13895 __Pyx_AddTraceback("pysam.libcvcf.VCF.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
13896 __pyx_r = NULL;
13897 __pyx_L0:;
13898 __Pyx_XDECREF(__pyx_v_id);
13899 __Pyx_XGIVEREF(__pyx_r);
13900 __Pyx_RefNannyFinishContext();
13901 return __pyx_r;
13902 }
13903
13904 /* "pysam/libcvcf.pyx":355
13905 * self.tabixfile = None
13906 *
13907 * def error(self,line,error,opt=None): # <<<<<<<<<<<<<<
13908 * if error in self._ignored_errors: return
13909 * errorlabel, errorstring = self._errors[error].split(':')
13910 */
13911
13912 /* Python wrapper */
13913 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_3error(PyObject *__pyx_self,
13914 #if CYTHON_METH_FASTCALL
13915 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
13916 #else
13917 PyObject *__pyx_args, PyObject *__pyx_kwds
13918 #endif
13919 ); /*proto*/
13920 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_2error, "VCF.error(self, line, error, opt=None)");
13921 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_3error = {"error", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_3error, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_2error};
13922 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_3error(PyObject *__pyx_self,
13923 #if CYTHON_METH_FASTCALL
13924 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
13925 #else
13926 PyObject *__pyx_args, PyObject *__pyx_kwds
13927 #endif
13928 ) {
13929 PyObject *__pyx_v_self = 0;
13930 PyObject *__pyx_v_line = 0;
13931 PyObject *__pyx_v_error = 0;
13932 PyObject *__pyx_v_opt = 0;
13933 #if !CYTHON_METH_FASTCALL
13934 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
13935 #endif
13936 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
13937 PyObject* values[4] = {0,0,0,0};
13938 int __pyx_lineno = 0;
13939 const char *__pyx_filename = NULL;
13940 int __pyx_clineno = 0;
13941 PyObject *__pyx_r = 0;
13942 __Pyx_RefNannyDeclarations
13943 __Pyx_RefNannySetupContext("error (wrapper)", 0);
13944 #if !CYTHON_METH_FASTCALL
13945 #if CYTHON_ASSUME_SAFE_MACROS
13946 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
13947 #else
13948 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
13949 #endif
13950 #endif
13951 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
13952 {
13953 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_line,&__pyx_n_s_error,&__pyx_n_s_opt,0};
13954 values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
13955 if (__pyx_kwds) {
13956 Py_ssize_t kw_args;
13957 switch (__pyx_nargs) {
13958 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
13959 CYTHON_FALLTHROUGH;
13960 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
13961 CYTHON_FALLTHROUGH;
13962 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
13963 CYTHON_FALLTHROUGH;
13964 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
13965 CYTHON_FALLTHROUGH;
13966 case 0: break;
13967 default: goto __pyx_L5_argtuple_error;
13968 }
13969 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
13970 switch (__pyx_nargs) {
13971 case 0:
13972 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
13973 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
13974 kw_args--;
13975 }
13976 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 355, __pyx_L3_error)
13977 else goto __pyx_L5_argtuple_error;
13978 CYTHON_FALLTHROUGH;
13979 case 1:
13980 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_line)) != 0)) {
13981 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
13982 kw_args--;
13983 }
13984 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 355, __pyx_L3_error)
13985 else {
13986 __Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, 1); __PYX_ERR(0, 355, __pyx_L3_error)
13987 }
13988 CYTHON_FALLTHROUGH;
13989 case 2:
13990 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_error)) != 0)) {
13991 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
13992 kw_args--;
13993 }
13994 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 355, __pyx_L3_error)
13995 else {
13996 __Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, 2); __PYX_ERR(0, 355, __pyx_L3_error)
13997 }
13998 CYTHON_FALLTHROUGH;
13999 case 3:
14000 if (kw_args > 0) {
14001 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_opt);
14002 if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
14003 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 355, __pyx_L3_error)
14004 }
14005 }
14006 if (unlikely(kw_args > 0)) {
14007 const Py_ssize_t kwd_pos_args = __pyx_nargs;
14008 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "error") < 0)) __PYX_ERR(0, 355, __pyx_L3_error)
14009 }
14010 } else {
14011 switch (__pyx_nargs) {
14012 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
14013 CYTHON_FALLTHROUGH;
14014 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
14015 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
14016 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
14017 break;
14018 default: goto __pyx_L5_argtuple_error;
14019 }
14020 }
14021 __pyx_v_self = values[0];
14022 __pyx_v_line = values[1];
14023 __pyx_v_error = values[2];
14024 __pyx_v_opt = values[3];
14025 }
14026 goto __pyx_L6_skip;
14027 __pyx_L5_argtuple_error:;
14028 __Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, __pyx_nargs); __PYX_ERR(0, 355, __pyx_L3_error)
14029 __pyx_L6_skip:;
14030 goto __pyx_L4_argument_unpacking_done;
14031 __pyx_L3_error:;
14032 {
14033 Py_ssize_t __pyx_temp;
14034 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
14035 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
14036 }
14037 }
14038 __Pyx_AddTraceback("pysam.libcvcf.VCF.error", __pyx_clineno, __pyx_lineno, __pyx_filename);
14039 __Pyx_RefNannyFinishContext();
14040 return NULL;
14041 __pyx_L4_argument_unpacking_done:;
14042 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_2error(__pyx_self, __pyx_v_self, __pyx_v_line, __pyx_v_error, __pyx_v_opt);
14043
14044 /* function exit code */
14045 {
14046 Py_ssize_t __pyx_temp;
14047 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
14048 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
14049 }
14050 }
14051 __Pyx_RefNannyFinishContext();
14052 return __pyx_r;
14053 }
14054
14055 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt) {
14056 PyObject *__pyx_v_errorlabel = NULL;
14057 PyObject *__pyx_v_errorstring = NULL;
14058 PyObject *__pyx_v_errwarn = NULL;
14059 PyObject *__pyx_r = NULL;
14060 __Pyx_RefNannyDeclarations
14061 PyObject *__pyx_t_1 = NULL;
14062 int __pyx_t_2;
14063 PyObject *__pyx_t_3 = NULL;
14064 PyObject *__pyx_t_4 = NULL;
14065 unsigned int __pyx_t_5;
14066 PyObject *__pyx_t_6 = NULL;
14067 PyObject *(*__pyx_t_7)(PyObject *);
14068 Py_ssize_t __pyx_t_8;
14069 Py_UCS4 __pyx_t_9;
14070 int __pyx_lineno = 0;
14071 const char *__pyx_filename = NULL;
14072 int __pyx_clineno = 0;
14073 __Pyx_RefNannySetupContext("error", 1);
14074
14075 /* "pysam/libcvcf.pyx":356
14076 *
14077 * def error(self,line,error,opt=None):
14078 * if error in self._ignored_errors: return # <<<<<<<<<<<<<<
14079 * errorlabel, errorstring = self._errors[error].split(':')
14080 * if opt: errorstring = errorstring % opt
14081 */
14082 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_ignored_errors); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 356, __pyx_L1_error)
14083 __Pyx_GOTREF(__pyx_t_1);
14084 __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_v_error, __pyx_t_1, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 356, __pyx_L1_error)
14085 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14086 if (__pyx_t_2) {
14087 __Pyx_XDECREF(__pyx_r);
14088 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
14089 goto __pyx_L0;
14090 }
14091
14092 /* "pysam/libcvcf.pyx":357
14093 * def error(self,line,error,opt=None):
14094 * if error in self._ignored_errors: return
14095 * errorlabel, errorstring = self._errors[error].split(':') # <<<<<<<<<<<<<<
14096 * if opt: errorstring = errorstring % opt
14097 * errwarn = ["Error","Warning"][error in self._warn_errors]
14098 */
14099 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_errors); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 357, __pyx_L1_error)
14100 __Pyx_GOTREF(__pyx_t_3);
14101 __pyx_t_4 = __Pyx_PyObject_GetItem(__pyx_t_3, __pyx_v_error); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 357, __pyx_L1_error)
14102 __Pyx_GOTREF(__pyx_t_4);
14103 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
14104 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_split); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 357, __pyx_L1_error)
14105 __Pyx_GOTREF(__pyx_t_3);
14106 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
14107 __pyx_t_4 = NULL;
14108 __pyx_t_5 = 0;
14109 #if CYTHON_UNPACK_METHODS
14110 if (likely(PyMethod_Check(__pyx_t_3))) {
14111 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
14112 if (likely(__pyx_t_4)) {
14113 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
14114 __Pyx_INCREF(__pyx_t_4);
14115 __Pyx_INCREF(function);
14116 __Pyx_DECREF_SET(__pyx_t_3, function);
14117 __pyx_t_5 = 1;
14118 }
14119 }
14120 #endif
14121 {
14122 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_kp_u__3};
14123 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
14124 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
14125 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 357, __pyx_L1_error)
14126 __Pyx_GOTREF(__pyx_t_1);
14127 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
14128 }
14129 if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
14130 PyObject* sequence = __pyx_t_1;
14131 Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
14132 if (unlikely(size != 2)) {
14133 if (size > 2) __Pyx_RaiseTooManyValuesError(2);
14134 else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
14135 __PYX_ERR(0, 357, __pyx_L1_error)
14136 }
14137 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
14138 if (likely(PyTuple_CheckExact(sequence))) {
14139 __pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
14140 __pyx_t_4 = PyTuple_GET_ITEM(sequence, 1);
14141 } else {
14142 __pyx_t_3 = PyList_GET_ITEM(sequence, 0);
14143 __pyx_t_4 = PyList_GET_ITEM(sequence, 1);
14144 }
14145 __Pyx_INCREF(__pyx_t_3);
14146 __Pyx_INCREF(__pyx_t_4);
14147 #else
14148 __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 357, __pyx_L1_error)
14149 __Pyx_GOTREF(__pyx_t_3);
14150 __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 357, __pyx_L1_error)
14151 __Pyx_GOTREF(__pyx_t_4);
14152 #endif
14153 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14154 } else {
14155 Py_ssize_t index = -1;
14156 __pyx_t_6 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 357, __pyx_L1_error)
14157 __Pyx_GOTREF(__pyx_t_6);
14158 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14159 __pyx_t_7 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_6);
14160 index = 0; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L4_unpacking_failed;
14161 __Pyx_GOTREF(__pyx_t_3);
14162 index = 1; __pyx_t_4 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_4)) goto __pyx_L4_unpacking_failed;
14163 __Pyx_GOTREF(__pyx_t_4);
14164 if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) __PYX_ERR(0, 357, __pyx_L1_error)
14165 __pyx_t_7 = NULL;
14166 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
14167 goto __pyx_L5_unpacking_done;
14168 __pyx_L4_unpacking_failed:;
14169 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
14170 __pyx_t_7 = NULL;
14171 if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
14172 __PYX_ERR(0, 357, __pyx_L1_error)
14173 __pyx_L5_unpacking_done:;
14174 }
14175 __pyx_v_errorlabel = __pyx_t_3;
14176 __pyx_t_3 = 0;
14177 __pyx_v_errorstring = __pyx_t_4;
14178 __pyx_t_4 = 0;
14179
14180 /* "pysam/libcvcf.pyx":358
14181 * if error in self._ignored_errors: return
14182 * errorlabel, errorstring = self._errors[error].split(':')
14183 * if opt: errorstring = errorstring % opt # <<<<<<<<<<<<<<
14184 * errwarn = ["Error","Warning"][error in self._warn_errors]
14185 * errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring)
14186 */
14187 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_opt); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 358, __pyx_L1_error)
14188 if (__pyx_t_2) {
14189 __pyx_t_1 = PyNumber_Remainder(__pyx_v_errorstring, __pyx_v_opt); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 358, __pyx_L1_error)
14190 __Pyx_GOTREF(__pyx_t_1);
14191 __Pyx_DECREF_SET(__pyx_v_errorstring, __pyx_t_1);
14192 __pyx_t_1 = 0;
14193 }
14194
14195 /* "pysam/libcvcf.pyx":359
14196 * errorlabel, errorstring = self._errors[error].split(':')
14197 * if opt: errorstring = errorstring % opt
14198 * errwarn = ["Error","Warning"][error in self._warn_errors] # <<<<<<<<<<<<<<
14199 * errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring)
14200 * if error in self._warn_errors: return
14201 */
14202 __pyx_t_1 = PyList_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 359, __pyx_L1_error)
14203 __Pyx_GOTREF(__pyx_t_1);
14204 __Pyx_INCREF(__pyx_n_u_Error);
14205 __Pyx_GIVEREF(__pyx_n_u_Error);
14206 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_u_Error)) __PYX_ERR(0, 359, __pyx_L1_error);
14207 __Pyx_INCREF(__pyx_n_u_Warning);
14208 __Pyx_GIVEREF(__pyx_n_u_Warning);
14209 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 1, __pyx_n_u_Warning)) __PYX_ERR(0, 359, __pyx_L1_error);
14210 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_warn_errors); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 359, __pyx_L1_error)
14211 __Pyx_GOTREF(__pyx_t_4);
14212 __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_v_error, __pyx_t_4, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 359, __pyx_L1_error)
14213 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
14214 __pyx_t_4 = __Pyx_GetItemInt_List(__pyx_t_1, __pyx_t_2, int, 1, __Pyx_PyBool_FromLong, 1, 1, 1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 359, __pyx_L1_error)
14215 __Pyx_GOTREF(__pyx_t_4);
14216 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14217 __pyx_v_errwarn = __pyx_t_4;
14218 __pyx_t_4 = 0;
14219
14220 /* "pysam/libcvcf.pyx":360
14221 * if opt: errorstring = errorstring % opt
14222 * errwarn = ["Error","Warning"][error in self._warn_errors]
14223 * errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring) # <<<<<<<<<<<<<<
14224 * if error in self._warn_errors: return
14225 * raise ValueError(errorstring)
14226 */
14227 __pyx_t_4 = PyTuple_New(11); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 360, __pyx_L1_error)
14228 __Pyx_GOTREF(__pyx_t_4);
14229 __pyx_t_8 = 0;
14230 __pyx_t_9 = 127;
14231 __Pyx_INCREF(__pyx_kp_u_in_line);
14232 __pyx_t_8 += 9;
14233 __Pyx_GIVEREF(__pyx_kp_u_in_line);
14234 PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_kp_u_in_line);
14235 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_lineno); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 360, __pyx_L1_error)
14236 __Pyx_GOTREF(__pyx_t_1);
14237 __pyx_t_3 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_1), __pyx_empty_unicode); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 360, __pyx_L1_error)
14238 __Pyx_GOTREF(__pyx_t_3);
14239 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14240 __pyx_t_9 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_3) > __pyx_t_9) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_3) : __pyx_t_9;
14241 __pyx_t_8 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_3);
14242 __Pyx_GIVEREF(__pyx_t_3);
14243 PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3);
14244 __pyx_t_3 = 0;
14245 __Pyx_INCREF(__pyx_kp_u__10);
14246 __pyx_t_8 += 3;
14247 __Pyx_GIVEREF(__pyx_kp_u__10);
14248 PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_kp_u__10);
14249 __pyx_t_3 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_line), __pyx_empty_unicode); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 360, __pyx_L1_error)
14250 __Pyx_GOTREF(__pyx_t_3);
14251 __pyx_t_9 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_3) > __pyx_t_9) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_3) : __pyx_t_9;
14252 __pyx_t_8 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_3);
14253 __Pyx_GIVEREF(__pyx_t_3);
14254 PyTuple_SET_ITEM(__pyx_t_4, 3, __pyx_t_3);
14255 __pyx_t_3 = 0;
14256 __Pyx_INCREF(__pyx_kp_u__11);
14257 __pyx_t_8 += 2;
14258 __Pyx_GIVEREF(__pyx_kp_u__11);
14259 PyTuple_SET_ITEM(__pyx_t_4, 4, __pyx_kp_u__11);
14260 __pyx_t_3 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_errwarn), __pyx_empty_unicode); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 360, __pyx_L1_error)
14261 __Pyx_GOTREF(__pyx_t_3);
14262 __pyx_t_9 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_3) > __pyx_t_9) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_3) : __pyx_t_9;
14263 __pyx_t_8 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_3);
14264 __Pyx_GIVEREF(__pyx_t_3);
14265 PyTuple_SET_ITEM(__pyx_t_4, 5, __pyx_t_3);
14266 __pyx_t_3 = 0;
14267 __Pyx_INCREF(__pyx_kp_u__12);
14268 __pyx_t_8 += 1;
14269 __Pyx_GIVEREF(__pyx_kp_u__12);
14270 PyTuple_SET_ITEM(__pyx_t_4, 6, __pyx_kp_u__12);
14271 __pyx_t_3 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_errorlabel), __pyx_empty_unicode); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 360, __pyx_L1_error)
14272 __Pyx_GOTREF(__pyx_t_3);
14273 __pyx_t_9 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_3) > __pyx_t_9) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_3) : __pyx_t_9;
14274 __pyx_t_8 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_3);
14275 __Pyx_GIVEREF(__pyx_t_3);
14276 PyTuple_SET_ITEM(__pyx_t_4, 7, __pyx_t_3);
14277 __pyx_t_3 = 0;
14278 __Pyx_INCREF(__pyx_kp_u__13);
14279 __pyx_t_8 += 2;
14280 __Pyx_GIVEREF(__pyx_kp_u__13);
14281 PyTuple_SET_ITEM(__pyx_t_4, 8, __pyx_kp_u__13);
14282 __pyx_t_3 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_errorstring), __pyx_empty_unicode); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 360, __pyx_L1_error)
14283 __Pyx_GOTREF(__pyx_t_3);
14284 __pyx_t_9 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_3) > __pyx_t_9) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_3) : __pyx_t_9;
14285 __pyx_t_8 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_3);
14286 __Pyx_GIVEREF(__pyx_t_3);
14287 PyTuple_SET_ITEM(__pyx_t_4, 9, __pyx_t_3);
14288 __pyx_t_3 = 0;
14289 __Pyx_INCREF(__pyx_kp_u__14);
14290 __pyx_t_8 += 1;
14291 __Pyx_GIVEREF(__pyx_kp_u__14);
14292 PyTuple_SET_ITEM(__pyx_t_4, 10, __pyx_kp_u__14);
14293 __pyx_t_3 = __Pyx_PyUnicode_Join(__pyx_t_4, 11, __pyx_t_8, __pyx_t_9); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 360, __pyx_L1_error)
14294 __Pyx_GOTREF(__pyx_t_3);
14295 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
14296 __pyx_t_4 = PyNumber_InPlaceAdd(__pyx_v_errorstring, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 360, __pyx_L1_error)
14297 __Pyx_GOTREF(__pyx_t_4);
14298 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
14299 __Pyx_DECREF_SET(__pyx_v_errorstring, __pyx_t_4);
14300 __pyx_t_4 = 0;
14301
14302 /* "pysam/libcvcf.pyx":361
14303 * errwarn = ["Error","Warning"][error in self._warn_errors]
14304 * errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring)
14305 * if error in self._warn_errors: return # <<<<<<<<<<<<<<
14306 * raise ValueError(errorstring)
14307 *
14308 */
14309 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_warn_errors); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 361, __pyx_L1_error)
14310 __Pyx_GOTREF(__pyx_t_4);
14311 __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_v_error, __pyx_t_4, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 361, __pyx_L1_error)
14312 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
14313 if (__pyx_t_2) {
14314 __Pyx_XDECREF(__pyx_r);
14315 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
14316 goto __pyx_L0;
14317 }
14318
14319 /* "pysam/libcvcf.pyx":362
14320 * errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring)
14321 * if error in self._warn_errors: return
14322 * raise ValueError(errorstring) # <<<<<<<<<<<<<<
14323 *
14324 * def parse_format(self,line,format,filter=False):
14325 */
14326 __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_v_errorstring); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 362, __pyx_L1_error)
14327 __Pyx_GOTREF(__pyx_t_4);
14328 __Pyx_Raise(__pyx_t_4, 0, 0, 0);
14329 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
14330 __PYX_ERR(0, 362, __pyx_L1_error)
14331
14332 /* "pysam/libcvcf.pyx":355
14333 * self.tabixfile = None
14334 *
14335 * def error(self,line,error,opt=None): # <<<<<<<<<<<<<<
14336 * if error in self._ignored_errors: return
14337 * errorlabel, errorstring = self._errors[error].split(':')
14338 */
14339
14340 /* function exit code */
14341 __pyx_L1_error:;
14342 __Pyx_XDECREF(__pyx_t_1);
14343 __Pyx_XDECREF(__pyx_t_3);
14344 __Pyx_XDECREF(__pyx_t_4);
14345 __Pyx_XDECREF(__pyx_t_6);
14346 __Pyx_AddTraceback("pysam.libcvcf.VCF.error", __pyx_clineno, __pyx_lineno, __pyx_filename);
14347 __pyx_r = NULL;
14348 __pyx_L0:;
14349 __Pyx_XDECREF(__pyx_v_errorlabel);
14350 __Pyx_XDECREF(__pyx_v_errorstring);
14351 __Pyx_XDECREF(__pyx_v_errwarn);
14352 __Pyx_XGIVEREF(__pyx_r);
14353 __Pyx_RefNannyFinishContext();
14354 return __pyx_r;
14355 }
14356
14357 /* "pysam/libcvcf.pyx":364
14358 * raise ValueError(errorstring)
14359 *
14360 * def parse_format(self,line,format,filter=False): # <<<<<<<<<<<<<<
14361 * if self._version == 40:
14362 * if not format.startswith('<'):
14363 */
14364
14365 /* Python wrapper */
14366 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_5parse_format(PyObject *__pyx_self,
14367 #if CYTHON_METH_FASTCALL
14368 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
14369 #else
14370 PyObject *__pyx_args, PyObject *__pyx_kwds
14371 #endif
14372 ); /*proto*/
14373 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_4parse_format, "VCF.parse_format(self, line, format, filter=False)");
14374 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_5parse_format = {"parse_format", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_5parse_format, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_4parse_format};
14375 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_5parse_format(PyObject *__pyx_self,
14376 #if CYTHON_METH_FASTCALL
14377 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
14378 #else
14379 PyObject *__pyx_args, PyObject *__pyx_kwds
14380 #endif
14381 ) {
14382 PyObject *__pyx_v_self = 0;
14383 PyObject *__pyx_v_line = 0;
14384 PyObject *__pyx_v_format = 0;
14385 PyObject *__pyx_v_filter = 0;
14386 #if !CYTHON_METH_FASTCALL
14387 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
14388 #endif
14389 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
14390 PyObject* values[4] = {0,0,0,0};
14391 int __pyx_lineno = 0;
14392 const char *__pyx_filename = NULL;
14393 int __pyx_clineno = 0;
14394 PyObject *__pyx_r = 0;
14395 __Pyx_RefNannyDeclarations
14396 __Pyx_RefNannySetupContext("parse_format (wrapper)", 0);
14397 #if !CYTHON_METH_FASTCALL
14398 #if CYTHON_ASSUME_SAFE_MACROS
14399 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
14400 #else
14401 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
14402 #endif
14403 #endif
14404 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
14405 {
14406 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_line,&__pyx_n_s_format,&__pyx_n_s_filter_2,0};
14407 values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False)));
14408 if (__pyx_kwds) {
14409 Py_ssize_t kw_args;
14410 switch (__pyx_nargs) {
14411 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
14412 CYTHON_FALLTHROUGH;
14413 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
14414 CYTHON_FALLTHROUGH;
14415 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
14416 CYTHON_FALLTHROUGH;
14417 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
14418 CYTHON_FALLTHROUGH;
14419 case 0: break;
14420 default: goto __pyx_L5_argtuple_error;
14421 }
14422 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
14423 switch (__pyx_nargs) {
14424 case 0:
14425 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
14426 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
14427 kw_args--;
14428 }
14429 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 364, __pyx_L3_error)
14430 else goto __pyx_L5_argtuple_error;
14431 CYTHON_FALLTHROUGH;
14432 case 1:
14433 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_line)) != 0)) {
14434 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
14435 kw_args--;
14436 }
14437 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 364, __pyx_L3_error)
14438 else {
14439 __Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, 1); __PYX_ERR(0, 364, __pyx_L3_error)
14440 }
14441 CYTHON_FALLTHROUGH;
14442 case 2:
14443 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_format)) != 0)) {
14444 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
14445 kw_args--;
14446 }
14447 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 364, __pyx_L3_error)
14448 else {
14449 __Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, 2); __PYX_ERR(0, 364, __pyx_L3_error)
14450 }
14451 CYTHON_FALLTHROUGH;
14452 case 3:
14453 if (kw_args > 0) {
14454 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filter_2);
14455 if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
14456 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 364, __pyx_L3_error)
14457 }
14458 }
14459 if (unlikely(kw_args > 0)) {
14460 const Py_ssize_t kwd_pos_args = __pyx_nargs;
14461 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "parse_format") < 0)) __PYX_ERR(0, 364, __pyx_L3_error)
14462 }
14463 } else {
14464 switch (__pyx_nargs) {
14465 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
14466 CYTHON_FALLTHROUGH;
14467 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
14468 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
14469 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
14470 break;
14471 default: goto __pyx_L5_argtuple_error;
14472 }
14473 }
14474 __pyx_v_self = values[0];
14475 __pyx_v_line = values[1];
14476 __pyx_v_format = values[2];
14477 __pyx_v_filter = values[3];
14478 }
14479 goto __pyx_L6_skip;
14480 __pyx_L5_argtuple_error:;
14481 __Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, __pyx_nargs); __PYX_ERR(0, 364, __pyx_L3_error)
14482 __pyx_L6_skip:;
14483 goto __pyx_L4_argument_unpacking_done;
14484 __pyx_L3_error:;
14485 {
14486 Py_ssize_t __pyx_temp;
14487 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
14488 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
14489 }
14490 }
14491 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_format", __pyx_clineno, __pyx_lineno, __pyx_filename);
14492 __Pyx_RefNannyFinishContext();
14493 return NULL;
14494 __pyx_L4_argument_unpacking_done:;
14495 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_4parse_format(__pyx_self, __pyx_v_self, __pyx_v_line, __pyx_v_format, __pyx_v_filter);
14496
14497 /* function exit code */
14498 {
14499 Py_ssize_t __pyx_temp;
14500 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
14501 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
14502 }
14503 }
14504 __Pyx_RefNannyFinishContext();
14505 return __pyx_r;
14506 }
14507
14508 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_format, PyObject *__pyx_v_filter) {
14509 PyObject *__pyx_v_data = NULL;
14510 PyObject *__pyx_v_idx = NULL;
14511 PyObject *__pyx_v_elts = NULL;
14512 PyObject *__pyx_v_first = NULL;
14513 PyObject *__pyx_v_rest = NULL;
14514 PyObject *__pyx_v_n = NULL;
14515 PyObject *__pyx_v_t = NULL;
14516 PyObject *__pyx_r = NULL;
14517 __Pyx_RefNannyDeclarations
14518 PyObject *__pyx_t_1 = NULL;
14519 int __pyx_t_2;
14520 PyObject *__pyx_t_3 = NULL;
14521 PyObject *__pyx_t_4 = NULL;
14522 unsigned int __pyx_t_5;
14523 int __pyx_t_6;
14524 PyObject *__pyx_t_7 = NULL;
14525 Py_ssize_t __pyx_t_8;
14526 int __pyx_t_9;
14527 PyObject *__pyx_t_10 = NULL;
14528 PyObject *__pyx_t_11 = NULL;
14529 PyObject *__pyx_t_12 = NULL;
14530 PyObject *__pyx_t_13 = NULL;
14531 PyObject *__pyx_t_14 = NULL;
14532 int __pyx_t_15;
14533 PyObject *__pyx_t_16 = NULL;
14534 int __pyx_lineno = 0;
14535 const char *__pyx_filename = NULL;
14536 int __pyx_clineno = 0;
14537 __Pyx_RefNannySetupContext("parse_format", 0);
14538 __Pyx_INCREF(__pyx_v_format);
14539
14540 /* "pysam/libcvcf.pyx":365
14541 *
14542 * def parse_format(self,line,format,filter=False):
14543 * if self._version == 40: # <<<<<<<<<<<<<<
14544 * if not format.startswith('<'):
14545 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
14546 */
14547 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_version); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 365, __pyx_L1_error)
14548 __Pyx_GOTREF(__pyx_t_1);
14549 __pyx_t_2 = (__Pyx_PyInt_BoolEqObjC(__pyx_t_1, __pyx_int_40, 40, 0)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 365, __pyx_L1_error)
14550 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14551 if (__pyx_t_2) {
14552
14553 /* "pysam/libcvcf.pyx":366
14554 * def parse_format(self,line,format,filter=False):
14555 * if self._version == 40:
14556 * if not format.startswith('<'): # <<<<<<<<<<<<<<
14557 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
14558 * format = "<"+format
14559 */
14560 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_format, __pyx_n_s_startswith); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 366, __pyx_L1_error)
14561 __Pyx_GOTREF(__pyx_t_3);
14562 __pyx_t_4 = NULL;
14563 __pyx_t_5 = 0;
14564 #if CYTHON_UNPACK_METHODS
14565 if (likely(PyMethod_Check(__pyx_t_3))) {
14566 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
14567 if (likely(__pyx_t_4)) {
14568 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
14569 __Pyx_INCREF(__pyx_t_4);
14570 __Pyx_INCREF(function);
14571 __Pyx_DECREF_SET(__pyx_t_3, function);
14572 __pyx_t_5 = 1;
14573 }
14574 }
14575 #endif
14576 {
14577 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_kp_u__15};
14578 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
14579 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
14580 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 366, __pyx_L1_error)
14581 __Pyx_GOTREF(__pyx_t_1);
14582 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
14583 }
14584 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 366, __pyx_L1_error)
14585 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14586 __pyx_t_6 = (!__pyx_t_2);
14587 if (__pyx_t_6) {
14588
14589 /* "pysam/libcvcf.pyx":367
14590 * if self._version == 40:
14591 * if not format.startswith('<'):
14592 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS) # <<<<<<<<<<<<<<
14593 * format = "<"+format
14594 * if not format.endswith('>'):
14595 */
14596 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 367, __pyx_L1_error)
14597 __Pyx_GOTREF(__pyx_t_3);
14598 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_V40_MISSING_ANGLE_BRACKETS); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 367, __pyx_L1_error)
14599 __Pyx_GOTREF(__pyx_t_4);
14600 __pyx_t_7 = NULL;
14601 __pyx_t_5 = 0;
14602 #if CYTHON_UNPACK_METHODS
14603 if (likely(PyMethod_Check(__pyx_t_3))) {
14604 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_3);
14605 if (likely(__pyx_t_7)) {
14606 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
14607 __Pyx_INCREF(__pyx_t_7);
14608 __Pyx_INCREF(function);
14609 __Pyx_DECREF_SET(__pyx_t_3, function);
14610 __pyx_t_5 = 1;
14611 }
14612 }
14613 #endif
14614 {
14615 PyObject *__pyx_callargs[3] = {__pyx_t_7, __pyx_v_line, __pyx_t_4};
14616 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
14617 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
14618 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
14619 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 367, __pyx_L1_error)
14620 __Pyx_GOTREF(__pyx_t_1);
14621 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
14622 }
14623 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14624
14625 /* "pysam/libcvcf.pyx":368
14626 * if not format.startswith('<'):
14627 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
14628 * format = "<"+format # <<<<<<<<<<<<<<
14629 * if not format.endswith('>'):
14630 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
14631 */
14632 __pyx_t_1 = PyNumber_Add(__pyx_kp_u__15, __pyx_v_format); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 368, __pyx_L1_error)
14633 __Pyx_GOTREF(__pyx_t_1);
14634 __Pyx_DECREF_SET(__pyx_v_format, __pyx_t_1);
14635 __pyx_t_1 = 0;
14636
14637 /* "pysam/libcvcf.pyx":366
14638 * def parse_format(self,line,format,filter=False):
14639 * if self._version == 40:
14640 * if not format.startswith('<'): # <<<<<<<<<<<<<<
14641 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
14642 * format = "<"+format
14643 */
14644 }
14645
14646 /* "pysam/libcvcf.pyx":369
14647 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
14648 * format = "<"+format
14649 * if not format.endswith('>'): # <<<<<<<<<<<<<<
14650 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
14651 * format += ">"
14652 */
14653 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_format, __pyx_n_s_endswith); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 369, __pyx_L1_error)
14654 __Pyx_GOTREF(__pyx_t_3);
14655 __pyx_t_4 = NULL;
14656 __pyx_t_5 = 0;
14657 #if CYTHON_UNPACK_METHODS
14658 if (likely(PyMethod_Check(__pyx_t_3))) {
14659 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
14660 if (likely(__pyx_t_4)) {
14661 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
14662 __Pyx_INCREF(__pyx_t_4);
14663 __Pyx_INCREF(function);
14664 __Pyx_DECREF_SET(__pyx_t_3, function);
14665 __pyx_t_5 = 1;
14666 }
14667 }
14668 #endif
14669 {
14670 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_kp_u__16};
14671 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
14672 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
14673 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 369, __pyx_L1_error)
14674 __Pyx_GOTREF(__pyx_t_1);
14675 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
14676 }
14677 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 369, __pyx_L1_error)
14678 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14679 __pyx_t_2 = (!__pyx_t_6);
14680 if (__pyx_t_2) {
14681
14682 /* "pysam/libcvcf.pyx":370
14683 * format = "<"+format
14684 * if not format.endswith('>'):
14685 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS) # <<<<<<<<<<<<<<
14686 * format += ">"
14687 * format = format[1:-1]
14688 */
14689 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 370, __pyx_L1_error)
14690 __Pyx_GOTREF(__pyx_t_3);
14691 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_V40_MISSING_ANGLE_BRACKETS); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 370, __pyx_L1_error)
14692 __Pyx_GOTREF(__pyx_t_4);
14693 __pyx_t_7 = NULL;
14694 __pyx_t_5 = 0;
14695 #if CYTHON_UNPACK_METHODS
14696 if (likely(PyMethod_Check(__pyx_t_3))) {
14697 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_3);
14698 if (likely(__pyx_t_7)) {
14699 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
14700 __Pyx_INCREF(__pyx_t_7);
14701 __Pyx_INCREF(function);
14702 __Pyx_DECREF_SET(__pyx_t_3, function);
14703 __pyx_t_5 = 1;
14704 }
14705 }
14706 #endif
14707 {
14708 PyObject *__pyx_callargs[3] = {__pyx_t_7, __pyx_v_line, __pyx_t_4};
14709 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
14710 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
14711 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
14712 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 370, __pyx_L1_error)
14713 __Pyx_GOTREF(__pyx_t_1);
14714 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
14715 }
14716 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14717
14718 /* "pysam/libcvcf.pyx":371
14719 * if not format.endswith('>'):
14720 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
14721 * format += ">" # <<<<<<<<<<<<<<
14722 * format = format[1:-1]
14723 * data = {'id':None,'number':None,'type':None,'descr':None}
14724 */
14725 __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_v_format, __pyx_kp_u__16); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 371, __pyx_L1_error)
14726 __Pyx_GOTREF(__pyx_t_1);
14727 __Pyx_DECREF_SET(__pyx_v_format, __pyx_t_1);
14728 __pyx_t_1 = 0;
14729
14730 /* "pysam/libcvcf.pyx":369
14731 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
14732 * format = "<"+format
14733 * if not format.endswith('>'): # <<<<<<<<<<<<<<
14734 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
14735 * format += ">"
14736 */
14737 }
14738
14739 /* "pysam/libcvcf.pyx":372
14740 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
14741 * format += ">"
14742 * format = format[1:-1] # <<<<<<<<<<<<<<
14743 * data = {'id':None,'number':None,'type':None,'descr':None}
14744 * idx = 0
14745 */
14746 __pyx_t_1 = __Pyx_PyObject_GetSlice(__pyx_v_format, 1, -1L, NULL, NULL, &__pyx_slice__17, 1, 1, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 372, __pyx_L1_error)
14747 __Pyx_GOTREF(__pyx_t_1);
14748 __Pyx_DECREF_SET(__pyx_v_format, __pyx_t_1);
14749 __pyx_t_1 = 0;
14750
14751 /* "pysam/libcvcf.pyx":365
14752 *
14753 * def parse_format(self,line,format,filter=False):
14754 * if self._version == 40: # <<<<<<<<<<<<<<
14755 * if not format.startswith('<'):
14756 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
14757 */
14758 }
14759
14760 /* "pysam/libcvcf.pyx":373
14761 * format += ">"
14762 * format = format[1:-1]
14763 * data = {'id':None,'number':None,'type':None,'descr':None} # <<<<<<<<<<<<<<
14764 * idx = 0
14765 * while len(format.strip())>0:
14766 */
14767 __pyx_t_1 = __Pyx_PyDict_NewPresized(4); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 373, __pyx_L1_error)
14768 __Pyx_GOTREF(__pyx_t_1);
14769 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_id_2, Py_None) < 0) __PYX_ERR(0, 373, __pyx_L1_error)
14770 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_number, Py_None) < 0) __PYX_ERR(0, 373, __pyx_L1_error)
14771 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_type, Py_None) < 0) __PYX_ERR(0, 373, __pyx_L1_error)
14772 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_descr, Py_None) < 0) __PYX_ERR(0, 373, __pyx_L1_error)
14773 __pyx_v_data = ((PyObject*)__pyx_t_1);
14774 __pyx_t_1 = 0;
14775
14776 /* "pysam/libcvcf.pyx":374
14777 * format = format[1:-1]
14778 * data = {'id':None,'number':None,'type':None,'descr':None}
14779 * idx = 0 # <<<<<<<<<<<<<<
14780 * while len(format.strip())>0:
14781 * elts = format.strip().split(',')
14782 */
14783 __Pyx_INCREF(__pyx_int_0);
14784 __pyx_v_idx = __pyx_int_0;
14785
14786 /* "pysam/libcvcf.pyx":375
14787 * data = {'id':None,'number':None,'type':None,'descr':None}
14788 * idx = 0
14789 * while len(format.strip())>0: # <<<<<<<<<<<<<<
14790 * elts = format.strip().split(',')
14791 * first, rest = elts[0], ','.join(elts[1:])
14792 */
14793 while (1) {
14794 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_format, __pyx_n_s_strip); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 375, __pyx_L1_error)
14795 __Pyx_GOTREF(__pyx_t_3);
14796 __pyx_t_4 = NULL;
14797 __pyx_t_5 = 0;
14798 #if CYTHON_UNPACK_METHODS
14799 if (likely(PyMethod_Check(__pyx_t_3))) {
14800 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
14801 if (likely(__pyx_t_4)) {
14802 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
14803 __Pyx_INCREF(__pyx_t_4);
14804 __Pyx_INCREF(function);
14805 __Pyx_DECREF_SET(__pyx_t_3, function);
14806 __pyx_t_5 = 1;
14807 }
14808 }
14809 #endif
14810 {
14811 PyObject *__pyx_callargs[2] = {__pyx_t_4, NULL};
14812 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 0+__pyx_t_5);
14813 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
14814 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 375, __pyx_L1_error)
14815 __Pyx_GOTREF(__pyx_t_1);
14816 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
14817 }
14818 __pyx_t_8 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_8 == ((Py_ssize_t)-1))) __PYX_ERR(0, 375, __pyx_L1_error)
14819 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14820 __pyx_t_2 = (__pyx_t_8 > 0);
14821 if (!__pyx_t_2) break;
14822
14823 /* "pysam/libcvcf.pyx":376
14824 * idx = 0
14825 * while len(format.strip())>0:
14826 * elts = format.strip().split(',') # <<<<<<<<<<<<<<
14827 * first, rest = elts[0], ','.join(elts[1:])
14828 * if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
14829 */
14830 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_format, __pyx_n_s_strip); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 376, __pyx_L1_error)
14831 __Pyx_GOTREF(__pyx_t_4);
14832 __pyx_t_7 = NULL;
14833 __pyx_t_5 = 0;
14834 #if CYTHON_UNPACK_METHODS
14835 if (likely(PyMethod_Check(__pyx_t_4))) {
14836 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_4);
14837 if (likely(__pyx_t_7)) {
14838 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
14839 __Pyx_INCREF(__pyx_t_7);
14840 __Pyx_INCREF(function);
14841 __Pyx_DECREF_SET(__pyx_t_4, function);
14842 __pyx_t_5 = 1;
14843 }
14844 }
14845 #endif
14846 {
14847 PyObject *__pyx_callargs[2] = {__pyx_t_7, NULL};
14848 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 0+__pyx_t_5);
14849 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
14850 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 376, __pyx_L1_error)
14851 __Pyx_GOTREF(__pyx_t_3);
14852 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
14853 }
14854 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_split); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 376, __pyx_L1_error)
14855 __Pyx_GOTREF(__pyx_t_4);
14856 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
14857 __pyx_t_3 = NULL;
14858 __pyx_t_5 = 0;
14859 #if CYTHON_UNPACK_METHODS
14860 if (likely(PyMethod_Check(__pyx_t_4))) {
14861 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_4);
14862 if (likely(__pyx_t_3)) {
14863 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
14864 __Pyx_INCREF(__pyx_t_3);
14865 __Pyx_INCREF(function);
14866 __Pyx_DECREF_SET(__pyx_t_4, function);
14867 __pyx_t_5 = 1;
14868 }
14869 }
14870 #endif
14871 {
14872 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_kp_u__2};
14873 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
14874 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
14875 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 376, __pyx_L1_error)
14876 __Pyx_GOTREF(__pyx_t_1);
14877 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
14878 }
14879 __Pyx_XDECREF_SET(__pyx_v_elts, __pyx_t_1);
14880 __pyx_t_1 = 0;
14881
14882 /* "pysam/libcvcf.pyx":377
14883 * while len(format.strip())>0:
14884 * elts = format.strip().split(',')
14885 * first, rest = elts[0], ','.join(elts[1:]) # <<<<<<<<<<<<<<
14886 * if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
14887 * if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
14888 */
14889 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_elts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 377, __pyx_L1_error)
14890 __Pyx_GOTREF(__pyx_t_1);
14891 __pyx_t_4 = __Pyx_PyObject_GetSlice(__pyx_v_elts, 1, 0, NULL, NULL, &__pyx_slice__18, 1, 0, 1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 377, __pyx_L1_error)
14892 __Pyx_GOTREF(__pyx_t_4);
14893 __pyx_t_3 = PyUnicode_Join(__pyx_kp_u__2, __pyx_t_4); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 377, __pyx_L1_error)
14894 __Pyx_GOTREF(__pyx_t_3);
14895 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
14896 __Pyx_XDECREF_SET(__pyx_v_first, __pyx_t_1);
14897 __pyx_t_1 = 0;
14898 __Pyx_XDECREF_SET(__pyx_v_rest, ((PyObject*)__pyx_t_3));
14899 __pyx_t_3 = 0;
14900
14901 /* "pysam/libcvcf.pyx":378
14902 * elts = format.strip().split(',')
14903 * first, rest = elts[0], ','.join(elts[1:])
14904 * if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')): # <<<<<<<<<<<<<<
14905 * if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
14906 * if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
14907 */
14908 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_first, __pyx_n_s_find); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 378, __pyx_L1_error)
14909 __Pyx_GOTREF(__pyx_t_1);
14910 __pyx_t_4 = NULL;
14911 __pyx_t_5 = 0;
14912 #if CYTHON_UNPACK_METHODS
14913 if (likely(PyMethod_Check(__pyx_t_1))) {
14914 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_1);
14915 if (likely(__pyx_t_4)) {
14916 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
14917 __Pyx_INCREF(__pyx_t_4);
14918 __Pyx_INCREF(function);
14919 __Pyx_DECREF_SET(__pyx_t_1, function);
14920 __pyx_t_5 = 1;
14921 }
14922 }
14923 #endif
14924 {
14925 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_kp_u__7};
14926 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
14927 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
14928 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 378, __pyx_L1_error)
14929 __Pyx_GOTREF(__pyx_t_3);
14930 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14931 }
14932 __pyx_t_6 = (__Pyx_PyInt_BoolEqObjC(__pyx_t_3, __pyx_int_neg_1, -1L, 0)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 378, __pyx_L1_error)
14933 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
14934 if (!__pyx_t_6) {
14935 } else {
14936 __pyx_t_2 = __pyx_t_6;
14937 goto __pyx_L9_bool_binop_done;
14938 }
14939 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_first, __pyx_n_s_find); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 378, __pyx_L1_error)
14940 __Pyx_GOTREF(__pyx_t_1);
14941 __pyx_t_4 = NULL;
14942 __pyx_t_5 = 0;
14943 #if CYTHON_UNPACK_METHODS
14944 if (likely(PyMethod_Check(__pyx_t_1))) {
14945 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_1);
14946 if (likely(__pyx_t_4)) {
14947 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
14948 __Pyx_INCREF(__pyx_t_4);
14949 __Pyx_INCREF(function);
14950 __Pyx_DECREF_SET(__pyx_t_1, function);
14951 __pyx_t_5 = 1;
14952 }
14953 }
14954 #endif
14955 {
14956 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_kp_u__19};
14957 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
14958 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
14959 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 378, __pyx_L1_error)
14960 __Pyx_GOTREF(__pyx_t_3);
14961 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14962 }
14963 __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_int_0, Py_GE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 378, __pyx_L1_error)
14964 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
14965 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 378, __pyx_L1_error)
14966 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
14967 if (__pyx_t_6) {
14968 } else {
14969 __pyx_t_2 = __pyx_t_6;
14970 goto __pyx_L9_bool_binop_done;
14971 }
14972 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_first, __pyx_n_s_find); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 378, __pyx_L1_error)
14973 __Pyx_GOTREF(__pyx_t_3);
14974 __pyx_t_4 = NULL;
14975 __pyx_t_5 = 0;
14976 #if CYTHON_UNPACK_METHODS
14977 if (likely(PyMethod_Check(__pyx_t_3))) {
14978 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
14979 if (likely(__pyx_t_4)) {
14980 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
14981 __Pyx_INCREF(__pyx_t_4);
14982 __Pyx_INCREF(function);
14983 __Pyx_DECREF_SET(__pyx_t_3, function);
14984 __pyx_t_5 = 1;
14985 }
14986 }
14987 #endif
14988 {
14989 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_kp_u__7};
14990 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
14991 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
14992 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 378, __pyx_L1_error)
14993 __Pyx_GOTREF(__pyx_t_1);
14994 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
14995 }
14996 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_first, __pyx_n_s_find); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 378, __pyx_L1_error)
14997 __Pyx_GOTREF(__pyx_t_4);
14998 __pyx_t_7 = NULL;
14999 __pyx_t_5 = 0;
15000 #if CYTHON_UNPACK_METHODS
15001 if (likely(PyMethod_Check(__pyx_t_4))) {
15002 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_4);
15003 if (likely(__pyx_t_7)) {
15004 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
15005 __Pyx_INCREF(__pyx_t_7);
15006 __Pyx_INCREF(function);
15007 __Pyx_DECREF_SET(__pyx_t_4, function);
15008 __pyx_t_5 = 1;
15009 }
15010 }
15011 #endif
15012 {
15013 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_kp_u__19};
15014 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
15015 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
15016 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 378, __pyx_L1_error)
15017 __Pyx_GOTREF(__pyx_t_3);
15018 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15019 }
15020 __pyx_t_4 = PyObject_RichCompare(__pyx_t_1, __pyx_t_3, Py_GT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 378, __pyx_L1_error)
15021 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
15022 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15023 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 378, __pyx_L1_error)
15024 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15025 __pyx_t_2 = __pyx_t_6;
15026 __pyx_L9_bool_binop_done:;
15027 if (__pyx_t_2) {
15028
15029 /* "pysam/libcvcf.pyx":379
15030 * first, rest = elts[0], ','.join(elts[1:])
15031 * if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
15032 * if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS) # <<<<<<<<<<<<<<
15033 * if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15034 * first = ["ID=","Number=","Type=","Description="][idx] + first
15035 */
15036 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_version); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 379, __pyx_L1_error)
15037 __Pyx_GOTREF(__pyx_t_4);
15038 __pyx_t_2 = (__Pyx_PyInt_BoolEqObjC(__pyx_t_4, __pyx_int_40, 40, 0)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 379, __pyx_L1_error)
15039 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15040 if (__pyx_t_2) {
15041 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 379, __pyx_L1_error)
15042 __Pyx_GOTREF(__pyx_t_3);
15043 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_V40_FORMAT_MUST_HAVE_NAMED_FIELD); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 379, __pyx_L1_error)
15044 __Pyx_GOTREF(__pyx_t_1);
15045 __pyx_t_7 = NULL;
15046 __pyx_t_5 = 0;
15047 #if CYTHON_UNPACK_METHODS
15048 if (likely(PyMethod_Check(__pyx_t_3))) {
15049 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_3);
15050 if (likely(__pyx_t_7)) {
15051 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
15052 __Pyx_INCREF(__pyx_t_7);
15053 __Pyx_INCREF(function);
15054 __Pyx_DECREF_SET(__pyx_t_3, function);
15055 __pyx_t_5 = 1;
15056 }
15057 }
15058 #endif
15059 {
15060 PyObject *__pyx_callargs[3] = {__pyx_t_7, __pyx_v_line, __pyx_t_1};
15061 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
15062 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
15063 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
15064 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 379, __pyx_L1_error)
15065 __Pyx_GOTREF(__pyx_t_4);
15066 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15067 }
15068 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15069 }
15070
15071 /* "pysam/libcvcf.pyx":380
15072 * if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
15073 * if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
15074 * if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
15075 * first = ["ID=","Number=","Type=","Description="][idx] + first
15076 * if first.startswith('ID='): data['id'] = first.split('=')[1]
15077 */
15078 __pyx_t_2 = (__Pyx_PyInt_BoolEqObjC(__pyx_v_idx, __pyx_int_4, 4, 0)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 380, __pyx_L1_error)
15079 if (__pyx_t_2) {
15080 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 380, __pyx_L1_error)
15081 __Pyx_GOTREF(__pyx_t_3);
15082 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_BADLY_FORMATTED_FORMAT_STRING); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 380, __pyx_L1_error)
15083 __Pyx_GOTREF(__pyx_t_1);
15084 __pyx_t_7 = NULL;
15085 __pyx_t_5 = 0;
15086 #if CYTHON_UNPACK_METHODS
15087 if (likely(PyMethod_Check(__pyx_t_3))) {
15088 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_3);
15089 if (likely(__pyx_t_7)) {
15090 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
15091 __Pyx_INCREF(__pyx_t_7);
15092 __Pyx_INCREF(function);
15093 __Pyx_DECREF_SET(__pyx_t_3, function);
15094 __pyx_t_5 = 1;
15095 }
15096 }
15097 #endif
15098 {
15099 PyObject *__pyx_callargs[3] = {__pyx_t_7, __pyx_v_line, __pyx_t_1};
15100 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
15101 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
15102 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
15103 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 380, __pyx_L1_error)
15104 __Pyx_GOTREF(__pyx_t_4);
15105 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15106 }
15107 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15108 }
15109
15110 /* "pysam/libcvcf.pyx":381
15111 * if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
15112 * if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15113 * first = ["ID=","Number=","Type=","Description="][idx] + first # <<<<<<<<<<<<<<
15114 * if first.startswith('ID='): data['id'] = first.split('=')[1]
15115 * elif first.startswith('Number='): data['number'] = first.split('=')[1]
15116 */
15117 __pyx_t_4 = PyList_New(4); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 381, __pyx_L1_error)
15118 __Pyx_GOTREF(__pyx_t_4);
15119 __Pyx_INCREF(__pyx_kp_u_ID);
15120 __Pyx_GIVEREF(__pyx_kp_u_ID);
15121 if (__Pyx_PyList_SET_ITEM(__pyx_t_4, 0, __pyx_kp_u_ID)) __PYX_ERR(0, 381, __pyx_L1_error);
15122 __Pyx_INCREF(__pyx_kp_u_Number);
15123 __Pyx_GIVEREF(__pyx_kp_u_Number);
15124 if (__Pyx_PyList_SET_ITEM(__pyx_t_4, 1, __pyx_kp_u_Number)) __PYX_ERR(0, 381, __pyx_L1_error);
15125 __Pyx_INCREF(__pyx_kp_u_Type);
15126 __Pyx_GIVEREF(__pyx_kp_u_Type);
15127 if (__Pyx_PyList_SET_ITEM(__pyx_t_4, 2, __pyx_kp_u_Type)) __PYX_ERR(0, 381, __pyx_L1_error);
15128 __Pyx_INCREF(__pyx_kp_u_Description);
15129 __Pyx_GIVEREF(__pyx_kp_u_Description);
15130 if (__Pyx_PyList_SET_ITEM(__pyx_t_4, 3, __pyx_kp_u_Description)) __PYX_ERR(0, 381, __pyx_L1_error);
15131 __pyx_t_3 = __Pyx_PyObject_GetItem(__pyx_t_4, __pyx_v_idx); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 381, __pyx_L1_error)
15132 __Pyx_GOTREF(__pyx_t_3);
15133 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15134 __pyx_t_4 = PyNumber_Add(__pyx_t_3, __pyx_v_first); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 381, __pyx_L1_error)
15135 __Pyx_GOTREF(__pyx_t_4);
15136 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15137 __Pyx_DECREF_SET(__pyx_v_first, __pyx_t_4);
15138 __pyx_t_4 = 0;
15139
15140 /* "pysam/libcvcf.pyx":378
15141 * elts = format.strip().split(',')
15142 * first, rest = elts[0], ','.join(elts[1:])
15143 * if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')): # <<<<<<<<<<<<<<
15144 * if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
15145 * if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15146 */
15147 }
15148
15149 /* "pysam/libcvcf.pyx":382
15150 * if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15151 * first = ["ID=","Number=","Type=","Description="][idx] + first
15152 * if first.startswith('ID='): data['id'] = first.split('=')[1] # <<<<<<<<<<<<<<
15153 * elif first.startswith('Number='): data['number'] = first.split('=')[1]
15154 * elif first.startswith('Type='): data['type'] = first.split('=')[1]
15155 */
15156 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_first, __pyx_n_s_startswith); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 382, __pyx_L1_error)
15157 __Pyx_GOTREF(__pyx_t_3);
15158 __pyx_t_1 = NULL;
15159 __pyx_t_5 = 0;
15160 #if CYTHON_UNPACK_METHODS
15161 if (likely(PyMethod_Check(__pyx_t_3))) {
15162 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_3);
15163 if (likely(__pyx_t_1)) {
15164 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
15165 __Pyx_INCREF(__pyx_t_1);
15166 __Pyx_INCREF(function);
15167 __Pyx_DECREF_SET(__pyx_t_3, function);
15168 __pyx_t_5 = 1;
15169 }
15170 }
15171 #endif
15172 {
15173 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_kp_u_ID};
15174 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
15175 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
15176 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 382, __pyx_L1_error)
15177 __Pyx_GOTREF(__pyx_t_4);
15178 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15179 }
15180 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 382, __pyx_L1_error)
15181 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15182 if (__pyx_t_2) {
15183 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_first, __pyx_n_s_split); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 382, __pyx_L1_error)
15184 __Pyx_GOTREF(__pyx_t_3);
15185 __pyx_t_1 = NULL;
15186 __pyx_t_5 = 0;
15187 #if CYTHON_UNPACK_METHODS
15188 if (likely(PyMethod_Check(__pyx_t_3))) {
15189 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_3);
15190 if (likely(__pyx_t_1)) {
15191 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
15192 __Pyx_INCREF(__pyx_t_1);
15193 __Pyx_INCREF(function);
15194 __Pyx_DECREF_SET(__pyx_t_3, function);
15195 __pyx_t_5 = 1;
15196 }
15197 }
15198 #endif
15199 {
15200 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_kp_u__7};
15201 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
15202 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
15203 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 382, __pyx_L1_error)
15204 __Pyx_GOTREF(__pyx_t_4);
15205 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15206 }
15207 __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_4, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 382, __pyx_L1_error)
15208 __Pyx_GOTREF(__pyx_t_3);
15209 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15210 if (unlikely((PyDict_SetItem(__pyx_v_data, __pyx_n_u_id_2, __pyx_t_3) < 0))) __PYX_ERR(0, 382, __pyx_L1_error)
15211 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15212 goto __pyx_L14;
15213 }
15214
15215 /* "pysam/libcvcf.pyx":383
15216 * first = ["ID=","Number=","Type=","Description="][idx] + first
15217 * if first.startswith('ID='): data['id'] = first.split('=')[1]
15218 * elif first.startswith('Number='): data['number'] = first.split('=')[1] # <<<<<<<<<<<<<<
15219 * elif first.startswith('Type='): data['type'] = first.split('=')[1]
15220 * elif first.startswith('Description='):
15221 */
15222 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_first, __pyx_n_s_startswith); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 383, __pyx_L1_error)
15223 __Pyx_GOTREF(__pyx_t_4);
15224 __pyx_t_1 = NULL;
15225 __pyx_t_5 = 0;
15226 #if CYTHON_UNPACK_METHODS
15227 if (likely(PyMethod_Check(__pyx_t_4))) {
15228 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_4);
15229 if (likely(__pyx_t_1)) {
15230 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
15231 __Pyx_INCREF(__pyx_t_1);
15232 __Pyx_INCREF(function);
15233 __Pyx_DECREF_SET(__pyx_t_4, function);
15234 __pyx_t_5 = 1;
15235 }
15236 }
15237 #endif
15238 {
15239 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_kp_u_Number};
15240 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
15241 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
15242 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 383, __pyx_L1_error)
15243 __Pyx_GOTREF(__pyx_t_3);
15244 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15245 }
15246 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 383, __pyx_L1_error)
15247 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15248 if (__pyx_t_2) {
15249 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_first, __pyx_n_s_split); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 383, __pyx_L1_error)
15250 __Pyx_GOTREF(__pyx_t_4);
15251 __pyx_t_1 = NULL;
15252 __pyx_t_5 = 0;
15253 #if CYTHON_UNPACK_METHODS
15254 if (likely(PyMethod_Check(__pyx_t_4))) {
15255 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_4);
15256 if (likely(__pyx_t_1)) {
15257 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
15258 __Pyx_INCREF(__pyx_t_1);
15259 __Pyx_INCREF(function);
15260 __Pyx_DECREF_SET(__pyx_t_4, function);
15261 __pyx_t_5 = 1;
15262 }
15263 }
15264 #endif
15265 {
15266 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_kp_u__7};
15267 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
15268 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
15269 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 383, __pyx_L1_error)
15270 __Pyx_GOTREF(__pyx_t_3);
15271 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15272 }
15273 __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 383, __pyx_L1_error)
15274 __Pyx_GOTREF(__pyx_t_4);
15275 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15276 if (unlikely((PyDict_SetItem(__pyx_v_data, __pyx_n_u_number, __pyx_t_4) < 0))) __PYX_ERR(0, 383, __pyx_L1_error)
15277 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15278 goto __pyx_L14;
15279 }
15280
15281 /* "pysam/libcvcf.pyx":384
15282 * if first.startswith('ID='): data['id'] = first.split('=')[1]
15283 * elif first.startswith('Number='): data['number'] = first.split('=')[1]
15284 * elif first.startswith('Type='): data['type'] = first.split('=')[1] # <<<<<<<<<<<<<<
15285 * elif first.startswith('Description='):
15286 * elts = format.split('"')
15287 */
15288 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_first, __pyx_n_s_startswith); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 384, __pyx_L1_error)
15289 __Pyx_GOTREF(__pyx_t_3);
15290 __pyx_t_1 = NULL;
15291 __pyx_t_5 = 0;
15292 #if CYTHON_UNPACK_METHODS
15293 if (likely(PyMethod_Check(__pyx_t_3))) {
15294 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_3);
15295 if (likely(__pyx_t_1)) {
15296 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
15297 __Pyx_INCREF(__pyx_t_1);
15298 __Pyx_INCREF(function);
15299 __Pyx_DECREF_SET(__pyx_t_3, function);
15300 __pyx_t_5 = 1;
15301 }
15302 }
15303 #endif
15304 {
15305 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_kp_u_Type};
15306 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
15307 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
15308 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 384, __pyx_L1_error)
15309 __Pyx_GOTREF(__pyx_t_4);
15310 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15311 }
15312 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 384, __pyx_L1_error)
15313 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15314 if (__pyx_t_2) {
15315 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_first, __pyx_n_s_split); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 384, __pyx_L1_error)
15316 __Pyx_GOTREF(__pyx_t_3);
15317 __pyx_t_1 = NULL;
15318 __pyx_t_5 = 0;
15319 #if CYTHON_UNPACK_METHODS
15320 if (likely(PyMethod_Check(__pyx_t_3))) {
15321 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_3);
15322 if (likely(__pyx_t_1)) {
15323 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
15324 __Pyx_INCREF(__pyx_t_1);
15325 __Pyx_INCREF(function);
15326 __Pyx_DECREF_SET(__pyx_t_3, function);
15327 __pyx_t_5 = 1;
15328 }
15329 }
15330 #endif
15331 {
15332 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_kp_u__7};
15333 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
15334 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
15335 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 384, __pyx_L1_error)
15336 __Pyx_GOTREF(__pyx_t_4);
15337 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15338 }
15339 __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_4, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 384, __pyx_L1_error)
15340 __Pyx_GOTREF(__pyx_t_3);
15341 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15342 if (unlikely((PyDict_SetItem(__pyx_v_data, __pyx_n_u_type, __pyx_t_3) < 0))) __PYX_ERR(0, 384, __pyx_L1_error)
15343 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15344 goto __pyx_L14;
15345 }
15346
15347 /* "pysam/libcvcf.pyx":385
15348 * elif first.startswith('Number='): data['number'] = first.split('=')[1]
15349 * elif first.startswith('Type='): data['type'] = first.split('=')[1]
15350 * elif first.startswith('Description='): # <<<<<<<<<<<<<<
15351 * elts = format.split('"')
15352 * if len(elts)<3:
15353 */
15354 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_first, __pyx_n_s_startswith); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 385, __pyx_L1_error)
15355 __Pyx_GOTREF(__pyx_t_4);
15356 __pyx_t_1 = NULL;
15357 __pyx_t_5 = 0;
15358 #if CYTHON_UNPACK_METHODS
15359 if (likely(PyMethod_Check(__pyx_t_4))) {
15360 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_4);
15361 if (likely(__pyx_t_1)) {
15362 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
15363 __Pyx_INCREF(__pyx_t_1);
15364 __Pyx_INCREF(function);
15365 __Pyx_DECREF_SET(__pyx_t_4, function);
15366 __pyx_t_5 = 1;
15367 }
15368 }
15369 #endif
15370 {
15371 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_kp_u_Description};
15372 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
15373 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
15374 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 385, __pyx_L1_error)
15375 __Pyx_GOTREF(__pyx_t_3);
15376 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15377 }
15378 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 385, __pyx_L1_error)
15379 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15380 if (__pyx_t_2) {
15381
15382 /* "pysam/libcvcf.pyx":386
15383 * elif first.startswith('Type='): data['type'] = first.split('=')[1]
15384 * elif first.startswith('Description='):
15385 * elts = format.split('"') # <<<<<<<<<<<<<<
15386 * if len(elts)<3:
15387 * self.error(line,self.FORMAT_MISSING_QUOTES)
15388 */
15389 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_format, __pyx_n_s_split); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 386, __pyx_L1_error)
15390 __Pyx_GOTREF(__pyx_t_4);
15391 __pyx_t_1 = NULL;
15392 __pyx_t_5 = 0;
15393 #if CYTHON_UNPACK_METHODS
15394 if (likely(PyMethod_Check(__pyx_t_4))) {
15395 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_4);
15396 if (likely(__pyx_t_1)) {
15397 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
15398 __Pyx_INCREF(__pyx_t_1);
15399 __Pyx_INCREF(function);
15400 __Pyx_DECREF_SET(__pyx_t_4, function);
15401 __pyx_t_5 = 1;
15402 }
15403 }
15404 #endif
15405 {
15406 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_kp_u__19};
15407 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
15408 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
15409 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 386, __pyx_L1_error)
15410 __Pyx_GOTREF(__pyx_t_3);
15411 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15412 }
15413 __Pyx_DECREF_SET(__pyx_v_elts, __pyx_t_3);
15414 __pyx_t_3 = 0;
15415
15416 /* "pysam/libcvcf.pyx":387
15417 * elif first.startswith('Description='):
15418 * elts = format.split('"')
15419 * if len(elts)<3: # <<<<<<<<<<<<<<
15420 * self.error(line,self.FORMAT_MISSING_QUOTES)
15421 * elts = first.split('=') + [rest]
15422 */
15423 __pyx_t_8 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_8 == ((Py_ssize_t)-1))) __PYX_ERR(0, 387, __pyx_L1_error)
15424 __pyx_t_2 = (__pyx_t_8 < 3);
15425 if (__pyx_t_2) {
15426
15427 /* "pysam/libcvcf.pyx":388
15428 * elts = format.split('"')
15429 * if len(elts)<3:
15430 * self.error(line,self.FORMAT_MISSING_QUOTES) # <<<<<<<<<<<<<<
15431 * elts = first.split('=') + [rest]
15432 * data['descr'] = elts[1]
15433 */
15434 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 388, __pyx_L1_error)
15435 __Pyx_GOTREF(__pyx_t_4);
15436 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_FORMAT_MISSING_QUOTES); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 388, __pyx_L1_error)
15437 __Pyx_GOTREF(__pyx_t_1);
15438 __pyx_t_7 = NULL;
15439 __pyx_t_5 = 0;
15440 #if CYTHON_UNPACK_METHODS
15441 if (likely(PyMethod_Check(__pyx_t_4))) {
15442 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_4);
15443 if (likely(__pyx_t_7)) {
15444 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
15445 __Pyx_INCREF(__pyx_t_7);
15446 __Pyx_INCREF(function);
15447 __Pyx_DECREF_SET(__pyx_t_4, function);
15448 __pyx_t_5 = 1;
15449 }
15450 }
15451 #endif
15452 {
15453 PyObject *__pyx_callargs[3] = {__pyx_t_7, __pyx_v_line, __pyx_t_1};
15454 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
15455 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
15456 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
15457 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 388, __pyx_L1_error)
15458 __Pyx_GOTREF(__pyx_t_3);
15459 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15460 }
15461 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15462
15463 /* "pysam/libcvcf.pyx":389
15464 * if len(elts)<3:
15465 * self.error(line,self.FORMAT_MISSING_QUOTES)
15466 * elts = first.split('=') + [rest] # <<<<<<<<<<<<<<
15467 * data['descr'] = elts[1]
15468 * rest = '"'.join(elts[2:])
15469 */
15470 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_first, __pyx_n_s_split); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 389, __pyx_L1_error)
15471 __Pyx_GOTREF(__pyx_t_4);
15472 __pyx_t_1 = NULL;
15473 __pyx_t_5 = 0;
15474 #if CYTHON_UNPACK_METHODS
15475 if (likely(PyMethod_Check(__pyx_t_4))) {
15476 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_4);
15477 if (likely(__pyx_t_1)) {
15478 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
15479 __Pyx_INCREF(__pyx_t_1);
15480 __Pyx_INCREF(function);
15481 __Pyx_DECREF_SET(__pyx_t_4, function);
15482 __pyx_t_5 = 1;
15483 }
15484 }
15485 #endif
15486 {
15487 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_kp_u__7};
15488 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
15489 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
15490 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 389, __pyx_L1_error)
15491 __Pyx_GOTREF(__pyx_t_3);
15492 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15493 }
15494 __pyx_t_4 = PyList_New(1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 389, __pyx_L1_error)
15495 __Pyx_GOTREF(__pyx_t_4);
15496 __Pyx_INCREF(__pyx_v_rest);
15497 __Pyx_GIVEREF(__pyx_v_rest);
15498 if (__Pyx_PyList_SET_ITEM(__pyx_t_4, 0, __pyx_v_rest)) __PYX_ERR(0, 389, __pyx_L1_error);
15499 __pyx_t_1 = PyNumber_Add(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 389, __pyx_L1_error)
15500 __Pyx_GOTREF(__pyx_t_1);
15501 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15502 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15503 __Pyx_DECREF_SET(__pyx_v_elts, __pyx_t_1);
15504 __pyx_t_1 = 0;
15505
15506 /* "pysam/libcvcf.pyx":387
15507 * elif first.startswith('Description='):
15508 * elts = format.split('"')
15509 * if len(elts)<3: # <<<<<<<<<<<<<<
15510 * self.error(line,self.FORMAT_MISSING_QUOTES)
15511 * elts = first.split('=') + [rest]
15512 */
15513 }
15514
15515 /* "pysam/libcvcf.pyx":390
15516 * self.error(line,self.FORMAT_MISSING_QUOTES)
15517 * elts = first.split('=') + [rest]
15518 * data['descr'] = elts[1] # <<<<<<<<<<<<<<
15519 * rest = '"'.join(elts[2:])
15520 * if rest.startswith(','): rest = rest[1:]
15521 */
15522 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_elts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 390, __pyx_L1_error)
15523 __Pyx_GOTREF(__pyx_t_1);
15524 if (unlikely((PyDict_SetItem(__pyx_v_data, __pyx_n_u_descr, __pyx_t_1) < 0))) __PYX_ERR(0, 390, __pyx_L1_error)
15525 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
15526
15527 /* "pysam/libcvcf.pyx":391
15528 * elts = first.split('=') + [rest]
15529 * data['descr'] = elts[1]
15530 * rest = '"'.join(elts[2:]) # <<<<<<<<<<<<<<
15531 * if rest.startswith(','): rest = rest[1:]
15532 * else:
15533 */
15534 __pyx_t_1 = __Pyx_PyObject_GetSlice(__pyx_v_elts, 2, 0, NULL, NULL, &__pyx_slice__20, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 391, __pyx_L1_error)
15535 __Pyx_GOTREF(__pyx_t_1);
15536 __pyx_t_4 = PyUnicode_Join(__pyx_kp_u__19, __pyx_t_1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 391, __pyx_L1_error)
15537 __Pyx_GOTREF(__pyx_t_4);
15538 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
15539 __Pyx_DECREF_SET(__pyx_v_rest, ((PyObject*)__pyx_t_4));
15540 __pyx_t_4 = 0;
15541
15542 /* "pysam/libcvcf.pyx":392
15543 * data['descr'] = elts[1]
15544 * rest = '"'.join(elts[2:])
15545 * if rest.startswith(','): rest = rest[1:] # <<<<<<<<<<<<<<
15546 * else:
15547 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15548 */
15549 if (unlikely(__pyx_v_rest == Py_None)) {
15550 PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%.30s'", "startswith");
15551 __PYX_ERR(0, 392, __pyx_L1_error)
15552 }
15553 __pyx_t_2 = __Pyx_PyUnicode_Tailmatch(__pyx_v_rest, __pyx_kp_u__2, 0, PY_SSIZE_T_MAX, -1); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 392, __pyx_L1_error)
15554 if (__pyx_t_2) {
15555 if (unlikely(__pyx_v_rest == Py_None)) {
15556 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
15557 __PYX_ERR(0, 392, __pyx_L1_error)
15558 }
15559 __pyx_t_4 = __Pyx_PyUnicode_Substring(__pyx_v_rest, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 392, __pyx_L1_error)
15560 __Pyx_GOTREF(__pyx_t_4);
15561 __Pyx_DECREF_SET(__pyx_v_rest, ((PyObject*)__pyx_t_4));
15562 __pyx_t_4 = 0;
15563 }
15564
15565 /* "pysam/libcvcf.pyx":385
15566 * elif first.startswith('Number='): data['number'] = first.split('=')[1]
15567 * elif first.startswith('Type='): data['type'] = first.split('=')[1]
15568 * elif first.startswith('Description='): # <<<<<<<<<<<<<<
15569 * elts = format.split('"')
15570 * if len(elts)<3:
15571 */
15572 goto __pyx_L14;
15573 }
15574
15575 /* "pysam/libcvcf.pyx":394
15576 * if rest.startswith(','): rest = rest[1:]
15577 * else:
15578 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
15579 * format = rest
15580 * idx += 1
15581 */
15582 /*else*/ {
15583 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 394, __pyx_L1_error)
15584 __Pyx_GOTREF(__pyx_t_1);
15585 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_BADLY_FORMATTED_FORMAT_STRING); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 394, __pyx_L1_error)
15586 __Pyx_GOTREF(__pyx_t_3);
15587 __pyx_t_7 = NULL;
15588 __pyx_t_5 = 0;
15589 #if CYTHON_UNPACK_METHODS
15590 if (likely(PyMethod_Check(__pyx_t_1))) {
15591 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_1);
15592 if (likely(__pyx_t_7)) {
15593 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
15594 __Pyx_INCREF(__pyx_t_7);
15595 __Pyx_INCREF(function);
15596 __Pyx_DECREF_SET(__pyx_t_1, function);
15597 __pyx_t_5 = 1;
15598 }
15599 }
15600 #endif
15601 {
15602 PyObject *__pyx_callargs[3] = {__pyx_t_7, __pyx_v_line, __pyx_t_3};
15603 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
15604 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
15605 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15606 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 394, __pyx_L1_error)
15607 __Pyx_GOTREF(__pyx_t_4);
15608 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
15609 }
15610 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15611 }
15612 __pyx_L14:;
15613
15614 /* "pysam/libcvcf.pyx":395
15615 * else:
15616 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15617 * format = rest # <<<<<<<<<<<<<<
15618 * idx += 1
15619 * if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings
15620 */
15621 __Pyx_INCREF(__pyx_v_rest);
15622 __Pyx_DECREF_SET(__pyx_v_format, __pyx_v_rest);
15623
15624 /* "pysam/libcvcf.pyx":396
15625 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15626 * format = rest
15627 * idx += 1 # <<<<<<<<<<<<<<
15628 * if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings
15629 * if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15630 */
15631 __pyx_t_4 = __Pyx_PyInt_AddObjC(__pyx_v_idx, __pyx_int_1, 1, 1, 0); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 396, __pyx_L1_error)
15632 __Pyx_GOTREF(__pyx_t_4);
15633 __Pyx_DECREF_SET(__pyx_v_idx, __pyx_t_4);
15634 __pyx_t_4 = 0;
15635
15636 /* "pysam/libcvcf.pyx":397
15637 * format = rest
15638 * idx += 1
15639 * if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings # <<<<<<<<<<<<<<
15640 * if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15641 * if 'descr' not in data:
15642 */
15643 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_filter); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 397, __pyx_L1_error)
15644 if (__pyx_t_6) {
15645 } else {
15646 __pyx_t_2 = __pyx_t_6;
15647 goto __pyx_L18_bool_binop_done;
15648 }
15649 __pyx_t_6 = (__Pyx_PyInt_BoolEqObjC(__pyx_v_idx, __pyx_int_1, 1, 0)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 397, __pyx_L1_error)
15650 __pyx_t_2 = __pyx_t_6;
15651 __pyx_L18_bool_binop_done:;
15652 if (__pyx_t_2) {
15653 __Pyx_INCREF(__pyx_int_3);
15654 __Pyx_DECREF_SET(__pyx_v_idx, __pyx_int_3);
15655 }
15656 }
15657
15658 /* "pysam/libcvcf.pyx":398
15659 * idx += 1
15660 * if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings
15661 * if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
15662 * if 'descr' not in data:
15663 * # missing description
15664 */
15665 __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_id_2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 398, __pyx_L1_error)
15666 __Pyx_GOTREF(__pyx_t_4);
15667 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 398, __pyx_L1_error)
15668 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15669 __pyx_t_6 = (!__pyx_t_2);
15670 if (__pyx_t_6) {
15671 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 398, __pyx_L1_error)
15672 __Pyx_GOTREF(__pyx_t_1);
15673 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_BADLY_FORMATTED_FORMAT_STRING); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 398, __pyx_L1_error)
15674 __Pyx_GOTREF(__pyx_t_3);
15675 __pyx_t_7 = NULL;
15676 __pyx_t_5 = 0;
15677 #if CYTHON_UNPACK_METHODS
15678 if (likely(PyMethod_Check(__pyx_t_1))) {
15679 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_1);
15680 if (likely(__pyx_t_7)) {
15681 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
15682 __Pyx_INCREF(__pyx_t_7);
15683 __Pyx_INCREF(function);
15684 __Pyx_DECREF_SET(__pyx_t_1, function);
15685 __pyx_t_5 = 1;
15686 }
15687 }
15688 #endif
15689 {
15690 PyObject *__pyx_callargs[3] = {__pyx_t_7, __pyx_v_line, __pyx_t_3};
15691 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
15692 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
15693 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15694 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 398, __pyx_L1_error)
15695 __Pyx_GOTREF(__pyx_t_4);
15696 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
15697 }
15698 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15699 }
15700
15701 /* "pysam/libcvcf.pyx":399
15702 * if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings
15703 * if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15704 * if 'descr' not in data: # <<<<<<<<<<<<<<
15705 * # missing description
15706 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15707 */
15708 __pyx_t_6 = (__Pyx_PyDict_ContainsTF(__pyx_n_u_descr, __pyx_v_data, Py_NE)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 399, __pyx_L1_error)
15709 if (__pyx_t_6) {
15710
15711 /* "pysam/libcvcf.pyx":401
15712 * if 'descr' not in data:
15713 * # missing description
15714 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
15715 * data['descr'] = ""
15716 * if not data['type'] and not data['number']:
15717 */
15718 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 401, __pyx_L1_error)
15719 __Pyx_GOTREF(__pyx_t_1);
15720 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_BADLY_FORMATTED_FORMAT_STRING); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 401, __pyx_L1_error)
15721 __Pyx_GOTREF(__pyx_t_3);
15722 __pyx_t_7 = NULL;
15723 __pyx_t_5 = 0;
15724 #if CYTHON_UNPACK_METHODS
15725 if (likely(PyMethod_Check(__pyx_t_1))) {
15726 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_1);
15727 if (likely(__pyx_t_7)) {
15728 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
15729 __Pyx_INCREF(__pyx_t_7);
15730 __Pyx_INCREF(function);
15731 __Pyx_DECREF_SET(__pyx_t_1, function);
15732 __pyx_t_5 = 1;
15733 }
15734 }
15735 #endif
15736 {
15737 PyObject *__pyx_callargs[3] = {__pyx_t_7, __pyx_v_line, __pyx_t_3};
15738 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
15739 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
15740 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15741 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 401, __pyx_L1_error)
15742 __Pyx_GOTREF(__pyx_t_4);
15743 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
15744 }
15745 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15746
15747 /* "pysam/libcvcf.pyx":402
15748 * # missing description
15749 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15750 * data['descr'] = "" # <<<<<<<<<<<<<<
15751 * if not data['type'] and not data['number']:
15752 * # fine, ##filter format
15753 */
15754 if (unlikely((PyDict_SetItem(__pyx_v_data, __pyx_n_u_descr, __pyx_kp_u_) < 0))) __PYX_ERR(0, 402, __pyx_L1_error)
15755
15756 /* "pysam/libcvcf.pyx":399
15757 * if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings
15758 * if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15759 * if 'descr' not in data: # <<<<<<<<<<<<<<
15760 * # missing description
15761 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15762 */
15763 }
15764
15765 /* "pysam/libcvcf.pyx":403
15766 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15767 * data['descr'] = ""
15768 * if not data['type'] and not data['number']: # <<<<<<<<<<<<<<
15769 * # fine, ##filter format
15770 * return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
15771 */
15772 __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_type); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 403, __pyx_L1_error)
15773 __Pyx_GOTREF(__pyx_t_4);
15774 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 403, __pyx_L1_error)
15775 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15776 __pyx_t_9 = (!__pyx_t_2);
15777 if (__pyx_t_9) {
15778 } else {
15779 __pyx_t_6 = __pyx_t_9;
15780 goto __pyx_L23_bool_binop_done;
15781 }
15782 __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_number); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 403, __pyx_L1_error)
15783 __Pyx_GOTREF(__pyx_t_4);
15784 __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_9 < 0))) __PYX_ERR(0, 403, __pyx_L1_error)
15785 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15786 __pyx_t_2 = (!__pyx_t_9);
15787 __pyx_t_6 = __pyx_t_2;
15788 __pyx_L23_bool_binop_done:;
15789 if (__pyx_t_6) {
15790
15791 /* "pysam/libcvcf.pyx":405
15792 * if not data['type'] and not data['number']:
15793 * # fine, ##filter format
15794 * return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.') # <<<<<<<<<<<<<<
15795 * if not data['type'] in ["Integer","Float","Character","String","Flag"]:
15796 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15797 */
15798 __Pyx_XDECREF(__pyx_r);
15799 __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 405, __pyx_L1_error)
15800 __Pyx_GOTREF(__pyx_t_1);
15801 __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_id_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 405, __pyx_L1_error)
15802 __Pyx_GOTREF(__pyx_t_3);
15803 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NUMBER); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 405, __pyx_L1_error)
15804 __Pyx_GOTREF(__pyx_t_7);
15805 __pyx_t_10 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_descr); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 405, __pyx_L1_error)
15806 __Pyx_GOTREF(__pyx_t_10);
15807 __pyx_t_11 = NULL;
15808 __pyx_t_5 = 0;
15809 #if CYTHON_UNPACK_METHODS
15810 if (unlikely(PyMethod_Check(__pyx_t_1))) {
15811 __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_1);
15812 if (likely(__pyx_t_11)) {
15813 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
15814 __Pyx_INCREF(__pyx_t_11);
15815 __Pyx_INCREF(function);
15816 __Pyx_DECREF_SET(__pyx_t_1, function);
15817 __pyx_t_5 = 1;
15818 }
15819 }
15820 #endif
15821 {
15822 PyObject *__pyx_callargs[7] = {__pyx_t_11, __pyx_t_3, __pyx_t_7, __pyx_int_0, __pyx_n_u_Flag, __pyx_t_10, __pyx_kp_u__5};
15823 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
15824 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
15825 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
15826 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
15827 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
15828 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 405, __pyx_L1_error)
15829 __Pyx_GOTREF(__pyx_t_4);
15830 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
15831 }
15832 __pyx_r = __pyx_t_4;
15833 __pyx_t_4 = 0;
15834 goto __pyx_L0;
15835
15836 /* "pysam/libcvcf.pyx":403
15837 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15838 * data['descr'] = ""
15839 * if not data['type'] and not data['number']: # <<<<<<<<<<<<<<
15840 * # fine, ##filter format
15841 * return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
15842 */
15843 }
15844
15845 /* "pysam/libcvcf.pyx":406
15846 * # fine, ##filter format
15847 * return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
15848 * if not data['type'] in ["Integer","Float","Character","String","Flag"]: # <<<<<<<<<<<<<<
15849 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15850 * # I would like a missing-value field, but it isn't there
15851 */
15852 __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_type); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 406, __pyx_L1_error)
15853 __Pyx_GOTREF(__pyx_t_4);
15854 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_4, __pyx_n_u_Integer, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 406, __pyx_L1_error)
15855 if (__pyx_t_2) {
15856 } else {
15857 __pyx_t_6 = __pyx_t_2;
15858 goto __pyx_L26_bool_binop_done;
15859 }
15860 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_4, __pyx_n_u_Float, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 406, __pyx_L1_error)
15861 if (__pyx_t_2) {
15862 } else {
15863 __pyx_t_6 = __pyx_t_2;
15864 goto __pyx_L26_bool_binop_done;
15865 }
15866 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_4, __pyx_n_u_Character, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 406, __pyx_L1_error)
15867 if (__pyx_t_2) {
15868 } else {
15869 __pyx_t_6 = __pyx_t_2;
15870 goto __pyx_L26_bool_binop_done;
15871 }
15872 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_4, __pyx_n_u_String, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 406, __pyx_L1_error)
15873 if (__pyx_t_2) {
15874 } else {
15875 __pyx_t_6 = __pyx_t_2;
15876 goto __pyx_L26_bool_binop_done;
15877 }
15878 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_4, __pyx_n_u_Flag, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 406, __pyx_L1_error)
15879 __pyx_t_6 = __pyx_t_2;
15880 __pyx_L26_bool_binop_done:;
15881 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15882 __pyx_t_2 = __pyx_t_6;
15883 if (__pyx_t_2) {
15884
15885 /* "pysam/libcvcf.pyx":407
15886 * return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
15887 * if not data['type'] in ["Integer","Float","Character","String","Flag"]:
15888 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
15889 * # I would like a missing-value field, but it isn't there
15890 * if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value
15891 */
15892 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 407, __pyx_L1_error)
15893 __Pyx_GOTREF(__pyx_t_1);
15894 __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_BADLY_FORMATTED_FORMAT_STRING); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 407, __pyx_L1_error)
15895 __Pyx_GOTREF(__pyx_t_10);
15896 __pyx_t_7 = NULL;
15897 __pyx_t_5 = 0;
15898 #if CYTHON_UNPACK_METHODS
15899 if (likely(PyMethod_Check(__pyx_t_1))) {
15900 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_1);
15901 if (likely(__pyx_t_7)) {
15902 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
15903 __Pyx_INCREF(__pyx_t_7);
15904 __Pyx_INCREF(function);
15905 __Pyx_DECREF_SET(__pyx_t_1, function);
15906 __pyx_t_5 = 1;
15907 }
15908 }
15909 #endif
15910 {
15911 PyObject *__pyx_callargs[3] = {__pyx_t_7, __pyx_v_line, __pyx_t_10};
15912 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
15913 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
15914 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
15915 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 407, __pyx_L1_error)
15916 __Pyx_GOTREF(__pyx_t_4);
15917 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
15918 }
15919 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15920
15921 /* "pysam/libcvcf.pyx":406
15922 * # fine, ##filter format
15923 * return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
15924 * if not data['type'] in ["Integer","Float","Character","String","Flag"]: # <<<<<<<<<<<<<<
15925 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15926 * # I would like a missing-value field, but it isn't there
15927 */
15928 }
15929
15930 /* "pysam/libcvcf.pyx":409
15931 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15932 * # I would like a missing-value field, but it isn't there
15933 * if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value # <<<<<<<<<<<<<<
15934 * else: data['missing'] = '.'
15935 * if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15936 */
15937 __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_type); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 409, __pyx_L1_error)
15938 __Pyx_GOTREF(__pyx_t_4);
15939 __pyx_t_6 = (__Pyx_PyUnicode_Equals(__pyx_t_4, __pyx_n_u_Integer, Py_EQ)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 409, __pyx_L1_error)
15940 if (!__pyx_t_6) {
15941 } else {
15942 __pyx_t_2 = __pyx_t_6;
15943 goto __pyx_L32_bool_binop_done;
15944 }
15945 __pyx_t_6 = (__Pyx_PyUnicode_Equals(__pyx_t_4, __pyx_n_u_Float, Py_EQ)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 409, __pyx_L1_error)
15946 __pyx_t_2 = __pyx_t_6;
15947 __pyx_L32_bool_binop_done:;
15948 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15949 __pyx_t_6 = __pyx_t_2;
15950 if (__pyx_t_6) {
15951 if (unlikely((PyDict_SetItem(__pyx_v_data, __pyx_n_u_missing, Py_None) < 0))) __PYX_ERR(0, 409, __pyx_L1_error)
15952 goto __pyx_L31;
15953 }
15954
15955 /* "pysam/libcvcf.pyx":410
15956 * # I would like a missing-value field, but it isn't there
15957 * if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value
15958 * else: data['missing'] = '.' # <<<<<<<<<<<<<<
15959 * if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
15960 * try:
15961 */
15962 /*else*/ {
15963 if (unlikely((PyDict_SetItem(__pyx_v_data, __pyx_n_u_missing, __pyx_kp_u__5) < 0))) __PYX_ERR(0, 410, __pyx_L1_error)
15964 }
15965 __pyx_L31:;
15966
15967 /* "pysam/libcvcf.pyx":411
15968 * if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value
15969 * else: data['missing'] = '.'
15970 * if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
15971 * try:
15972 * n = int(data['number'])
15973 */
15974 __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_number); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 411, __pyx_L1_error)
15975 __Pyx_GOTREF(__pyx_t_4);
15976 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 411, __pyx_L1_error)
15977 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
15978 __pyx_t_2 = (!__pyx_t_6);
15979 if (__pyx_t_2) {
15980 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 411, __pyx_L1_error)
15981 __Pyx_GOTREF(__pyx_t_1);
15982 __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_BADLY_FORMATTED_FORMAT_STRING); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 411, __pyx_L1_error)
15983 __Pyx_GOTREF(__pyx_t_10);
15984 __pyx_t_7 = NULL;
15985 __pyx_t_5 = 0;
15986 #if CYTHON_UNPACK_METHODS
15987 if (likely(PyMethod_Check(__pyx_t_1))) {
15988 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_1);
15989 if (likely(__pyx_t_7)) {
15990 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
15991 __Pyx_INCREF(__pyx_t_7);
15992 __Pyx_INCREF(function);
15993 __Pyx_DECREF_SET(__pyx_t_1, function);
15994 __pyx_t_5 = 1;
15995 }
15996 }
15997 #endif
15998 {
15999 PyObject *__pyx_callargs[3] = {__pyx_t_7, __pyx_v_line, __pyx_t_10};
16000 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
16001 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
16002 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
16003 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 411, __pyx_L1_error)
16004 __Pyx_GOTREF(__pyx_t_4);
16005 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16006 }
16007 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
16008 }
16009
16010 /* "pysam/libcvcf.pyx":412
16011 * else: data['missing'] = '.'
16012 * if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
16013 * try: # <<<<<<<<<<<<<<
16014 * n = int(data['number'])
16015 * t = self.NT_NUMBER
16016 */
16017 {
16018 __Pyx_PyThreadState_declare
16019 __Pyx_PyThreadState_assign
16020 __Pyx_ExceptionSave(&__pyx_t_12, &__pyx_t_13, &__pyx_t_14);
16021 __Pyx_XGOTREF(__pyx_t_12);
16022 __Pyx_XGOTREF(__pyx_t_13);
16023 __Pyx_XGOTREF(__pyx_t_14);
16024 /*try:*/ {
16025
16026 /* "pysam/libcvcf.pyx":413
16027 * if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
16028 * try:
16029 * n = int(data['number']) # <<<<<<<<<<<<<<
16030 * t = self.NT_NUMBER
16031 * except ValueError:
16032 */
16033 __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_number); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 413, __pyx_L35_error)
16034 __Pyx_GOTREF(__pyx_t_4);
16035 __pyx_t_1 = __Pyx_PyNumber_Int(__pyx_t_4); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 413, __pyx_L35_error)
16036 __Pyx_GOTREF(__pyx_t_1);
16037 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
16038 __pyx_v_n = __pyx_t_1;
16039 __pyx_t_1 = 0;
16040
16041 /* "pysam/libcvcf.pyx":414
16042 * try:
16043 * n = int(data['number'])
16044 * t = self.NT_NUMBER # <<<<<<<<<<<<<<
16045 * except ValueError:
16046 * n = -1
16047 */
16048 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NUMBER); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 414, __pyx_L35_error)
16049 __Pyx_GOTREF(__pyx_t_1);
16050 __pyx_v_t = __pyx_t_1;
16051 __pyx_t_1 = 0;
16052
16053 /* "pysam/libcvcf.pyx":412
16054 * else: data['missing'] = '.'
16055 * if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
16056 * try: # <<<<<<<<<<<<<<
16057 * n = int(data['number'])
16058 * t = self.NT_NUMBER
16059 */
16060 }
16061 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
16062 __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
16063 __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
16064 goto __pyx_L40_try_end;
16065 __pyx_L35_error:;
16066 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
16067 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
16068 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
16069 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
16070 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
16071 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
16072
16073 /* "pysam/libcvcf.pyx":415
16074 * n = int(data['number'])
16075 * t = self.NT_NUMBER
16076 * except ValueError: # <<<<<<<<<<<<<<
16077 * n = -1
16078 * if data['number'] == '.': t = self.NT_UNKNOWN
16079 */
16080 __pyx_t_15 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_ValueError);
16081 if (__pyx_t_15) {
16082 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_format", __pyx_clineno, __pyx_lineno, __pyx_filename);
16083 if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_4, &__pyx_t_10) < 0) __PYX_ERR(0, 415, __pyx_L37_except_error)
16084 __Pyx_XGOTREF(__pyx_t_1);
16085 __Pyx_XGOTREF(__pyx_t_4);
16086 __Pyx_XGOTREF(__pyx_t_10);
16087
16088 /* "pysam/libcvcf.pyx":416
16089 * t = self.NT_NUMBER
16090 * except ValueError:
16091 * n = -1 # <<<<<<<<<<<<<<
16092 * if data['number'] == '.': t = self.NT_UNKNOWN
16093 * elif data['number'] == '#alleles': t = self.NT_ALLELES
16094 */
16095 __Pyx_INCREF(__pyx_int_neg_1);
16096 __Pyx_XDECREF_SET(__pyx_v_n, __pyx_int_neg_1);
16097
16098 /* "pysam/libcvcf.pyx":417
16099 * except ValueError:
16100 * n = -1
16101 * if data['number'] == '.': t = self.NT_UNKNOWN # <<<<<<<<<<<<<<
16102 * elif data['number'] == '#alleles': t = self.NT_ALLELES
16103 * elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
16104 */
16105 __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_number); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 417, __pyx_L37_except_error)
16106 __Pyx_GOTREF(__pyx_t_7);
16107 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_7, __pyx_kp_u__5, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 417, __pyx_L37_except_error)
16108 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
16109 if (__pyx_t_2) {
16110 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_UNKNOWN); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 417, __pyx_L37_except_error)
16111 __Pyx_GOTREF(__pyx_t_7);
16112 __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_7);
16113 __pyx_t_7 = 0;
16114 goto __pyx_L43;
16115 }
16116
16117 /* "pysam/libcvcf.pyx":418
16118 * n = -1
16119 * if data['number'] == '.': t = self.NT_UNKNOWN
16120 * elif data['number'] == '#alleles': t = self.NT_ALLELES # <<<<<<<<<<<<<<
16121 * elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
16122 * elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
16123 */
16124 __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_number); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 418, __pyx_L37_except_error)
16125 __Pyx_GOTREF(__pyx_t_7);
16126 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_7, __pyx_kp_u_alleles, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 418, __pyx_L37_except_error)
16127 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
16128 if (__pyx_t_2) {
16129 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_ALLELES); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 418, __pyx_L37_except_error)
16130 __Pyx_GOTREF(__pyx_t_7);
16131 __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_7);
16132 __pyx_t_7 = 0;
16133 goto __pyx_L43;
16134 }
16135
16136 /* "pysam/libcvcf.pyx":419
16137 * if data['number'] == '.': t = self.NT_UNKNOWN
16138 * elif data['number'] == '#alleles': t = self.NT_ALLELES
16139 * elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES # <<<<<<<<<<<<<<
16140 * elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
16141 * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
16142 */
16143 __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_number); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 419, __pyx_L37_except_error)
16144 __Pyx_GOTREF(__pyx_t_7);
16145 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_7, __pyx_kp_u_nonref_alleles, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 419, __pyx_L37_except_error)
16146 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
16147 if (__pyx_t_2) {
16148 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NR_ALLELES); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 419, __pyx_L37_except_error)
16149 __Pyx_GOTREF(__pyx_t_7);
16150 __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_7);
16151 __pyx_t_7 = 0;
16152 goto __pyx_L43;
16153 }
16154
16155 /* "pysam/libcvcf.pyx":420
16156 * elif data['number'] == '#alleles': t = self.NT_ALLELES
16157 * elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
16158 * elif data['number'] == '#genotypes': t = self.NT_GENOTYPES # <<<<<<<<<<<<<<
16159 * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
16160 * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
16161 */
16162 __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_number); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 420, __pyx_L37_except_error)
16163 __Pyx_GOTREF(__pyx_t_7);
16164 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_7, __pyx_kp_u_genotypes, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 420, __pyx_L37_except_error)
16165 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
16166 if (__pyx_t_2) {
16167 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_GENOTYPES); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 420, __pyx_L37_except_error)
16168 __Pyx_GOTREF(__pyx_t_7);
16169 __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_7);
16170 __pyx_t_7 = 0;
16171 goto __pyx_L43;
16172 }
16173
16174 /* "pysam/libcvcf.pyx":421
16175 * elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
16176 * elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
16177 * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES # <<<<<<<<<<<<<<
16178 * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
16179 * # abbreviations added in VCF version v4.1
16180 */
16181 __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_number); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 421, __pyx_L37_except_error)
16182 __Pyx_GOTREF(__pyx_t_7);
16183 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_7, __pyx_kp_u_phased_genotypes, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 421, __pyx_L37_except_error)
16184 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
16185 if (__pyx_t_2) {
16186 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 421, __pyx_L37_except_error)
16187 __Pyx_GOTREF(__pyx_t_7);
16188 __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_7);
16189 __pyx_t_7 = 0;
16190 goto __pyx_L43;
16191 }
16192
16193 /* "pysam/libcvcf.pyx":422
16194 * elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
16195 * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
16196 * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES # <<<<<<<<<<<<<<
16197 * # abbreviations added in VCF version v4.1
16198 * elif data['number'] == 'A': t = self.NT_ALLELES
16199 */
16200 __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_number); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 422, __pyx_L37_except_error)
16201 __Pyx_GOTREF(__pyx_t_7);
16202 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_7, __pyx_kp_u_phased_genotypes, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 422, __pyx_L37_except_error)
16203 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
16204 if (__pyx_t_2) {
16205 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 422, __pyx_L37_except_error)
16206 __Pyx_GOTREF(__pyx_t_7);
16207 __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_7);
16208 __pyx_t_7 = 0;
16209 goto __pyx_L43;
16210 }
16211
16212 /* "pysam/libcvcf.pyx":424
16213 * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
16214 * # abbreviations added in VCF version v4.1
16215 * elif data['number'] == 'A': t = self.NT_ALLELES # <<<<<<<<<<<<<<
16216 * elif data['number'] == 'G': t = self.NT_GENOTYPES
16217 * else:
16218 */
16219 __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_number); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 424, __pyx_L37_except_error)
16220 __Pyx_GOTREF(__pyx_t_7);
16221 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_7, __pyx_n_u_A, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 424, __pyx_L37_except_error)
16222 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
16223 if (__pyx_t_2) {
16224 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_ALLELES); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 424, __pyx_L37_except_error)
16225 __Pyx_GOTREF(__pyx_t_7);
16226 __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_7);
16227 __pyx_t_7 = 0;
16228 goto __pyx_L43;
16229 }
16230
16231 /* "pysam/libcvcf.pyx":425
16232 * # abbreviations added in VCF version v4.1
16233 * elif data['number'] == 'A': t = self.NT_ALLELES
16234 * elif data['number'] == 'G': t = self.NT_GENOTYPES # <<<<<<<<<<<<<<
16235 * else:
16236 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
16237 */
16238 __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_number); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 425, __pyx_L37_except_error)
16239 __Pyx_GOTREF(__pyx_t_7);
16240 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_t_7, __pyx_n_u_G, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 425, __pyx_L37_except_error)
16241 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
16242 if (__pyx_t_2) {
16243 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_GENOTYPES); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 425, __pyx_L37_except_error)
16244 __Pyx_GOTREF(__pyx_t_7);
16245 __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_7);
16246 __pyx_t_7 = 0;
16247 goto __pyx_L43;
16248 }
16249
16250 /* "pysam/libcvcf.pyx":427
16251 * elif data['number'] == 'G': t = self.NT_GENOTYPES
16252 * else:
16253 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
16254 * # if number is 0 - type must be Flag
16255 * if n == 0 and data['type'] != 'Flag':
16256 */
16257 /*else*/ {
16258 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 427, __pyx_L37_except_error)
16259 __Pyx_GOTREF(__pyx_t_3);
16260 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_BADLY_FORMATTED_FORMAT_STRING); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 427, __pyx_L37_except_error)
16261 __Pyx_GOTREF(__pyx_t_11);
16262 __pyx_t_16 = NULL;
16263 __pyx_t_5 = 0;
16264 #if CYTHON_UNPACK_METHODS
16265 if (likely(PyMethod_Check(__pyx_t_3))) {
16266 __pyx_t_16 = PyMethod_GET_SELF(__pyx_t_3);
16267 if (likely(__pyx_t_16)) {
16268 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
16269 __Pyx_INCREF(__pyx_t_16);
16270 __Pyx_INCREF(function);
16271 __Pyx_DECREF_SET(__pyx_t_3, function);
16272 __pyx_t_5 = 1;
16273 }
16274 }
16275 #endif
16276 {
16277 PyObject *__pyx_callargs[3] = {__pyx_t_16, __pyx_v_line, __pyx_t_11};
16278 __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
16279 __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
16280 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
16281 if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 427, __pyx_L37_except_error)
16282 __Pyx_GOTREF(__pyx_t_7);
16283 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
16284 }
16285 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
16286 }
16287 __pyx_L43:;
16288 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
16289 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
16290 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
16291 goto __pyx_L36_exception_handled;
16292 }
16293 goto __pyx_L37_except_error;
16294
16295 /* "pysam/libcvcf.pyx":412
16296 * else: data['missing'] = '.'
16297 * if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
16298 * try: # <<<<<<<<<<<<<<
16299 * n = int(data['number'])
16300 * t = self.NT_NUMBER
16301 */
16302 __pyx_L37_except_error:;
16303 __Pyx_XGIVEREF(__pyx_t_12);
16304 __Pyx_XGIVEREF(__pyx_t_13);
16305 __Pyx_XGIVEREF(__pyx_t_14);
16306 __Pyx_ExceptionReset(__pyx_t_12, __pyx_t_13, __pyx_t_14);
16307 goto __pyx_L1_error;
16308 __pyx_L36_exception_handled:;
16309 __Pyx_XGIVEREF(__pyx_t_12);
16310 __Pyx_XGIVEREF(__pyx_t_13);
16311 __Pyx_XGIVEREF(__pyx_t_14);
16312 __Pyx_ExceptionReset(__pyx_t_12, __pyx_t_13, __pyx_t_14);
16313 __pyx_L40_try_end:;
16314 }
16315
16316 /* "pysam/libcvcf.pyx":429
16317 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
16318 * # if number is 0 - type must be Flag
16319 * if n == 0 and data['type'] != 'Flag': # <<<<<<<<<<<<<<
16320 * self.error( line, self.ZERO_FOR_NON_FLAG_FIELD)
16321 * # force type 'Flag' if no number
16322 */
16323 __pyx_t_6 = (__Pyx_PyInt_BoolEqObjC(__pyx_v_n, __pyx_int_0, 0, 0)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 429, __pyx_L1_error)
16324 if (__pyx_t_6) {
16325 } else {
16326 __pyx_t_2 = __pyx_t_6;
16327 goto __pyx_L45_bool_binop_done;
16328 }
16329 __pyx_t_10 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_type); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 429, __pyx_L1_error)
16330 __Pyx_GOTREF(__pyx_t_10);
16331 __pyx_t_6 = (__Pyx_PyUnicode_Equals(__pyx_t_10, __pyx_n_u_Flag, Py_NE)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 429, __pyx_L1_error)
16332 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
16333 __pyx_t_2 = __pyx_t_6;
16334 __pyx_L45_bool_binop_done:;
16335 if (__pyx_t_2) {
16336
16337 /* "pysam/libcvcf.pyx":430
16338 * # if number is 0 - type must be Flag
16339 * if n == 0 and data['type'] != 'Flag':
16340 * self.error( line, self.ZERO_FOR_NON_FLAG_FIELD) # <<<<<<<<<<<<<<
16341 * # force type 'Flag' if no number
16342 * data['type'] = 'Flag'
16343 */
16344 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 430, __pyx_L1_error)
16345 __Pyx_GOTREF(__pyx_t_4);
16346 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_ZERO_FOR_NON_FLAG_FIELD); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 430, __pyx_L1_error)
16347 __Pyx_GOTREF(__pyx_t_1);
16348 __pyx_t_7 = NULL;
16349 __pyx_t_5 = 0;
16350 #if CYTHON_UNPACK_METHODS
16351 if (likely(PyMethod_Check(__pyx_t_4))) {
16352 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_4);
16353 if (likely(__pyx_t_7)) {
16354 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
16355 __Pyx_INCREF(__pyx_t_7);
16356 __Pyx_INCREF(function);
16357 __Pyx_DECREF_SET(__pyx_t_4, function);
16358 __pyx_t_5 = 1;
16359 }
16360 }
16361 #endif
16362 {
16363 PyObject *__pyx_callargs[3] = {__pyx_t_7, __pyx_v_line, __pyx_t_1};
16364 __pyx_t_10 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 2+__pyx_t_5);
16365 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
16366 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16367 if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 430, __pyx_L1_error)
16368 __Pyx_GOTREF(__pyx_t_10);
16369 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
16370 }
16371 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
16372
16373 /* "pysam/libcvcf.pyx":432
16374 * self.error( line, self.ZERO_FOR_NON_FLAG_FIELD)
16375 * # force type 'Flag' if no number
16376 * data['type'] = 'Flag' # <<<<<<<<<<<<<<
16377 *
16378 * return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
16379 */
16380 if (unlikely((PyDict_SetItem(__pyx_v_data, __pyx_n_u_type, __pyx_n_u_Flag) < 0))) __PYX_ERR(0, 432, __pyx_L1_error)
16381
16382 /* "pysam/libcvcf.pyx":429
16383 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
16384 * # if number is 0 - type must be Flag
16385 * if n == 0 and data['type'] != 'Flag': # <<<<<<<<<<<<<<
16386 * self.error( line, self.ZERO_FOR_NON_FLAG_FIELD)
16387 * # force type 'Flag' if no number
16388 */
16389 }
16390
16391 /* "pysam/libcvcf.pyx":434
16392 * data['type'] = 'Flag'
16393 *
16394 * return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing']) # <<<<<<<<<<<<<<
16395 *
16396 * def format_format( self, fmt, filter=False ):
16397 */
16398 __Pyx_XDECREF(__pyx_r);
16399 __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 434, __pyx_L1_error)
16400 __Pyx_GOTREF(__pyx_t_4);
16401 __pyx_t_1 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_id_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 434, __pyx_L1_error)
16402 __Pyx_GOTREF(__pyx_t_1);
16403 if (unlikely(!__pyx_v_t)) { __Pyx_RaiseUnboundLocalError("t"); __PYX_ERR(0, 434, __pyx_L1_error) }
16404 __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_type); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 434, __pyx_L1_error)
16405 __Pyx_GOTREF(__pyx_t_7);
16406 __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_descr); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 434, __pyx_L1_error)
16407 __Pyx_GOTREF(__pyx_t_3);
16408 __pyx_t_11 = __Pyx_PyDict_GetItem(__pyx_v_data, __pyx_n_u_missing); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 434, __pyx_L1_error)
16409 __Pyx_GOTREF(__pyx_t_11);
16410 __pyx_t_16 = NULL;
16411 __pyx_t_5 = 0;
16412 #if CYTHON_UNPACK_METHODS
16413 if (unlikely(PyMethod_Check(__pyx_t_4))) {
16414 __pyx_t_16 = PyMethod_GET_SELF(__pyx_t_4);
16415 if (likely(__pyx_t_16)) {
16416 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
16417 __Pyx_INCREF(__pyx_t_16);
16418 __Pyx_INCREF(function);
16419 __Pyx_DECREF_SET(__pyx_t_4, function);
16420 __pyx_t_5 = 1;
16421 }
16422 }
16423 #endif
16424 {
16425 PyObject *__pyx_callargs[7] = {__pyx_t_16, __pyx_t_1, __pyx_v_t, __pyx_v_n, __pyx_t_7, __pyx_t_3, __pyx_t_11};
16426 __pyx_t_10 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
16427 __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
16428 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16429 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
16430 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
16431 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
16432 if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 434, __pyx_L1_error)
16433 __Pyx_GOTREF(__pyx_t_10);
16434 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
16435 }
16436 __pyx_r = __pyx_t_10;
16437 __pyx_t_10 = 0;
16438 goto __pyx_L0;
16439
16440 /* "pysam/libcvcf.pyx":364
16441 * raise ValueError(errorstring)
16442 *
16443 * def parse_format(self,line,format,filter=False): # <<<<<<<<<<<<<<
16444 * if self._version == 40:
16445 * if not format.startswith('<'):
16446 */
16447
16448 /* function exit code */
16449 __pyx_L1_error:;
16450 __Pyx_XDECREF(__pyx_t_1);
16451 __Pyx_XDECREF(__pyx_t_3);
16452 __Pyx_XDECREF(__pyx_t_4);
16453 __Pyx_XDECREF(__pyx_t_7);
16454 __Pyx_XDECREF(__pyx_t_10);
16455 __Pyx_XDECREF(__pyx_t_11);
16456 __Pyx_XDECREF(__pyx_t_16);
16457 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_format", __pyx_clineno, __pyx_lineno, __pyx_filename);
16458 __pyx_r = NULL;
16459 __pyx_L0:;
16460 __Pyx_XDECREF(__pyx_v_data);
16461 __Pyx_XDECREF(__pyx_v_idx);
16462 __Pyx_XDECREF(__pyx_v_elts);
16463 __Pyx_XDECREF(__pyx_v_first);
16464 __Pyx_XDECREF(__pyx_v_rest);
16465 __Pyx_XDECREF(__pyx_v_n);
16466 __Pyx_XDECREF(__pyx_v_t);
16467 __Pyx_XDECREF(__pyx_v_format);
16468 __Pyx_XGIVEREF(__pyx_r);
16469 __Pyx_RefNannyFinishContext();
16470 return __pyx_r;
16471 }
16472
16473 /* "pysam/libcvcf.pyx":436
16474 * return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
16475 *
16476 * def format_format( self, fmt, filter=False ): # <<<<<<<<<<<<<<
16477 * values = [('ID',fmt.id)]
16478 * if fmt.number != None and not filter:
16479 */
16480
16481 /* Python wrapper */
16482 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_7format_format(PyObject *__pyx_self,
16483 #if CYTHON_METH_FASTCALL
16484 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
16485 #else
16486 PyObject *__pyx_args, PyObject *__pyx_kwds
16487 #endif
16488 ); /*proto*/
16489 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_6format_format, "VCF.format_format(self, fmt, filter=False)");
16490 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_7format_format = {"format_format", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_7format_format, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_6format_format};
16491 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_7format_format(PyObject *__pyx_self,
16492 #if CYTHON_METH_FASTCALL
16493 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
16494 #else
16495 PyObject *__pyx_args, PyObject *__pyx_kwds
16496 #endif
16497 ) {
16498 PyObject *__pyx_v_self = 0;
16499 PyObject *__pyx_v_fmt = 0;
16500 PyObject *__pyx_v_filter = 0;
16501 #if !CYTHON_METH_FASTCALL
16502 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
16503 #endif
16504 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
16505 PyObject* values[3] = {0,0,0};
16506 int __pyx_lineno = 0;
16507 const char *__pyx_filename = NULL;
16508 int __pyx_clineno = 0;
16509 PyObject *__pyx_r = 0;
16510 __Pyx_RefNannyDeclarations
16511 __Pyx_RefNannySetupContext("format_format (wrapper)", 0);
16512 #if !CYTHON_METH_FASTCALL
16513 #if CYTHON_ASSUME_SAFE_MACROS
16514 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
16515 #else
16516 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
16517 #endif
16518 #endif
16519 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
16520 {
16521 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_fmt,&__pyx_n_s_filter_2,0};
16522 values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False)));
16523 if (__pyx_kwds) {
16524 Py_ssize_t kw_args;
16525 switch (__pyx_nargs) {
16526 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
16527 CYTHON_FALLTHROUGH;
16528 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
16529 CYTHON_FALLTHROUGH;
16530 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
16531 CYTHON_FALLTHROUGH;
16532 case 0: break;
16533 default: goto __pyx_L5_argtuple_error;
16534 }
16535 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
16536 switch (__pyx_nargs) {
16537 case 0:
16538 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
16539 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
16540 kw_args--;
16541 }
16542 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 436, __pyx_L3_error)
16543 else goto __pyx_L5_argtuple_error;
16544 CYTHON_FALLTHROUGH;
16545 case 1:
16546 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_fmt)) != 0)) {
16547 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
16548 kw_args--;
16549 }
16550 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 436, __pyx_L3_error)
16551 else {
16552 __Pyx_RaiseArgtupleInvalid("format_format", 0, 2, 3, 1); __PYX_ERR(0, 436, __pyx_L3_error)
16553 }
16554 CYTHON_FALLTHROUGH;
16555 case 2:
16556 if (kw_args > 0) {
16557 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filter_2);
16558 if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
16559 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 436, __pyx_L3_error)
16560 }
16561 }
16562 if (unlikely(kw_args > 0)) {
16563 const Py_ssize_t kwd_pos_args = __pyx_nargs;
16564 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "format_format") < 0)) __PYX_ERR(0, 436, __pyx_L3_error)
16565 }
16566 } else {
16567 switch (__pyx_nargs) {
16568 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
16569 CYTHON_FALLTHROUGH;
16570 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
16571 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
16572 break;
16573 default: goto __pyx_L5_argtuple_error;
16574 }
16575 }
16576 __pyx_v_self = values[0];
16577 __pyx_v_fmt = values[1];
16578 __pyx_v_filter = values[2];
16579 }
16580 goto __pyx_L6_skip;
16581 __pyx_L5_argtuple_error:;
16582 __Pyx_RaiseArgtupleInvalid("format_format", 0, 2, 3, __pyx_nargs); __PYX_ERR(0, 436, __pyx_L3_error)
16583 __pyx_L6_skip:;
16584 goto __pyx_L4_argument_unpacking_done;
16585 __pyx_L3_error:;
16586 {
16587 Py_ssize_t __pyx_temp;
16588 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
16589 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
16590 }
16591 }
16592 __Pyx_AddTraceback("pysam.libcvcf.VCF.format_format", __pyx_clineno, __pyx_lineno, __pyx_filename);
16593 __Pyx_RefNannyFinishContext();
16594 return NULL;
16595 __pyx_L4_argument_unpacking_done:;
16596 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_6format_format(__pyx_self, __pyx_v_self, __pyx_v_fmt, __pyx_v_filter);
16597
16598 /* function exit code */
16599 {
16600 Py_ssize_t __pyx_temp;
16601 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
16602 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
16603 }
16604 }
16605 __Pyx_RefNannyFinishContext();
16606 return __pyx_r;
16607 }
16608
16609 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fmt, PyObject *__pyx_v_filter) {
16610 PyObject *__pyx_v_values = NULL;
16611 PyObject *__pyx_v_nmb = NULL;
16612 PyObject *__pyx_v_format = NULL;
16613 CYTHON_UNUSED PyObject *__pyx_7genexpr__pyx_v_k = NULL;
16614 PyObject *__pyx_7genexpr__pyx_v_v = NULL;
16615 PyObject *__pyx_8genexpr1__pyx_v_k = NULL;
16616 PyObject *__pyx_8genexpr1__pyx_v_v = NULL;
16617 PyObject *__pyx_r = NULL;
16618 __Pyx_RefNannyDeclarations
16619 PyObject *__pyx_t_1 = NULL;
16620 PyObject *__pyx_t_2 = NULL;
16621 int __pyx_t_3;
16622 int __pyx_t_4;
16623 int __pyx_t_5;
16624 PyObject *__pyx_t_6 = NULL;
16625 int __pyx_t_7;
16626 Py_ssize_t __pyx_t_8;
16627 PyObject *__pyx_t_9 = NULL;
16628 PyObject *__pyx_t_10 = NULL;
16629 PyObject *__pyx_t_11 = NULL;
16630 PyObject *(*__pyx_t_12)(PyObject *);
16631 Py_ssize_t __pyx_t_13;
16632 Py_UCS4 __pyx_t_14;
16633 int __pyx_lineno = 0;
16634 const char *__pyx_filename = NULL;
16635 int __pyx_clineno = 0;
16636 __Pyx_RefNannySetupContext("format_format", 1);
16637
16638 /* "pysam/libcvcf.pyx":437
16639 *
16640 * def format_format( self, fmt, filter=False ):
16641 * values = [('ID',fmt.id)] # <<<<<<<<<<<<<<
16642 * if fmt.number != None and not filter:
16643 * if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
16644 */
16645 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_id_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 437, __pyx_L1_error)
16646 __Pyx_GOTREF(__pyx_t_1);
16647 __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 437, __pyx_L1_error)
16648 __Pyx_GOTREF(__pyx_t_2);
16649 __Pyx_INCREF(__pyx_n_u_ID_2);
16650 __Pyx_GIVEREF(__pyx_n_u_ID_2);
16651 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_n_u_ID_2)) __PYX_ERR(0, 437, __pyx_L1_error);
16652 __Pyx_GIVEREF(__pyx_t_1);
16653 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1)) __PYX_ERR(0, 437, __pyx_L1_error);
16654 __pyx_t_1 = 0;
16655 __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 437, __pyx_L1_error)
16656 __Pyx_GOTREF(__pyx_t_1);
16657 __Pyx_GIVEREF(__pyx_t_2);
16658 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_2)) __PYX_ERR(0, 437, __pyx_L1_error);
16659 __pyx_t_2 = 0;
16660 __pyx_v_values = ((PyObject*)__pyx_t_1);
16661 __pyx_t_1 = 0;
16662
16663 /* "pysam/libcvcf.pyx":438
16664 * def format_format( self, fmt, filter=False ):
16665 * values = [('ID',fmt.id)]
16666 * if fmt.number != None and not filter: # <<<<<<<<<<<<<<
16667 * if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
16668 * elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
16669 */
16670 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_number); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 438, __pyx_L1_error)
16671 __Pyx_GOTREF(__pyx_t_1);
16672 __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 438, __pyx_L1_error)
16673 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16674 __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(0, 438, __pyx_L1_error)
16675 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
16676 if (__pyx_t_4) {
16677 } else {
16678 __pyx_t_3 = __pyx_t_4;
16679 goto __pyx_L4_bool_binop_done;
16680 }
16681 __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_filter); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(0, 438, __pyx_L1_error)
16682 __pyx_t_5 = (!__pyx_t_4);
16683 __pyx_t_3 = __pyx_t_5;
16684 __pyx_L4_bool_binop_done:;
16685 if (__pyx_t_3) {
16686
16687 /* "pysam/libcvcf.pyx":439
16688 * values = [('ID',fmt.id)]
16689 * if fmt.number != None and not filter:
16690 * if fmt.numbertype == self.NT_UNKNOWN: nmb = "." # <<<<<<<<<<<<<<
16691 * elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
16692 * elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
16693 */
16694 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 439, __pyx_L1_error)
16695 __Pyx_GOTREF(__pyx_t_2);
16696 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_UNKNOWN); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 439, __pyx_L1_error)
16697 __Pyx_GOTREF(__pyx_t_1);
16698 __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 439, __pyx_L1_error)
16699 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
16700 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16701 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 439, __pyx_L1_error)
16702 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
16703 if (__pyx_t_3) {
16704 __Pyx_INCREF(__pyx_kp_u__5);
16705 __pyx_v_nmb = __pyx_kp_u__5;
16706 goto __pyx_L6;
16707 }
16708
16709 /* "pysam/libcvcf.pyx":440
16710 * if fmt.number != None and not filter:
16711 * if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
16712 * elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number) # <<<<<<<<<<<<<<
16713 * elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
16714 * elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
16715 */
16716 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 440, __pyx_L1_error)
16717 __Pyx_GOTREF(__pyx_t_6);
16718 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NUMBER); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 440, __pyx_L1_error)
16719 __Pyx_GOTREF(__pyx_t_1);
16720 __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 440, __pyx_L1_error)
16721 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
16722 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16723 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 440, __pyx_L1_error)
16724 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
16725 if (__pyx_t_3) {
16726 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_number); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 440, __pyx_L1_error)
16727 __Pyx_GOTREF(__pyx_t_2);
16728 __pyx_t_1 = __Pyx_PyObject_Unicode(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 440, __pyx_L1_error)
16729 __Pyx_GOTREF(__pyx_t_1);
16730 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
16731 __pyx_v_nmb = __pyx_t_1;
16732 __pyx_t_1 = 0;
16733 goto __pyx_L6;
16734 }
16735
16736 /* "pysam/libcvcf.pyx":441
16737 * if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
16738 * elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
16739 * elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles" # <<<<<<<<<<<<<<
16740 * elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
16741 * elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes"
16742 */
16743 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 441, __pyx_L1_error)
16744 __Pyx_GOTREF(__pyx_t_1);
16745 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_ALLELES); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 441, __pyx_L1_error)
16746 __Pyx_GOTREF(__pyx_t_2);
16747 __pyx_t_6 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 441, __pyx_L1_error)
16748 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16749 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
16750 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 441, __pyx_L1_error)
16751 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
16752 if (__pyx_t_3) {
16753 __Pyx_INCREF(__pyx_kp_u_alleles);
16754 __pyx_v_nmb = __pyx_kp_u_alleles;
16755 goto __pyx_L6;
16756 }
16757
16758 /* "pysam/libcvcf.pyx":442
16759 * elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
16760 * elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
16761 * elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles" # <<<<<<<<<<<<<<
16762 * elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes"
16763 * elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes"
16764 */
16765 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 442, __pyx_L1_error)
16766 __Pyx_GOTREF(__pyx_t_6);
16767 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NR_ALLELES); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 442, __pyx_L1_error)
16768 __Pyx_GOTREF(__pyx_t_2);
16769 __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 442, __pyx_L1_error)
16770 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
16771 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
16772 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 442, __pyx_L1_error)
16773 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16774 if (__pyx_t_3) {
16775 __Pyx_INCREF(__pyx_kp_u_nonref_alleles);
16776 __pyx_v_nmb = __pyx_kp_u_nonref_alleles;
16777 goto __pyx_L6;
16778 }
16779
16780 /* "pysam/libcvcf.pyx":443
16781 * elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
16782 * elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
16783 * elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes" # <<<<<<<<<<<<<<
16784 * elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes"
16785 * else:
16786 */
16787 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 443, __pyx_L1_error)
16788 __Pyx_GOTREF(__pyx_t_1);
16789 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_GENOTYPES); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 443, __pyx_L1_error)
16790 __Pyx_GOTREF(__pyx_t_2);
16791 __pyx_t_6 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 443, __pyx_L1_error)
16792 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16793 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
16794 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 443, __pyx_L1_error)
16795 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
16796 if (__pyx_t_3) {
16797 __Pyx_INCREF(__pyx_kp_u_genotypes);
16798 __pyx_v_nmb = __pyx_kp_u_genotypes;
16799 goto __pyx_L6;
16800 }
16801
16802 /* "pysam/libcvcf.pyx":444
16803 * elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
16804 * elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes"
16805 * elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes" # <<<<<<<<<<<<<<
16806 * else:
16807 * raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
16808 */
16809 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 444, __pyx_L1_error)
16810 __Pyx_GOTREF(__pyx_t_6);
16811 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 444, __pyx_L1_error)
16812 __Pyx_GOTREF(__pyx_t_2);
16813 __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 444, __pyx_L1_error)
16814 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
16815 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
16816 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 444, __pyx_L1_error)
16817 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16818 if (likely(__pyx_t_3)) {
16819 __Pyx_INCREF(__pyx_kp_u_phased_genotypes);
16820 __pyx_v_nmb = __pyx_kp_u_phased_genotypes;
16821 goto __pyx_L6;
16822 }
16823
16824 /* "pysam/libcvcf.pyx":446
16825 * elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes"
16826 * else:
16827 * raise ValueError("Unknown number type encountered: %s" % fmt.numbertype) # <<<<<<<<<<<<<<
16828 * values.append( ('Number',nmb) )
16829 * values.append( ('Type', fmt.type) )
16830 */
16831 /*else*/ {
16832 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 446, __pyx_L1_error)
16833 __Pyx_GOTREF(__pyx_t_1);
16834 __pyx_t_2 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_Unknown_number_type_encountered, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 446, __pyx_L1_error)
16835 __Pyx_GOTREF(__pyx_t_2);
16836 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16837 __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 446, __pyx_L1_error)
16838 __Pyx_GOTREF(__pyx_t_1);
16839 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
16840 __Pyx_Raise(__pyx_t_1, 0, 0, 0);
16841 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16842 __PYX_ERR(0, 446, __pyx_L1_error)
16843 }
16844 __pyx_L6:;
16845
16846 /* "pysam/libcvcf.pyx":447
16847 * else:
16848 * raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
16849 * values.append( ('Number',nmb) ) # <<<<<<<<<<<<<<
16850 * values.append( ('Type', fmt.type) )
16851 * values.append( ('Description', '"' + fmt.description + '"') )
16852 */
16853 __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 447, __pyx_L1_error)
16854 __Pyx_GOTREF(__pyx_t_1);
16855 __Pyx_INCREF(__pyx_n_u_Number_2);
16856 __Pyx_GIVEREF(__pyx_n_u_Number_2);
16857 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_n_u_Number_2)) __PYX_ERR(0, 447, __pyx_L1_error);
16858 __Pyx_INCREF(__pyx_v_nmb);
16859 __Pyx_GIVEREF(__pyx_v_nmb);
16860 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_nmb)) __PYX_ERR(0, 447, __pyx_L1_error);
16861 __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 447, __pyx_L1_error)
16862 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16863
16864 /* "pysam/libcvcf.pyx":448
16865 * raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
16866 * values.append( ('Number',nmb) )
16867 * values.append( ('Type', fmt.type) ) # <<<<<<<<<<<<<<
16868 * values.append( ('Description', '"' + fmt.description + '"') )
16869 * if self._version == 33:
16870 */
16871 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 448, __pyx_L1_error)
16872 __Pyx_GOTREF(__pyx_t_1);
16873 __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 448, __pyx_L1_error)
16874 __Pyx_GOTREF(__pyx_t_2);
16875 __Pyx_INCREF(__pyx_n_u_Type_2);
16876 __Pyx_GIVEREF(__pyx_n_u_Type_2);
16877 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_n_u_Type_2)) __PYX_ERR(0, 448, __pyx_L1_error);
16878 __Pyx_GIVEREF(__pyx_t_1);
16879 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1)) __PYX_ERR(0, 448, __pyx_L1_error);
16880 __pyx_t_1 = 0;
16881 __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_values, __pyx_t_2); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 448, __pyx_L1_error)
16882 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
16883
16884 /* "pysam/libcvcf.pyx":438
16885 * def format_format( self, fmt, filter=False ):
16886 * values = [('ID',fmt.id)]
16887 * if fmt.number != None and not filter: # <<<<<<<<<<<<<<
16888 * if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
16889 * elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
16890 */
16891 }
16892
16893 /* "pysam/libcvcf.pyx":449
16894 * values.append( ('Number',nmb) )
16895 * values.append( ('Type', fmt.type) )
16896 * values.append( ('Description', '"' + fmt.description + '"') ) # <<<<<<<<<<<<<<
16897 * if self._version == 33:
16898 * format = ",".join([v for k,v in values])
16899 */
16900 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_description); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 449, __pyx_L1_error)
16901 __Pyx_GOTREF(__pyx_t_2);
16902 __pyx_t_1 = PyNumber_Add(__pyx_kp_u__19, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 449, __pyx_L1_error)
16903 __Pyx_GOTREF(__pyx_t_1);
16904 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
16905 __pyx_t_2 = PyNumber_Add(__pyx_t_1, __pyx_kp_u__19); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 449, __pyx_L1_error)
16906 __Pyx_GOTREF(__pyx_t_2);
16907 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16908 __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 449, __pyx_L1_error)
16909 __Pyx_GOTREF(__pyx_t_1);
16910 __Pyx_INCREF(__pyx_n_u_Description_2);
16911 __Pyx_GIVEREF(__pyx_n_u_Description_2);
16912 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_n_u_Description_2)) __PYX_ERR(0, 449, __pyx_L1_error);
16913 __Pyx_GIVEREF(__pyx_t_2);
16914 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_2)) __PYX_ERR(0, 449, __pyx_L1_error);
16915 __pyx_t_2 = 0;
16916 __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 449, __pyx_L1_error)
16917 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16918
16919 /* "pysam/libcvcf.pyx":450
16920 * values.append( ('Type', fmt.type) )
16921 * values.append( ('Description', '"' + fmt.description + '"') )
16922 * if self._version == 33: # <<<<<<<<<<<<<<
16923 * format = ",".join([v for k,v in values])
16924 * else:
16925 */
16926 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_version); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 450, __pyx_L1_error)
16927 __Pyx_GOTREF(__pyx_t_1);
16928 __pyx_t_3 = (__Pyx_PyInt_BoolEqObjC(__pyx_t_1, __pyx_int_33, 33, 0)); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 450, __pyx_L1_error)
16929 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
16930 if (__pyx_t_3) {
16931
16932 /* "pysam/libcvcf.pyx":451
16933 * values.append( ('Description', '"' + fmt.description + '"') )
16934 * if self._version == 33:
16935 * format = ",".join([v for k,v in values]) # <<<<<<<<<<<<<<
16936 * else:
16937 * format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">"
16938 */
16939 { /* enter inner scope */
16940 __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 451, __pyx_L10_error)
16941 __Pyx_GOTREF(__pyx_t_1);
16942 __pyx_t_2 = __pyx_v_values; __Pyx_INCREF(__pyx_t_2);
16943 __pyx_t_8 = 0;
16944 for (;;) {
16945 {
16946 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2);
16947 #if !CYTHON_ASSUME_SAFE_MACROS
16948 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 451, __pyx_L10_error)
16949 #endif
16950 if (__pyx_t_8 >= __pyx_temp) break;
16951 }
16952 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
16953 __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_6); __pyx_t_8++; if (unlikely((0 < 0))) __PYX_ERR(0, 451, __pyx_L10_error)
16954 #else
16955 __pyx_t_6 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 451, __pyx_L10_error)
16956 __Pyx_GOTREF(__pyx_t_6);
16957 #endif
16958 if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) {
16959 PyObject* sequence = __pyx_t_6;
16960 Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
16961 if (unlikely(size != 2)) {
16962 if (size > 2) __Pyx_RaiseTooManyValuesError(2);
16963 else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
16964 __PYX_ERR(0, 451, __pyx_L10_error)
16965 }
16966 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
16967 if (likely(PyTuple_CheckExact(sequence))) {
16968 __pyx_t_9 = PyTuple_GET_ITEM(sequence, 0);
16969 __pyx_t_10 = PyTuple_GET_ITEM(sequence, 1);
16970 } else {
16971 __pyx_t_9 = PyList_GET_ITEM(sequence, 0);
16972 __pyx_t_10 = PyList_GET_ITEM(sequence, 1);
16973 }
16974 __Pyx_INCREF(__pyx_t_9);
16975 __Pyx_INCREF(__pyx_t_10);
16976 #else
16977 __pyx_t_9 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 451, __pyx_L10_error)
16978 __Pyx_GOTREF(__pyx_t_9);
16979 __pyx_t_10 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 451, __pyx_L10_error)
16980 __Pyx_GOTREF(__pyx_t_10);
16981 #endif
16982 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
16983 } else {
16984 Py_ssize_t index = -1;
16985 __pyx_t_11 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 451, __pyx_L10_error)
16986 __Pyx_GOTREF(__pyx_t_11);
16987 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
16988 __pyx_t_12 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_11);
16989 index = 0; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L13_unpacking_failed;
16990 __Pyx_GOTREF(__pyx_t_9);
16991 index = 1; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L13_unpacking_failed;
16992 __Pyx_GOTREF(__pyx_t_10);
16993 if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 2) < 0) __PYX_ERR(0, 451, __pyx_L10_error)
16994 __pyx_t_12 = NULL;
16995 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
16996 goto __pyx_L14_unpacking_done;
16997 __pyx_L13_unpacking_failed:;
16998 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
16999 __pyx_t_12 = NULL;
17000 if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
17001 __PYX_ERR(0, 451, __pyx_L10_error)
17002 __pyx_L14_unpacking_done:;
17003 }
17004 __Pyx_XDECREF_SET(__pyx_7genexpr__pyx_v_k, __pyx_t_9);
17005 __pyx_t_9 = 0;
17006 __Pyx_XDECREF_SET(__pyx_7genexpr__pyx_v_v, __pyx_t_10);
17007 __pyx_t_10 = 0;
17008 if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_7genexpr__pyx_v_v))) __PYX_ERR(0, 451, __pyx_L10_error)
17009 }
17010 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17011 __Pyx_XDECREF(__pyx_7genexpr__pyx_v_k); __pyx_7genexpr__pyx_v_k = 0;
17012 __Pyx_XDECREF(__pyx_7genexpr__pyx_v_v); __pyx_7genexpr__pyx_v_v = 0;
17013 goto __pyx_L16_exit_scope;
17014 __pyx_L10_error:;
17015 __Pyx_XDECREF(__pyx_7genexpr__pyx_v_k); __pyx_7genexpr__pyx_v_k = 0;
17016 __Pyx_XDECREF(__pyx_7genexpr__pyx_v_v); __pyx_7genexpr__pyx_v_v = 0;
17017 goto __pyx_L1_error;
17018 __pyx_L16_exit_scope:;
17019 } /* exit inner scope */
17020 __pyx_t_2 = PyUnicode_Join(__pyx_kp_u__2, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 451, __pyx_L1_error)
17021 __Pyx_GOTREF(__pyx_t_2);
17022 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
17023 __pyx_v_format = ((PyObject*)__pyx_t_2);
17024 __pyx_t_2 = 0;
17025
17026 /* "pysam/libcvcf.pyx":450
17027 * values.append( ('Type', fmt.type) )
17028 * values.append( ('Description', '"' + fmt.description + '"') )
17029 * if self._version == 33: # <<<<<<<<<<<<<<
17030 * format = ",".join([v for k,v in values])
17031 * else:
17032 */
17033 goto __pyx_L7;
17034 }
17035
17036 /* "pysam/libcvcf.pyx":453
17037 * format = ",".join([v for k,v in values])
17038 * else:
17039 * format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">" # <<<<<<<<<<<<<<
17040 * return format
17041 *
17042 */
17043 /*else*/ {
17044 { /* enter inner scope */
17045 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 453, __pyx_L19_error)
17046 __Pyx_GOTREF(__pyx_t_2);
17047 __pyx_t_1 = __pyx_v_values; __Pyx_INCREF(__pyx_t_1);
17048 __pyx_t_8 = 0;
17049 for (;;) {
17050 {
17051 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1);
17052 #if !CYTHON_ASSUME_SAFE_MACROS
17053 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 453, __pyx_L19_error)
17054 #endif
17055 if (__pyx_t_8 >= __pyx_temp) break;
17056 }
17057 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
17058 __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_6); __pyx_t_8++; if (unlikely((0 < 0))) __PYX_ERR(0, 453, __pyx_L19_error)
17059 #else
17060 __pyx_t_6 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 453, __pyx_L19_error)
17061 __Pyx_GOTREF(__pyx_t_6);
17062 #endif
17063 if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) {
17064 PyObject* sequence = __pyx_t_6;
17065 Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
17066 if (unlikely(size != 2)) {
17067 if (size > 2) __Pyx_RaiseTooManyValuesError(2);
17068 else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
17069 __PYX_ERR(0, 453, __pyx_L19_error)
17070 }
17071 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
17072 if (likely(PyTuple_CheckExact(sequence))) {
17073 __pyx_t_10 = PyTuple_GET_ITEM(sequence, 0);
17074 __pyx_t_9 = PyTuple_GET_ITEM(sequence, 1);
17075 } else {
17076 __pyx_t_10 = PyList_GET_ITEM(sequence, 0);
17077 __pyx_t_9 = PyList_GET_ITEM(sequence, 1);
17078 }
17079 __Pyx_INCREF(__pyx_t_10);
17080 __Pyx_INCREF(__pyx_t_9);
17081 #else
17082 __pyx_t_10 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 453, __pyx_L19_error)
17083 __Pyx_GOTREF(__pyx_t_10);
17084 __pyx_t_9 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 453, __pyx_L19_error)
17085 __Pyx_GOTREF(__pyx_t_9);
17086 #endif
17087 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
17088 } else {
17089 Py_ssize_t index = -1;
17090 __pyx_t_11 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 453, __pyx_L19_error)
17091 __Pyx_GOTREF(__pyx_t_11);
17092 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
17093 __pyx_t_12 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_11);
17094 index = 0; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L22_unpacking_failed;
17095 __Pyx_GOTREF(__pyx_t_10);
17096 index = 1; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L22_unpacking_failed;
17097 __Pyx_GOTREF(__pyx_t_9);
17098 if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 2) < 0) __PYX_ERR(0, 453, __pyx_L19_error)
17099 __pyx_t_12 = NULL;
17100 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
17101 goto __pyx_L23_unpacking_done;
17102 __pyx_L22_unpacking_failed:;
17103 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
17104 __pyx_t_12 = NULL;
17105 if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
17106 __PYX_ERR(0, 453, __pyx_L19_error)
17107 __pyx_L23_unpacking_done:;
17108 }
17109 __Pyx_XDECREF_SET(__pyx_8genexpr1__pyx_v_k, __pyx_t_10);
17110 __pyx_t_10 = 0;
17111 __Pyx_XDECREF_SET(__pyx_8genexpr1__pyx_v_v, __pyx_t_9);
17112 __pyx_t_9 = 0;
17113 __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 453, __pyx_L19_error)
17114 __Pyx_GOTREF(__pyx_t_6);
17115 __pyx_t_13 = 0;
17116 __pyx_t_14 = 127;
17117 __pyx_t_9 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_8genexpr1__pyx_v_k), __pyx_empty_unicode); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 453, __pyx_L19_error)
17118 __Pyx_GOTREF(__pyx_t_9);
17119 __pyx_t_14 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_9) > __pyx_t_14) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_9) : __pyx_t_14;
17120 __pyx_t_13 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_9);
17121 __Pyx_GIVEREF(__pyx_t_9);
17122 PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_9);
17123 __pyx_t_9 = 0;
17124 __Pyx_INCREF(__pyx_kp_u__7);
17125 __pyx_t_13 += 1;
17126 __Pyx_GIVEREF(__pyx_kp_u__7);
17127 PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_kp_u__7);
17128 __pyx_t_9 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_8genexpr1__pyx_v_v), __pyx_empty_unicode); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 453, __pyx_L19_error)
17129 __Pyx_GOTREF(__pyx_t_9);
17130 __pyx_t_14 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_9) > __pyx_t_14) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_9) : __pyx_t_14;
17131 __pyx_t_13 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_9);
17132 __Pyx_GIVEREF(__pyx_t_9);
17133 PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_9);
17134 __pyx_t_9 = 0;
17135 __pyx_t_9 = __Pyx_PyUnicode_Join(__pyx_t_6, 3, __pyx_t_13, __pyx_t_14); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 453, __pyx_L19_error)
17136 __Pyx_GOTREF(__pyx_t_9);
17137 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
17138 if (unlikely(__Pyx_ListComp_Append(__pyx_t_2, (PyObject*)__pyx_t_9))) __PYX_ERR(0, 453, __pyx_L19_error)
17139 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
17140 }
17141 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
17142 __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_k); __pyx_8genexpr1__pyx_v_k = 0;
17143 __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_v); __pyx_8genexpr1__pyx_v_v = 0;
17144 goto __pyx_L25_exit_scope;
17145 __pyx_L19_error:;
17146 __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_k); __pyx_8genexpr1__pyx_v_k = 0;
17147 __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_v); __pyx_8genexpr1__pyx_v_v = 0;
17148 goto __pyx_L1_error;
17149 __pyx_L25_exit_scope:;
17150 } /* exit inner scope */
17151 __pyx_t_1 = PyUnicode_Join(__pyx_kp_u__2, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 453, __pyx_L1_error)
17152 __Pyx_GOTREF(__pyx_t_1);
17153 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17154 __pyx_t_2 = __Pyx_PyUnicode_Concat(__pyx_kp_u__15, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 453, __pyx_L1_error)
17155 __Pyx_GOTREF(__pyx_t_2);
17156 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
17157 __pyx_t_1 = __Pyx_PyUnicode_ConcatInPlace(__pyx_t_2, __pyx_kp_u__16); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 453, __pyx_L1_error)
17158 __Pyx_GOTREF(__pyx_t_1);
17159 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17160 __pyx_v_format = ((PyObject*)__pyx_t_1);
17161 __pyx_t_1 = 0;
17162 }
17163 __pyx_L7:;
17164
17165 /* "pysam/libcvcf.pyx":454
17166 * else:
17167 * format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">"
17168 * return format # <<<<<<<<<<<<<<
17169 *
17170 * def get_expected(self, format, formatdict, alt):
17171 */
17172 __Pyx_XDECREF(__pyx_r);
17173 __Pyx_INCREF(__pyx_v_format);
17174 __pyx_r = __pyx_v_format;
17175 goto __pyx_L0;
17176
17177 /* "pysam/libcvcf.pyx":436
17178 * return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
17179 *
17180 * def format_format( self, fmt, filter=False ): # <<<<<<<<<<<<<<
17181 * values = [('ID',fmt.id)]
17182 * if fmt.number != None and not filter:
17183 */
17184
17185 /* function exit code */
17186 __pyx_L1_error:;
17187 __Pyx_XDECREF(__pyx_t_1);
17188 __Pyx_XDECREF(__pyx_t_2);
17189 __Pyx_XDECREF(__pyx_t_6);
17190 __Pyx_XDECREF(__pyx_t_9);
17191 __Pyx_XDECREF(__pyx_t_10);
17192 __Pyx_XDECREF(__pyx_t_11);
17193 __Pyx_AddTraceback("pysam.libcvcf.VCF.format_format", __pyx_clineno, __pyx_lineno, __pyx_filename);
17194 __pyx_r = NULL;
17195 __pyx_L0:;
17196 __Pyx_XDECREF(__pyx_v_values);
17197 __Pyx_XDECREF(__pyx_v_nmb);
17198 __Pyx_XDECREF(__pyx_v_format);
17199 __Pyx_XDECREF(__pyx_7genexpr__pyx_v_k);
17200 __Pyx_XDECREF(__pyx_7genexpr__pyx_v_v);
17201 __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_k);
17202 __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_v);
17203 __Pyx_XGIVEREF(__pyx_r);
17204 __Pyx_RefNannyFinishContext();
17205 return __pyx_r;
17206 }
17207
17208 /* "pysam/libcvcf.pyx":456
17209 * return format
17210 *
17211 * def get_expected(self, format, formatdict, alt): # <<<<<<<<<<<<<<
17212 * fmt = formatdict[format]
17213 * if fmt.numbertype == self.NT_UNKNOWN: return -1
17214 */
17215
17216 /* Python wrapper */
17217 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_9get_expected(PyObject *__pyx_self,
17218 #if CYTHON_METH_FASTCALL
17219 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
17220 #else
17221 PyObject *__pyx_args, PyObject *__pyx_kwds
17222 #endif
17223 ); /*proto*/
17224 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_8get_expected, "VCF.get_expected(self, format, formatdict, alt)");
17225 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_9get_expected = {"get_expected", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_9get_expected, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_8get_expected};
17226 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_9get_expected(PyObject *__pyx_self,
17227 #if CYTHON_METH_FASTCALL
17228 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
17229 #else
17230 PyObject *__pyx_args, PyObject *__pyx_kwds
17231 #endif
17232 ) {
17233 PyObject *__pyx_v_self = 0;
17234 PyObject *__pyx_v_format = 0;
17235 PyObject *__pyx_v_formatdict = 0;
17236 PyObject *__pyx_v_alt = 0;
17237 #if !CYTHON_METH_FASTCALL
17238 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
17239 #endif
17240 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
17241 PyObject* values[4] = {0,0,0,0};
17242 int __pyx_lineno = 0;
17243 const char *__pyx_filename = NULL;
17244 int __pyx_clineno = 0;
17245 PyObject *__pyx_r = 0;
17246 __Pyx_RefNannyDeclarations
17247 __Pyx_RefNannySetupContext("get_expected (wrapper)", 0);
17248 #if !CYTHON_METH_FASTCALL
17249 #if CYTHON_ASSUME_SAFE_MACROS
17250 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
17251 #else
17252 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
17253 #endif
17254 #endif
17255 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
17256 {
17257 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_format,&__pyx_n_s_formatdict,&__pyx_n_s_alt,0};
17258 if (__pyx_kwds) {
17259 Py_ssize_t kw_args;
17260 switch (__pyx_nargs) {
17261 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
17262 CYTHON_FALLTHROUGH;
17263 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
17264 CYTHON_FALLTHROUGH;
17265 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
17266 CYTHON_FALLTHROUGH;
17267 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
17268 CYTHON_FALLTHROUGH;
17269 case 0: break;
17270 default: goto __pyx_L5_argtuple_error;
17271 }
17272 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
17273 switch (__pyx_nargs) {
17274 case 0:
17275 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
17276 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
17277 kw_args--;
17278 }
17279 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 456, __pyx_L3_error)
17280 else goto __pyx_L5_argtuple_error;
17281 CYTHON_FALLTHROUGH;
17282 case 1:
17283 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_format)) != 0)) {
17284 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
17285 kw_args--;
17286 }
17287 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 456, __pyx_L3_error)
17288 else {
17289 __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 1); __PYX_ERR(0, 456, __pyx_L3_error)
17290 }
17291 CYTHON_FALLTHROUGH;
17292 case 2:
17293 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_formatdict)) != 0)) {
17294 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
17295 kw_args--;
17296 }
17297 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 456, __pyx_L3_error)
17298 else {
17299 __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 2); __PYX_ERR(0, 456, __pyx_L3_error)
17300 }
17301 CYTHON_FALLTHROUGH;
17302 case 3:
17303 if (likely((values[3] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_alt)) != 0)) {
17304 (void)__Pyx_Arg_NewRef_FASTCALL(values[3]);
17305 kw_args--;
17306 }
17307 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 456, __pyx_L3_error)
17308 else {
17309 __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 3); __PYX_ERR(0, 456, __pyx_L3_error)
17310 }
17311 }
17312 if (unlikely(kw_args > 0)) {
17313 const Py_ssize_t kwd_pos_args = __pyx_nargs;
17314 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "get_expected") < 0)) __PYX_ERR(0, 456, __pyx_L3_error)
17315 }
17316 } else if (unlikely(__pyx_nargs != 4)) {
17317 goto __pyx_L5_argtuple_error;
17318 } else {
17319 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
17320 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
17321 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
17322 values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
17323 }
17324 __pyx_v_self = values[0];
17325 __pyx_v_format = values[1];
17326 __pyx_v_formatdict = values[2];
17327 __pyx_v_alt = values[3];
17328 }
17329 goto __pyx_L6_skip;
17330 __pyx_L5_argtuple_error:;
17331 __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, __pyx_nargs); __PYX_ERR(0, 456, __pyx_L3_error)
17332 __pyx_L6_skip:;
17333 goto __pyx_L4_argument_unpacking_done;
17334 __pyx_L3_error:;
17335 {
17336 Py_ssize_t __pyx_temp;
17337 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
17338 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
17339 }
17340 }
17341 __Pyx_AddTraceback("pysam.libcvcf.VCF.get_expected", __pyx_clineno, __pyx_lineno, __pyx_filename);
17342 __Pyx_RefNannyFinishContext();
17343 return NULL;
17344 __pyx_L4_argument_unpacking_done:;
17345 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_8get_expected(__pyx_self, __pyx_v_self, __pyx_v_format, __pyx_v_formatdict, __pyx_v_alt);
17346
17347 /* function exit code */
17348 {
17349 Py_ssize_t __pyx_temp;
17350 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
17351 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
17352 }
17353 }
17354 __Pyx_RefNannyFinishContext();
17355 return __pyx_r;
17356 }
17357
17358 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_alt) {
17359 PyObject *__pyx_v_fmt = NULL;
17360 PyObject *__pyx_r = NULL;
17361 __Pyx_RefNannyDeclarations
17362 PyObject *__pyx_t_1 = NULL;
17363 PyObject *__pyx_t_2 = NULL;
17364 PyObject *__pyx_t_3 = NULL;
17365 int __pyx_t_4;
17366 Py_ssize_t __pyx_t_5;
17367 Py_ssize_t __pyx_t_6;
17368 int __pyx_lineno = 0;
17369 const char *__pyx_filename = NULL;
17370 int __pyx_clineno = 0;
17371 __Pyx_RefNannySetupContext("get_expected", 1);
17372
17373 /* "pysam/libcvcf.pyx":457
17374 *
17375 * def get_expected(self, format, formatdict, alt):
17376 * fmt = formatdict[format] # <<<<<<<<<<<<<<
17377 * if fmt.numbertype == self.NT_UNKNOWN: return -1
17378 * if fmt.numbertype == self.NT_NUMBER: return fmt.number
17379 */
17380 __pyx_t_1 = __Pyx_PyObject_GetItem(__pyx_v_formatdict, __pyx_v_format); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 457, __pyx_L1_error)
17381 __Pyx_GOTREF(__pyx_t_1);
17382 __pyx_v_fmt = __pyx_t_1;
17383 __pyx_t_1 = 0;
17384
17385 /* "pysam/libcvcf.pyx":458
17386 * def get_expected(self, format, formatdict, alt):
17387 * fmt = formatdict[format]
17388 * if fmt.numbertype == self.NT_UNKNOWN: return -1 # <<<<<<<<<<<<<<
17389 * if fmt.numbertype == self.NT_NUMBER: return fmt.number
17390 * if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
17391 */
17392 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 458, __pyx_L1_error)
17393 __Pyx_GOTREF(__pyx_t_1);
17394 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_UNKNOWN); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 458, __pyx_L1_error)
17395 __Pyx_GOTREF(__pyx_t_2);
17396 __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 458, __pyx_L1_error)
17397 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
17398 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17399 __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(0, 458, __pyx_L1_error)
17400 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
17401 if (__pyx_t_4) {
17402 __Pyx_XDECREF(__pyx_r);
17403 __Pyx_INCREF(__pyx_int_neg_1);
17404 __pyx_r = __pyx_int_neg_1;
17405 goto __pyx_L0;
17406 }
17407
17408 /* "pysam/libcvcf.pyx":459
17409 * fmt = formatdict[format]
17410 * if fmt.numbertype == self.NT_UNKNOWN: return -1
17411 * if fmt.numbertype == self.NT_NUMBER: return fmt.number # <<<<<<<<<<<<<<
17412 * if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
17413 * if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
17414 */
17415 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 459, __pyx_L1_error)
17416 __Pyx_GOTREF(__pyx_t_3);
17417 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NUMBER); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 459, __pyx_L1_error)
17418 __Pyx_GOTREF(__pyx_t_2);
17419 __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 459, __pyx_L1_error)
17420 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
17421 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17422 __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(0, 459, __pyx_L1_error)
17423 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
17424 if (__pyx_t_4) {
17425 __Pyx_XDECREF(__pyx_r);
17426 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_number); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 459, __pyx_L1_error)
17427 __Pyx_GOTREF(__pyx_t_1);
17428 __pyx_r = __pyx_t_1;
17429 __pyx_t_1 = 0;
17430 goto __pyx_L0;
17431 }
17432
17433 /* "pysam/libcvcf.pyx":460
17434 * if fmt.numbertype == self.NT_UNKNOWN: return -1
17435 * if fmt.numbertype == self.NT_NUMBER: return fmt.number
17436 * if fmt.numbertype == self.NT_ALLELES: return len(alt)+1 # <<<<<<<<<<<<<<
17437 * if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
17438 * if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
17439 */
17440 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 460, __pyx_L1_error)
17441 __Pyx_GOTREF(__pyx_t_1);
17442 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_ALLELES); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 460, __pyx_L1_error)
17443 __Pyx_GOTREF(__pyx_t_2);
17444 __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 460, __pyx_L1_error)
17445 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
17446 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17447 __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(0, 460, __pyx_L1_error)
17448 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
17449 if (__pyx_t_4) {
17450 __Pyx_XDECREF(__pyx_r);
17451 __pyx_t_5 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 460, __pyx_L1_error)
17452 __pyx_t_3 = PyInt_FromSsize_t((__pyx_t_5 + 1)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 460, __pyx_L1_error)
17453 __Pyx_GOTREF(__pyx_t_3);
17454 __pyx_r = __pyx_t_3;
17455 __pyx_t_3 = 0;
17456 goto __pyx_L0;
17457 }
17458
17459 /* "pysam/libcvcf.pyx":461
17460 * if fmt.numbertype == self.NT_NUMBER: return fmt.number
17461 * if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
17462 * if fmt.numbertype == self.NT_NR_ALLELES: return len(alt) # <<<<<<<<<<<<<<
17463 * if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
17464 * if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1)
17465 */
17466 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 461, __pyx_L1_error)
17467 __Pyx_GOTREF(__pyx_t_3);
17468 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NR_ALLELES); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 461, __pyx_L1_error)
17469 __Pyx_GOTREF(__pyx_t_2);
17470 __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 461, __pyx_L1_error)
17471 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
17472 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17473 __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(0, 461, __pyx_L1_error)
17474 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
17475 if (__pyx_t_4) {
17476 __Pyx_XDECREF(__pyx_r);
17477 __pyx_t_5 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 461, __pyx_L1_error)
17478 __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_5); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 461, __pyx_L1_error)
17479 __Pyx_GOTREF(__pyx_t_1);
17480 __pyx_r = __pyx_t_1;
17481 __pyx_t_1 = 0;
17482 goto __pyx_L0;
17483 }
17484
17485 /* "pysam/libcvcf.pyx":462
17486 * if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
17487 * if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
17488 * if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2 # <<<<<<<<<<<<<<
17489 * if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1)
17490 * return 0
17491 */
17492 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 462, __pyx_L1_error)
17493 __Pyx_GOTREF(__pyx_t_1);
17494 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_GENOTYPES); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 462, __pyx_L1_error)
17495 __Pyx_GOTREF(__pyx_t_2);
17496 __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 462, __pyx_L1_error)
17497 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
17498 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17499 __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(0, 462, __pyx_L1_error)
17500 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
17501 if (__pyx_t_4) {
17502 __Pyx_XDECREF(__pyx_r);
17503 __pyx_t_5 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 462, __pyx_L1_error)
17504 __pyx_t_6 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 462, __pyx_L1_error)
17505 __pyx_t_3 = PyInt_FromSsize_t(__Pyx_div_Py_ssize_t(((__pyx_t_5 + 1) * (__pyx_t_6 + 2)), 2)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 462, __pyx_L1_error)
17506 __Pyx_GOTREF(__pyx_t_3);
17507 __pyx_r = __pyx_t_3;
17508 __pyx_t_3 = 0;
17509 goto __pyx_L0;
17510 }
17511
17512 /* "pysam/libcvcf.pyx":463
17513 * if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
17514 * if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
17515 * if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1) # <<<<<<<<<<<<<<
17516 * return 0
17517 *
17518 */
17519 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_fmt, __pyx_n_s_numbertype); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 463, __pyx_L1_error)
17520 __Pyx_GOTREF(__pyx_t_3);
17521 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 463, __pyx_L1_error)
17522 __Pyx_GOTREF(__pyx_t_2);
17523 __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 463, __pyx_L1_error)
17524 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
17525 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17526 __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(0, 463, __pyx_L1_error)
17527 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
17528 if (__pyx_t_4) {
17529 __Pyx_XDECREF(__pyx_r);
17530 __pyx_t_6 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 463, __pyx_L1_error)
17531 __pyx_t_5 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 463, __pyx_L1_error)
17532 __pyx_t_1 = PyInt_FromSsize_t(((__pyx_t_6 + 1) * (__pyx_t_5 + 1))); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 463, __pyx_L1_error)
17533 __Pyx_GOTREF(__pyx_t_1);
17534 __pyx_r = __pyx_t_1;
17535 __pyx_t_1 = 0;
17536 goto __pyx_L0;
17537 }
17538
17539 /* "pysam/libcvcf.pyx":464
17540 * if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
17541 * if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1)
17542 * return 0 # <<<<<<<<<<<<<<
17543 *
17544 *
17545 */
17546 __Pyx_XDECREF(__pyx_r);
17547 __Pyx_INCREF(__pyx_int_0);
17548 __pyx_r = __pyx_int_0;
17549 goto __pyx_L0;
17550
17551 /* "pysam/libcvcf.pyx":456
17552 * return format
17553 *
17554 * def get_expected(self, format, formatdict, alt): # <<<<<<<<<<<<<<
17555 * fmt = formatdict[format]
17556 * if fmt.numbertype == self.NT_UNKNOWN: return -1
17557 */
17558
17559 /* function exit code */
17560 __pyx_L1_error:;
17561 __Pyx_XDECREF(__pyx_t_1);
17562 __Pyx_XDECREF(__pyx_t_2);
17563 __Pyx_XDECREF(__pyx_t_3);
17564 __Pyx_AddTraceback("pysam.libcvcf.VCF.get_expected", __pyx_clineno, __pyx_lineno, __pyx_filename);
17565 __pyx_r = NULL;
17566 __pyx_L0:;
17567 __Pyx_XDECREF(__pyx_v_fmt);
17568 __Pyx_XGIVEREF(__pyx_r);
17569 __Pyx_RefNannyFinishContext();
17570 return __pyx_r;
17571 }
17572
17573 /* "pysam/libcvcf.pyx":467
17574 *
17575 *
17576 * def _add_definition(self, formatdict, key, data, line ): # <<<<<<<<<<<<<<
17577 * if key in formatdict: return
17578 * self.error(line,self.ERROR_UNKNOWN_KEY,key)
17579 */
17580
17581 /* Python wrapper */
17582 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_11_add_definition(PyObject *__pyx_self,
17583 #if CYTHON_METH_FASTCALL
17584 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
17585 #else
17586 PyObject *__pyx_args, PyObject *__pyx_kwds
17587 #endif
17588 ); /*proto*/
17589 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_10_add_definition, "VCF._add_definition(self, formatdict, key, data, line)");
17590 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_11_add_definition = {"_add_definition", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_11_add_definition, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_10_add_definition};
17591 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_11_add_definition(PyObject *__pyx_self,
17592 #if CYTHON_METH_FASTCALL
17593 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
17594 #else
17595 PyObject *__pyx_args, PyObject *__pyx_kwds
17596 #endif
17597 ) {
17598 PyObject *__pyx_v_self = 0;
17599 PyObject *__pyx_v_formatdict = 0;
17600 PyObject *__pyx_v_key = 0;
17601 PyObject *__pyx_v_data = 0;
17602 PyObject *__pyx_v_line = 0;
17603 #if !CYTHON_METH_FASTCALL
17604 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
17605 #endif
17606 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
17607 PyObject* values[5] = {0,0,0,0,0};
17608 int __pyx_lineno = 0;
17609 const char *__pyx_filename = NULL;
17610 int __pyx_clineno = 0;
17611 PyObject *__pyx_r = 0;
17612 __Pyx_RefNannyDeclarations
17613 __Pyx_RefNannySetupContext("_add_definition (wrapper)", 0);
17614 #if !CYTHON_METH_FASTCALL
17615 #if CYTHON_ASSUME_SAFE_MACROS
17616 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
17617 #else
17618 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
17619 #endif
17620 #endif
17621 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
17622 {
17623 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_formatdict,&__pyx_n_s_key,&__pyx_n_s_data,&__pyx_n_s_line,0};
17624 if (__pyx_kwds) {
17625 Py_ssize_t kw_args;
17626 switch (__pyx_nargs) {
17627 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
17628 CYTHON_FALLTHROUGH;
17629 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
17630 CYTHON_FALLTHROUGH;
17631 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
17632 CYTHON_FALLTHROUGH;
17633 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
17634 CYTHON_FALLTHROUGH;
17635 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
17636 CYTHON_FALLTHROUGH;
17637 case 0: break;
17638 default: goto __pyx_L5_argtuple_error;
17639 }
17640 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
17641 switch (__pyx_nargs) {
17642 case 0:
17643 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
17644 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
17645 kw_args--;
17646 }
17647 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 467, __pyx_L3_error)
17648 else goto __pyx_L5_argtuple_error;
17649 CYTHON_FALLTHROUGH;
17650 case 1:
17651 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_formatdict)) != 0)) {
17652 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
17653 kw_args--;
17654 }
17655 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 467, __pyx_L3_error)
17656 else {
17657 __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 1); __PYX_ERR(0, 467, __pyx_L3_error)
17658 }
17659 CYTHON_FALLTHROUGH;
17660 case 2:
17661 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_key)) != 0)) {
17662 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
17663 kw_args--;
17664 }
17665 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 467, __pyx_L3_error)
17666 else {
17667 __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 2); __PYX_ERR(0, 467, __pyx_L3_error)
17668 }
17669 CYTHON_FALLTHROUGH;
17670 case 3:
17671 if (likely((values[3] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_data)) != 0)) {
17672 (void)__Pyx_Arg_NewRef_FASTCALL(values[3]);
17673 kw_args--;
17674 }
17675 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 467, __pyx_L3_error)
17676 else {
17677 __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 3); __PYX_ERR(0, 467, __pyx_L3_error)
17678 }
17679 CYTHON_FALLTHROUGH;
17680 case 4:
17681 if (likely((values[4] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_line)) != 0)) {
17682 (void)__Pyx_Arg_NewRef_FASTCALL(values[4]);
17683 kw_args--;
17684 }
17685 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 467, __pyx_L3_error)
17686 else {
17687 __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 4); __PYX_ERR(0, 467, __pyx_L3_error)
17688 }
17689 }
17690 if (unlikely(kw_args > 0)) {
17691 const Py_ssize_t kwd_pos_args = __pyx_nargs;
17692 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "_add_definition") < 0)) __PYX_ERR(0, 467, __pyx_L3_error)
17693 }
17694 } else if (unlikely(__pyx_nargs != 5)) {
17695 goto __pyx_L5_argtuple_error;
17696 } else {
17697 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
17698 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
17699 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
17700 values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
17701 values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
17702 }
17703 __pyx_v_self = values[0];
17704 __pyx_v_formatdict = values[1];
17705 __pyx_v_key = values[2];
17706 __pyx_v_data = values[3];
17707 __pyx_v_line = values[4];
17708 }
17709 goto __pyx_L6_skip;
17710 __pyx_L5_argtuple_error:;
17711 __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, __pyx_nargs); __PYX_ERR(0, 467, __pyx_L3_error)
17712 __pyx_L6_skip:;
17713 goto __pyx_L4_argument_unpacking_done;
17714 __pyx_L3_error:;
17715 {
17716 Py_ssize_t __pyx_temp;
17717 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
17718 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
17719 }
17720 }
17721 __Pyx_AddTraceback("pysam.libcvcf.VCF._add_definition", __pyx_clineno, __pyx_lineno, __pyx_filename);
17722 __Pyx_RefNannyFinishContext();
17723 return NULL;
17724 __pyx_L4_argument_unpacking_done:;
17725 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_10_add_definition(__pyx_self, __pyx_v_self, __pyx_v_formatdict, __pyx_v_key, __pyx_v_data, __pyx_v_line);
17726
17727 /* function exit code */
17728 {
17729 Py_ssize_t __pyx_temp;
17730 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
17731 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
17732 }
17733 }
17734 __Pyx_RefNannyFinishContext();
17735 return __pyx_r;
17736 }
17737
17738 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_key, PyObject *__pyx_v_data, PyObject *__pyx_v_line) {
17739 PyObject *__pyx_r = NULL;
17740 __Pyx_RefNannyDeclarations
17741 int __pyx_t_1;
17742 PyObject *__pyx_t_2 = NULL;
17743 PyObject *__pyx_t_3 = NULL;
17744 PyObject *__pyx_t_4 = NULL;
17745 PyObject *__pyx_t_5 = NULL;
17746 unsigned int __pyx_t_6;
17747 int __pyx_lineno = 0;
17748 const char *__pyx_filename = NULL;
17749 int __pyx_clineno = 0;
17750 __Pyx_RefNannySetupContext("_add_definition", 0);
17751 __Pyx_INCREF(__pyx_v_data);
17752
17753 /* "pysam/libcvcf.pyx":468
17754 *
17755 * def _add_definition(self, formatdict, key, data, line ):
17756 * if key in formatdict: return # <<<<<<<<<<<<<<
17757 * self.error(line,self.ERROR_UNKNOWN_KEY,key)
17758 * if data == None:
17759 */
17760 __pyx_t_1 = (__Pyx_PySequence_ContainsTF(__pyx_v_key, __pyx_v_formatdict, Py_EQ)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 468, __pyx_L1_error)
17761 if (__pyx_t_1) {
17762 __Pyx_XDECREF(__pyx_r);
17763 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
17764 goto __pyx_L0;
17765 }
17766
17767 /* "pysam/libcvcf.pyx":469
17768 * def _add_definition(self, formatdict, key, data, line ):
17769 * if key in formatdict: return
17770 * self.error(line,self.ERROR_UNKNOWN_KEY,key) # <<<<<<<<<<<<<<
17771 * if data == None:
17772 * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
17773 */
17774 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 469, __pyx_L1_error)
17775 __Pyx_GOTREF(__pyx_t_3);
17776 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_ERROR_UNKNOWN_KEY); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 469, __pyx_L1_error)
17777 __Pyx_GOTREF(__pyx_t_4);
17778 __pyx_t_5 = NULL;
17779 __pyx_t_6 = 0;
17780 #if CYTHON_UNPACK_METHODS
17781 if (likely(PyMethod_Check(__pyx_t_3))) {
17782 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_3);
17783 if (likely(__pyx_t_5)) {
17784 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
17785 __Pyx_INCREF(__pyx_t_5);
17786 __Pyx_INCREF(function);
17787 __Pyx_DECREF_SET(__pyx_t_3, function);
17788 __pyx_t_6 = 1;
17789 }
17790 }
17791 #endif
17792 {
17793 PyObject *__pyx_callargs[4] = {__pyx_t_5, __pyx_v_line, __pyx_t_4, __pyx_v_key};
17794 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_6, 3+__pyx_t_6);
17795 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
17796 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
17797 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 469, __pyx_L1_error)
17798 __Pyx_GOTREF(__pyx_t_2);
17799 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
17800 }
17801 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17802
17803 /* "pysam/libcvcf.pyx":470
17804 * if key in formatdict: return
17805 * self.error(line,self.ERROR_UNKNOWN_KEY,key)
17806 * if data == None: # <<<<<<<<<<<<<<
17807 * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
17808 * return
17809 */
17810 __pyx_t_2 = PyObject_RichCompare(__pyx_v_data, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 470, __pyx_L1_error)
17811 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 470, __pyx_L1_error)
17812 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17813 if (__pyx_t_1) {
17814
17815 /* "pysam/libcvcf.pyx":471
17816 * self.error(line,self.ERROR_UNKNOWN_KEY,key)
17817 * if data == None:
17818 * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".") # <<<<<<<<<<<<<<
17819 * return
17820 * if data == []: data = [""] # unsure what type -- say string
17821 */
17822 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 471, __pyx_L1_error)
17823 __Pyx_GOTREF(__pyx_t_3);
17824 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NUMBER); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 471, __pyx_L1_error)
17825 __Pyx_GOTREF(__pyx_t_4);
17826 __pyx_t_5 = NULL;
17827 __pyx_t_6 = 0;
17828 #if CYTHON_UNPACK_METHODS
17829 if (unlikely(PyMethod_Check(__pyx_t_3))) {
17830 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_3);
17831 if (likely(__pyx_t_5)) {
17832 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
17833 __Pyx_INCREF(__pyx_t_5);
17834 __Pyx_INCREF(function);
17835 __Pyx_DECREF_SET(__pyx_t_3, function);
17836 __pyx_t_6 = 1;
17837 }
17838 }
17839 #endif
17840 {
17841 PyObject *__pyx_callargs[7] = {__pyx_t_5, __pyx_v_key, __pyx_t_4, __pyx_int_0, __pyx_n_u_Flag, __pyx_kp_u_Undefined_tag, __pyx_kp_u__5};
17842 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_6, 6+__pyx_t_6);
17843 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
17844 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
17845 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 471, __pyx_L1_error)
17846 __Pyx_GOTREF(__pyx_t_2);
17847 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
17848 }
17849 if (unlikely((PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_2) < 0))) __PYX_ERR(0, 471, __pyx_L1_error)
17850 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17851
17852 /* "pysam/libcvcf.pyx":472
17853 * if data == None:
17854 * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
17855 * return # <<<<<<<<<<<<<<
17856 * if data == []: data = [""] # unsure what type -- say string
17857 * if type(data[0]) == type(0.0):
17858 */
17859 __Pyx_XDECREF(__pyx_r);
17860 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
17861 goto __pyx_L0;
17862
17863 /* "pysam/libcvcf.pyx":470
17864 * if key in formatdict: return
17865 * self.error(line,self.ERROR_UNKNOWN_KEY,key)
17866 * if data == None: # <<<<<<<<<<<<<<
17867 * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
17868 * return
17869 */
17870 }
17871
17872 /* "pysam/libcvcf.pyx":473
17873 * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
17874 * return
17875 * if data == []: data = [""] # unsure what type -- say string # <<<<<<<<<<<<<<
17876 * if type(data[0]) == type(0.0):
17877 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
17878 */
17879 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 473, __pyx_L1_error)
17880 __Pyx_GOTREF(__pyx_t_2);
17881 __pyx_t_3 = PyObject_RichCompare(__pyx_v_data, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 473, __pyx_L1_error)
17882 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17883 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 473, __pyx_L1_error)
17884 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
17885 if (__pyx_t_1) {
17886 __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 473, __pyx_L1_error)
17887 __Pyx_GOTREF(__pyx_t_3);
17888 __Pyx_INCREF(__pyx_kp_u_);
17889 __Pyx_GIVEREF(__pyx_kp_u_);
17890 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 0, __pyx_kp_u_)) __PYX_ERR(0, 473, __pyx_L1_error);
17891 __Pyx_DECREF_SET(__pyx_v_data, __pyx_t_3);
17892 __pyx_t_3 = 0;
17893 }
17894
17895 /* "pysam/libcvcf.pyx":474
17896 * return
17897 * if data == []: data = [""] # unsure what type -- say string
17898 * if type(data[0]) == type(0.0): # <<<<<<<<<<<<<<
17899 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
17900 * return
17901 */
17902 __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_data, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 474, __pyx_L1_error)
17903 __Pyx_GOTREF(__pyx_t_3);
17904 __pyx_t_2 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_3)), ((PyObject *)Py_TYPE(__pyx_float_0_0)), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 474, __pyx_L1_error)
17905 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
17906 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 474, __pyx_L1_error)
17907 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17908 if (__pyx_t_1) {
17909
17910 /* "pysam/libcvcf.pyx":475
17911 * if data == []: data = [""] # unsure what type -- say string
17912 * if type(data[0]) == type(0.0):
17913 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None) # <<<<<<<<<<<<<<
17914 * return
17915 * if type(data[0]) == type(0):
17916 */
17917 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 475, __pyx_L1_error)
17918 __Pyx_GOTREF(__pyx_t_3);
17919 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_UNKNOWN); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 475, __pyx_L1_error)
17920 __Pyx_GOTREF(__pyx_t_4);
17921 __pyx_t_5 = NULL;
17922 __pyx_t_6 = 0;
17923 #if CYTHON_UNPACK_METHODS
17924 if (unlikely(PyMethod_Check(__pyx_t_3))) {
17925 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_3);
17926 if (likely(__pyx_t_5)) {
17927 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
17928 __Pyx_INCREF(__pyx_t_5);
17929 __Pyx_INCREF(function);
17930 __Pyx_DECREF_SET(__pyx_t_3, function);
17931 __pyx_t_6 = 1;
17932 }
17933 }
17934 #endif
17935 {
17936 PyObject *__pyx_callargs[7] = {__pyx_t_5, __pyx_v_key, __pyx_t_4, __pyx_int_neg_1, __pyx_n_u_Float, __pyx_kp_u_Undefined_tag, Py_None};
17937 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_6, 6+__pyx_t_6);
17938 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
17939 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
17940 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 475, __pyx_L1_error)
17941 __Pyx_GOTREF(__pyx_t_2);
17942 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
17943 }
17944 if (unlikely((PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_2) < 0))) __PYX_ERR(0, 475, __pyx_L1_error)
17945 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17946
17947 /* "pysam/libcvcf.pyx":476
17948 * if type(data[0]) == type(0.0):
17949 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
17950 * return # <<<<<<<<<<<<<<
17951 * if type(data[0]) == type(0):
17952 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
17953 */
17954 __Pyx_XDECREF(__pyx_r);
17955 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
17956 goto __pyx_L0;
17957
17958 /* "pysam/libcvcf.pyx":474
17959 * return
17960 * if data == []: data = [""] # unsure what type -- say string
17961 * if type(data[0]) == type(0.0): # <<<<<<<<<<<<<<
17962 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
17963 * return
17964 */
17965 }
17966
17967 /* "pysam/libcvcf.pyx":477
17968 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
17969 * return
17970 * if type(data[0]) == type(0): # <<<<<<<<<<<<<<
17971 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
17972 * return
17973 */
17974 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_data, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 477, __pyx_L1_error)
17975 __Pyx_GOTREF(__pyx_t_2);
17976 __pyx_t_3 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_2)), ((PyObject *)Py_TYPE(__pyx_int_0)), Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 477, __pyx_L1_error)
17977 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
17978 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 477, __pyx_L1_error)
17979 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
17980 if (__pyx_t_1) {
17981
17982 /* "pysam/libcvcf.pyx":478
17983 * return
17984 * if type(data[0]) == type(0):
17985 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None) # <<<<<<<<<<<<<<
17986 * return
17987 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".")
17988 */
17989 __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 478, __pyx_L1_error)
17990 __Pyx_GOTREF(__pyx_t_2);
17991 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_UNKNOWN); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 478, __pyx_L1_error)
17992 __Pyx_GOTREF(__pyx_t_4);
17993 __pyx_t_5 = NULL;
17994 __pyx_t_6 = 0;
17995 #if CYTHON_UNPACK_METHODS
17996 if (unlikely(PyMethod_Check(__pyx_t_2))) {
17997 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_2);
17998 if (likely(__pyx_t_5)) {
17999 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
18000 __Pyx_INCREF(__pyx_t_5);
18001 __Pyx_INCREF(function);
18002 __Pyx_DECREF_SET(__pyx_t_2, function);
18003 __pyx_t_6 = 1;
18004 }
18005 }
18006 #endif
18007 {
18008 PyObject *__pyx_callargs[7] = {__pyx_t_5, __pyx_v_key, __pyx_t_4, __pyx_int_neg_1, __pyx_n_u_Integer, __pyx_kp_u_Undefined_tag, Py_None};
18009 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_6, 6+__pyx_t_6);
18010 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
18011 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
18012 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 478, __pyx_L1_error)
18013 __Pyx_GOTREF(__pyx_t_3);
18014 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
18015 }
18016 if (unlikely((PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_3) < 0))) __PYX_ERR(0, 478, __pyx_L1_error)
18017 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
18018
18019 /* "pysam/libcvcf.pyx":479
18020 * if type(data[0]) == type(0):
18021 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
18022 * return # <<<<<<<<<<<<<<
18023 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".")
18024 *
18025 */
18026 __Pyx_XDECREF(__pyx_r);
18027 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
18028 goto __pyx_L0;
18029
18030 /* "pysam/libcvcf.pyx":477
18031 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
18032 * return
18033 * if type(data[0]) == type(0): # <<<<<<<<<<<<<<
18034 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
18035 * return
18036 */
18037 }
18038
18039 /* "pysam/libcvcf.pyx":480
18040 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
18041 * return
18042 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".") # <<<<<<<<<<<<<<
18043 *
18044 *
18045 */
18046 __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 480, __pyx_L1_error)
18047 __Pyx_GOTREF(__pyx_t_2);
18048 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_UNKNOWN); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 480, __pyx_L1_error)
18049 __Pyx_GOTREF(__pyx_t_4);
18050 __pyx_t_5 = NULL;
18051 __pyx_t_6 = 0;
18052 #if CYTHON_UNPACK_METHODS
18053 if (unlikely(PyMethod_Check(__pyx_t_2))) {
18054 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_2);
18055 if (likely(__pyx_t_5)) {
18056 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
18057 __Pyx_INCREF(__pyx_t_5);
18058 __Pyx_INCREF(function);
18059 __Pyx_DECREF_SET(__pyx_t_2, function);
18060 __pyx_t_6 = 1;
18061 }
18062 }
18063 #endif
18064 {
18065 PyObject *__pyx_callargs[7] = {__pyx_t_5, __pyx_v_key, __pyx_t_4, __pyx_int_neg_1, __pyx_n_u_String, __pyx_kp_u_Undefined_tag, __pyx_kp_u__5};
18066 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_6, 6+__pyx_t_6);
18067 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
18068 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
18069 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 480, __pyx_L1_error)
18070 __Pyx_GOTREF(__pyx_t_3);
18071 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
18072 }
18073 if (unlikely((PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_3) < 0))) __PYX_ERR(0, 480, __pyx_L1_error)
18074 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
18075
18076 /* "pysam/libcvcf.pyx":467
18077 *
18078 *
18079 * def _add_definition(self, formatdict, key, data, line ): # <<<<<<<<<<<<<<
18080 * if key in formatdict: return
18081 * self.error(line,self.ERROR_UNKNOWN_KEY,key)
18082 */
18083
18084 /* function exit code */
18085 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
18086 goto __pyx_L0;
18087 __pyx_L1_error:;
18088 __Pyx_XDECREF(__pyx_t_2);
18089 __Pyx_XDECREF(__pyx_t_3);
18090 __Pyx_XDECREF(__pyx_t_4);
18091 __Pyx_XDECREF(__pyx_t_5);
18092 __Pyx_AddTraceback("pysam.libcvcf.VCF._add_definition", __pyx_clineno, __pyx_lineno, __pyx_filename);
18093 __pyx_r = NULL;
18094 __pyx_L0:;
18095 __Pyx_XDECREF(__pyx_v_data);
18096 __Pyx_XGIVEREF(__pyx_r);
18097 __Pyx_RefNannyFinishContext();
18098 return __pyx_r;
18099 }
18100
18101 /* "pysam/libcvcf.pyx":484
18102 *
18103 * # todo: trim trailing missing values
18104 * def format_formatdata( self, data, format, key=True, value=True, separator=":" ): # <<<<<<<<<<<<<<
18105 * output, sdata = [], []
18106 * if type(data) == type([]): # for FORMAT field, make data with dummy values
18107 */
18108
18109 /* Python wrapper */
18110 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_13format_formatdata(PyObject *__pyx_self,
18111 #if CYTHON_METH_FASTCALL
18112 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
18113 #else
18114 PyObject *__pyx_args, PyObject *__pyx_kwds
18115 #endif
18116 ); /*proto*/
18117 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_12format_formatdata, "VCF.format_formatdata(self, data, format, key=True, value=True, separator=u':')");
18118 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_13format_formatdata = {"format_formatdata", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_13format_formatdata, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_12format_formatdata};
18119 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_13format_formatdata(PyObject *__pyx_self,
18120 #if CYTHON_METH_FASTCALL
18121 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
18122 #else
18123 PyObject *__pyx_args, PyObject *__pyx_kwds
18124 #endif
18125 ) {
18126 PyObject *__pyx_v_self = 0;
18127 PyObject *__pyx_v_data = 0;
18128 PyObject *__pyx_v_format = 0;
18129 PyObject *__pyx_v_key = 0;
18130 PyObject *__pyx_v_value = 0;
18131 PyObject *__pyx_v_separator = 0;
18132 #if !CYTHON_METH_FASTCALL
18133 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
18134 #endif
18135 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
18136 PyObject* values[6] = {0,0,0,0,0,0};
18137 int __pyx_lineno = 0;
18138 const char *__pyx_filename = NULL;
18139 int __pyx_clineno = 0;
18140 PyObject *__pyx_r = 0;
18141 __Pyx_RefNannyDeclarations
18142 __Pyx_RefNannySetupContext("format_formatdata (wrapper)", 0);
18143 #if !CYTHON_METH_FASTCALL
18144 #if CYTHON_ASSUME_SAFE_MACROS
18145 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
18146 #else
18147 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
18148 #endif
18149 #endif
18150 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
18151 {
18152 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_data,&__pyx_n_s_format,&__pyx_n_s_key,&__pyx_n_s_value,&__pyx_n_s_separator,0};
18153 values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_True)));
18154 values[4] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_True)));
18155 values[5] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject*)__pyx_kp_u__3)));
18156 if (__pyx_kwds) {
18157 Py_ssize_t kw_args;
18158 switch (__pyx_nargs) {
18159 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
18160 CYTHON_FALLTHROUGH;
18161 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
18162 CYTHON_FALLTHROUGH;
18163 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
18164 CYTHON_FALLTHROUGH;
18165 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
18166 CYTHON_FALLTHROUGH;
18167 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
18168 CYTHON_FALLTHROUGH;
18169 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
18170 CYTHON_FALLTHROUGH;
18171 case 0: break;
18172 default: goto __pyx_L5_argtuple_error;
18173 }
18174 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
18175 switch (__pyx_nargs) {
18176 case 0:
18177 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
18178 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
18179 kw_args--;
18180 }
18181 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 484, __pyx_L3_error)
18182 else goto __pyx_L5_argtuple_error;
18183 CYTHON_FALLTHROUGH;
18184 case 1:
18185 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_data)) != 0)) {
18186 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
18187 kw_args--;
18188 }
18189 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 484, __pyx_L3_error)
18190 else {
18191 __Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, 1); __PYX_ERR(0, 484, __pyx_L3_error)
18192 }
18193 CYTHON_FALLTHROUGH;
18194 case 2:
18195 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_format)) != 0)) {
18196 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
18197 kw_args--;
18198 }
18199 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 484, __pyx_L3_error)
18200 else {
18201 __Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, 2); __PYX_ERR(0, 484, __pyx_L3_error)
18202 }
18203 CYTHON_FALLTHROUGH;
18204 case 3:
18205 if (kw_args > 0) {
18206 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_key);
18207 if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
18208 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 484, __pyx_L3_error)
18209 }
18210 CYTHON_FALLTHROUGH;
18211 case 4:
18212 if (kw_args > 0) {
18213 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_value);
18214 if (value) { values[4] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
18215 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 484, __pyx_L3_error)
18216 }
18217 CYTHON_FALLTHROUGH;
18218 case 5:
18219 if (kw_args > 0) {
18220 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_separator);
18221 if (value) { values[5] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
18222 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 484, __pyx_L3_error)
18223 }
18224 }
18225 if (unlikely(kw_args > 0)) {
18226 const Py_ssize_t kwd_pos_args = __pyx_nargs;
18227 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "format_formatdata") < 0)) __PYX_ERR(0, 484, __pyx_L3_error)
18228 }
18229 } else {
18230 switch (__pyx_nargs) {
18231 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
18232 CYTHON_FALLTHROUGH;
18233 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
18234 CYTHON_FALLTHROUGH;
18235 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
18236 CYTHON_FALLTHROUGH;
18237 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
18238 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
18239 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
18240 break;
18241 default: goto __pyx_L5_argtuple_error;
18242 }
18243 }
18244 __pyx_v_self = values[0];
18245 __pyx_v_data = values[1];
18246 __pyx_v_format = values[2];
18247 __pyx_v_key = values[3];
18248 __pyx_v_value = values[4];
18249 __pyx_v_separator = values[5];
18250 }
18251 goto __pyx_L6_skip;
18252 __pyx_L5_argtuple_error:;
18253 __Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, __pyx_nargs); __PYX_ERR(0, 484, __pyx_L3_error)
18254 __pyx_L6_skip:;
18255 goto __pyx_L4_argument_unpacking_done;
18256 __pyx_L3_error:;
18257 {
18258 Py_ssize_t __pyx_temp;
18259 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
18260 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
18261 }
18262 }
18263 __Pyx_AddTraceback("pysam.libcvcf.VCF.format_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename);
18264 __Pyx_RefNannyFinishContext();
18265 return NULL;
18266 __pyx_L4_argument_unpacking_done:;
18267 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_12format_formatdata(__pyx_self, __pyx_v_self, __pyx_v_data, __pyx_v_format, __pyx_v_key, __pyx_v_value, __pyx_v_separator);
18268
18269 /* function exit code */
18270 {
18271 Py_ssize_t __pyx_temp;
18272 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
18273 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
18274 }
18275 }
18276 __Pyx_RefNannyFinishContext();
18277 return __pyx_r;
18278 }
18279
18280 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_data, PyObject *__pyx_v_format, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_separator) {
18281 PyObject *__pyx_v_output = NULL;
18282 PyObject *__pyx_v_sdata = NULL;
18283 PyObject *__pyx_v_d = NULL;
18284 PyObject *__pyx_v_k = NULL;
18285 PyObject *__pyx_v_idx = NULL;
18286 PyObject *__pyx_v_v = NULL;
18287 PyObject *__pyx_v_last = NULL;
18288 PyObject *__pyx_r = NULL;
18289 __Pyx_RefNannyDeclarations
18290 PyObject *__pyx_t_1 = NULL;
18291 PyObject *__pyx_t_2 = NULL;
18292 int __pyx_t_3;
18293 Py_ssize_t __pyx_t_4;
18294 PyObject *(*__pyx_t_5)(PyObject *);
18295 PyObject *__pyx_t_6 = NULL;
18296 PyObject *__pyx_t_7 = NULL;
18297 PyObject *__pyx_t_8 = NULL;
18298 unsigned int __pyx_t_9;
18299 Py_ssize_t __pyx_t_10;
18300 PyObject *(*__pyx_t_11)(PyObject *);
18301 int __pyx_t_12;
18302 PyObject *(*__pyx_t_13)(PyObject *);
18303 int __pyx_t_14;
18304 int __pyx_lineno = 0;
18305 const char *__pyx_filename = NULL;
18306 int __pyx_clineno = 0;
18307 __Pyx_RefNannySetupContext("format_formatdata", 0);
18308 __Pyx_INCREF(__pyx_v_data);
18309
18310 /* "pysam/libcvcf.pyx":485
18311 * # todo: trim trailing missing values
18312 * def format_formatdata( self, data, format, key=True, value=True, separator=":" ):
18313 * output, sdata = [], [] # <<<<<<<<<<<<<<
18314 * if type(data) == type([]): # for FORMAT field, make data with dummy values
18315 * d = {}
18316 */
18317 __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 485, __pyx_L1_error)
18318 __Pyx_GOTREF(__pyx_t_1);
18319 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 485, __pyx_L1_error)
18320 __Pyx_GOTREF(__pyx_t_2);
18321 __pyx_v_output = ((PyObject*)__pyx_t_1);
18322 __pyx_t_1 = 0;
18323 __pyx_v_sdata = ((PyObject*)__pyx_t_2);
18324 __pyx_t_2 = 0;
18325
18326 /* "pysam/libcvcf.pyx":486
18327 * def format_formatdata( self, data, format, key=True, value=True, separator=":" ):
18328 * output, sdata = [], []
18329 * if type(data) == type([]): # for FORMAT field, make data with dummy values # <<<<<<<<<<<<<<
18330 * d = {}
18331 * for k in data: d[k] = []
18332 */
18333 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 486, __pyx_L1_error)
18334 __Pyx_GOTREF(__pyx_t_2);
18335 __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(__pyx_t_2)), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 486, __pyx_L1_error)
18336 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
18337 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 486, __pyx_L1_error)
18338 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
18339 if (__pyx_t_3) {
18340
18341 /* "pysam/libcvcf.pyx":487
18342 * output, sdata = [], []
18343 * if type(data) == type([]): # for FORMAT field, make data with dummy values
18344 * d = {} # <<<<<<<<<<<<<<
18345 * for k in data: d[k] = []
18346 * data = d
18347 */
18348 __pyx_t_1 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 487, __pyx_L1_error)
18349 __Pyx_GOTREF(__pyx_t_1);
18350 __pyx_v_d = ((PyObject*)__pyx_t_1);
18351 __pyx_t_1 = 0;
18352
18353 /* "pysam/libcvcf.pyx":488
18354 * if type(data) == type([]): # for FORMAT field, make data with dummy values
18355 * d = {}
18356 * for k in data: d[k] = [] # <<<<<<<<<<<<<<
18357 * data = d
18358 * # convert missing values; and silently add definitions if required
18359 */
18360 if (likely(PyList_CheckExact(__pyx_v_data)) || PyTuple_CheckExact(__pyx_v_data)) {
18361 __pyx_t_1 = __pyx_v_data; __Pyx_INCREF(__pyx_t_1);
18362 __pyx_t_4 = 0;
18363 __pyx_t_5 = NULL;
18364 } else {
18365 __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_data); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 488, __pyx_L1_error)
18366 __Pyx_GOTREF(__pyx_t_1);
18367 __pyx_t_5 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 488, __pyx_L1_error)
18368 }
18369 for (;;) {
18370 if (likely(!__pyx_t_5)) {
18371 if (likely(PyList_CheckExact(__pyx_t_1))) {
18372 {
18373 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1);
18374 #if !CYTHON_ASSUME_SAFE_MACROS
18375 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 488, __pyx_L1_error)
18376 #endif
18377 if (__pyx_t_4 >= __pyx_temp) break;
18378 }
18379 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
18380 __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 488, __pyx_L1_error)
18381 #else
18382 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 488, __pyx_L1_error)
18383 __Pyx_GOTREF(__pyx_t_2);
18384 #endif
18385 } else {
18386 {
18387 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1);
18388 #if !CYTHON_ASSUME_SAFE_MACROS
18389 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 488, __pyx_L1_error)
18390 #endif
18391 if (__pyx_t_4 >= __pyx_temp) break;
18392 }
18393 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
18394 __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 488, __pyx_L1_error)
18395 #else
18396 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 488, __pyx_L1_error)
18397 __Pyx_GOTREF(__pyx_t_2);
18398 #endif
18399 }
18400 } else {
18401 __pyx_t_2 = __pyx_t_5(__pyx_t_1);
18402 if (unlikely(!__pyx_t_2)) {
18403 PyObject* exc_type = PyErr_Occurred();
18404 if (exc_type) {
18405 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
18406 else __PYX_ERR(0, 488, __pyx_L1_error)
18407 }
18408 break;
18409 }
18410 __Pyx_GOTREF(__pyx_t_2);
18411 }
18412 __Pyx_XDECREF_SET(__pyx_v_k, __pyx_t_2);
18413 __pyx_t_2 = 0;
18414 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 488, __pyx_L1_error)
18415 __Pyx_GOTREF(__pyx_t_2);
18416 if (unlikely((PyDict_SetItem(__pyx_v_d, __pyx_v_k, __pyx_t_2) < 0))) __PYX_ERR(0, 488, __pyx_L1_error)
18417 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
18418 }
18419 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
18420
18421 /* "pysam/libcvcf.pyx":489
18422 * d = {}
18423 * for k in data: d[k] = []
18424 * data = d # <<<<<<<<<<<<<<
18425 * # convert missing values; and silently add definitions if required
18426 * for k in data:
18427 */
18428 __Pyx_INCREF(__pyx_v_d);
18429 __Pyx_DECREF_SET(__pyx_v_data, __pyx_v_d);
18430
18431 /* "pysam/libcvcf.pyx":486
18432 * def format_formatdata( self, data, format, key=True, value=True, separator=":" ):
18433 * output, sdata = [], []
18434 * if type(data) == type([]): # for FORMAT field, make data with dummy values # <<<<<<<<<<<<<<
18435 * d = {}
18436 * for k in data: d[k] = []
18437 */
18438 }
18439
18440 /* "pysam/libcvcf.pyx":491
18441 * data = d
18442 * # convert missing values; and silently add definitions if required
18443 * for k in data: # <<<<<<<<<<<<<<
18444 * self._add_definition( format, k, data[k], "(output)" )
18445 * for idx,v in enumerate(data[k]):
18446 */
18447 if (likely(PyList_CheckExact(__pyx_v_data)) || PyTuple_CheckExact(__pyx_v_data)) {
18448 __pyx_t_1 = __pyx_v_data; __Pyx_INCREF(__pyx_t_1);
18449 __pyx_t_4 = 0;
18450 __pyx_t_5 = NULL;
18451 } else {
18452 __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_data); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 491, __pyx_L1_error)
18453 __Pyx_GOTREF(__pyx_t_1);
18454 __pyx_t_5 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 491, __pyx_L1_error)
18455 }
18456 for (;;) {
18457 if (likely(!__pyx_t_5)) {
18458 if (likely(PyList_CheckExact(__pyx_t_1))) {
18459 {
18460 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1);
18461 #if !CYTHON_ASSUME_SAFE_MACROS
18462 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 491, __pyx_L1_error)
18463 #endif
18464 if (__pyx_t_4 >= __pyx_temp) break;
18465 }
18466 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
18467 __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 491, __pyx_L1_error)
18468 #else
18469 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 491, __pyx_L1_error)
18470 __Pyx_GOTREF(__pyx_t_2);
18471 #endif
18472 } else {
18473 {
18474 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1);
18475 #if !CYTHON_ASSUME_SAFE_MACROS
18476 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 491, __pyx_L1_error)
18477 #endif
18478 if (__pyx_t_4 >= __pyx_temp) break;
18479 }
18480 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
18481 __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 491, __pyx_L1_error)
18482 #else
18483 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 491, __pyx_L1_error)
18484 __Pyx_GOTREF(__pyx_t_2);
18485 #endif
18486 }
18487 } else {
18488 __pyx_t_2 = __pyx_t_5(__pyx_t_1);
18489 if (unlikely(!__pyx_t_2)) {
18490 PyObject* exc_type = PyErr_Occurred();
18491 if (exc_type) {
18492 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
18493 else __PYX_ERR(0, 491, __pyx_L1_error)
18494 }
18495 break;
18496 }
18497 __Pyx_GOTREF(__pyx_t_2);
18498 }
18499 __Pyx_XDECREF_SET(__pyx_v_k, __pyx_t_2);
18500 __pyx_t_2 = 0;
18501
18502 /* "pysam/libcvcf.pyx":492
18503 * # convert missing values; and silently add definitions if required
18504 * for k in data:
18505 * self._add_definition( format, k, data[k], "(output)" ) # <<<<<<<<<<<<<<
18506 * for idx,v in enumerate(data[k]):
18507 * if v == format[k].missingvalue: data[k][idx] = "."
18508 */
18509 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_add_definition); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 492, __pyx_L1_error)
18510 __Pyx_GOTREF(__pyx_t_6);
18511 __pyx_t_7 = __Pyx_PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 492, __pyx_L1_error)
18512 __Pyx_GOTREF(__pyx_t_7);
18513 __pyx_t_8 = NULL;
18514 __pyx_t_9 = 0;
18515 #if CYTHON_UNPACK_METHODS
18516 if (likely(PyMethod_Check(__pyx_t_6))) {
18517 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_6);
18518 if (likely(__pyx_t_8)) {
18519 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
18520 __Pyx_INCREF(__pyx_t_8);
18521 __Pyx_INCREF(function);
18522 __Pyx_DECREF_SET(__pyx_t_6, function);
18523 __pyx_t_9 = 1;
18524 }
18525 }
18526 #endif
18527 {
18528 PyObject *__pyx_callargs[5] = {__pyx_t_8, __pyx_v_format, __pyx_v_k, __pyx_t_7, __pyx_kp_u_output};
18529 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_9, 4+__pyx_t_9);
18530 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
18531 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
18532 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 492, __pyx_L1_error)
18533 __Pyx_GOTREF(__pyx_t_2);
18534 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
18535 }
18536 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
18537
18538 /* "pysam/libcvcf.pyx":493
18539 * for k in data:
18540 * self._add_definition( format, k, data[k], "(output)" )
18541 * for idx,v in enumerate(data[k]): # <<<<<<<<<<<<<<
18542 * if v == format[k].missingvalue: data[k][idx] = "."
18543 * # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
18544 */
18545 __Pyx_INCREF(__pyx_int_0);
18546 __pyx_t_2 = __pyx_int_0;
18547 __pyx_t_6 = __Pyx_PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 493, __pyx_L1_error)
18548 __Pyx_GOTREF(__pyx_t_6);
18549 if (likely(PyList_CheckExact(__pyx_t_6)) || PyTuple_CheckExact(__pyx_t_6)) {
18550 __pyx_t_7 = __pyx_t_6; __Pyx_INCREF(__pyx_t_7);
18551 __pyx_t_10 = 0;
18552 __pyx_t_11 = NULL;
18553 } else {
18554 __pyx_t_10 = -1; __pyx_t_7 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 493, __pyx_L1_error)
18555 __Pyx_GOTREF(__pyx_t_7);
18556 __pyx_t_11 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_7); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 493, __pyx_L1_error)
18557 }
18558 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
18559 for (;;) {
18560 if (likely(!__pyx_t_11)) {
18561 if (likely(PyList_CheckExact(__pyx_t_7))) {
18562 {
18563 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_7);
18564 #if !CYTHON_ASSUME_SAFE_MACROS
18565 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 493, __pyx_L1_error)
18566 #endif
18567 if (__pyx_t_10 >= __pyx_temp) break;
18568 }
18569 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
18570 __pyx_t_6 = PyList_GET_ITEM(__pyx_t_7, __pyx_t_10); __Pyx_INCREF(__pyx_t_6); __pyx_t_10++; if (unlikely((0 < 0))) __PYX_ERR(0, 493, __pyx_L1_error)
18571 #else
18572 __pyx_t_6 = __Pyx_PySequence_ITEM(__pyx_t_7, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 493, __pyx_L1_error)
18573 __Pyx_GOTREF(__pyx_t_6);
18574 #endif
18575 } else {
18576 {
18577 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_7);
18578 #if !CYTHON_ASSUME_SAFE_MACROS
18579 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 493, __pyx_L1_error)
18580 #endif
18581 if (__pyx_t_10 >= __pyx_temp) break;
18582 }
18583 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
18584 __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_7, __pyx_t_10); __Pyx_INCREF(__pyx_t_6); __pyx_t_10++; if (unlikely((0 < 0))) __PYX_ERR(0, 493, __pyx_L1_error)
18585 #else
18586 __pyx_t_6 = __Pyx_PySequence_ITEM(__pyx_t_7, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 493, __pyx_L1_error)
18587 __Pyx_GOTREF(__pyx_t_6);
18588 #endif
18589 }
18590 } else {
18591 __pyx_t_6 = __pyx_t_11(__pyx_t_7);
18592 if (unlikely(!__pyx_t_6)) {
18593 PyObject* exc_type = PyErr_Occurred();
18594 if (exc_type) {
18595 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
18596 else __PYX_ERR(0, 493, __pyx_L1_error)
18597 }
18598 break;
18599 }
18600 __Pyx_GOTREF(__pyx_t_6);
18601 }
18602 __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_6);
18603 __pyx_t_6 = 0;
18604 __Pyx_INCREF(__pyx_t_2);
18605 __Pyx_XDECREF_SET(__pyx_v_idx, __pyx_t_2);
18606 __pyx_t_6 = __Pyx_PyInt_AddObjC(__pyx_t_2, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 493, __pyx_L1_error)
18607 __Pyx_GOTREF(__pyx_t_6);
18608 __Pyx_DECREF(__pyx_t_2);
18609 __pyx_t_2 = __pyx_t_6;
18610 __pyx_t_6 = 0;
18611
18612 /* "pysam/libcvcf.pyx":494
18613 * self._add_definition( format, k, data[k], "(output)" )
18614 * for idx,v in enumerate(data[k]):
18615 * if v == format[k].missingvalue: data[k][idx] = "." # <<<<<<<<<<<<<<
18616 * # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
18617 * for k in data:
18618 */
18619 __pyx_t_6 = __Pyx_PyObject_GetItem(__pyx_v_format, __pyx_v_k); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 494, __pyx_L1_error)
18620 __Pyx_GOTREF(__pyx_t_6);
18621 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_missingvalue); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 494, __pyx_L1_error)
18622 __Pyx_GOTREF(__pyx_t_8);
18623 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
18624 __pyx_t_6 = PyObject_RichCompare(__pyx_v_v, __pyx_t_8, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 494, __pyx_L1_error)
18625 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
18626 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 494, __pyx_L1_error)
18627 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
18628 if (__pyx_t_3) {
18629 __pyx_t_6 = __Pyx_PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 494, __pyx_L1_error)
18630 __Pyx_GOTREF(__pyx_t_6);
18631 if (unlikely((PyObject_SetItem(__pyx_t_6, __pyx_v_idx, __pyx_kp_u__5) < 0))) __PYX_ERR(0, 494, __pyx_L1_error)
18632 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
18633 }
18634
18635 /* "pysam/libcvcf.pyx":493
18636 * for k in data:
18637 * self._add_definition( format, k, data[k], "(output)" )
18638 * for idx,v in enumerate(data[k]): # <<<<<<<<<<<<<<
18639 * if v == format[k].missingvalue: data[k][idx] = "."
18640 * # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
18641 */
18642 }
18643 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
18644 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
18645
18646 /* "pysam/libcvcf.pyx":491
18647 * data = d
18648 * # convert missing values; and silently add definitions if required
18649 * for k in data: # <<<<<<<<<<<<<<
18650 * self._add_definition( format, k, data[k], "(output)" )
18651 * for idx,v in enumerate(data[k]):
18652 */
18653 }
18654 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
18655
18656 /* "pysam/libcvcf.pyx":496
18657 * if v == format[k].missingvalue: data[k][idx] = "."
18658 * # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
18659 * for k in data: # <<<<<<<<<<<<<<
18660 * if k != 'GT': sdata.append( (k,data[k]) )
18661 * sdata.sort()
18662 */
18663 if (likely(PyList_CheckExact(__pyx_v_data)) || PyTuple_CheckExact(__pyx_v_data)) {
18664 __pyx_t_1 = __pyx_v_data; __Pyx_INCREF(__pyx_t_1);
18665 __pyx_t_4 = 0;
18666 __pyx_t_5 = NULL;
18667 } else {
18668 __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_data); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 496, __pyx_L1_error)
18669 __Pyx_GOTREF(__pyx_t_1);
18670 __pyx_t_5 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 496, __pyx_L1_error)
18671 }
18672 for (;;) {
18673 if (likely(!__pyx_t_5)) {
18674 if (likely(PyList_CheckExact(__pyx_t_1))) {
18675 {
18676 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1);
18677 #if !CYTHON_ASSUME_SAFE_MACROS
18678 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 496, __pyx_L1_error)
18679 #endif
18680 if (__pyx_t_4 >= __pyx_temp) break;
18681 }
18682 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
18683 __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 496, __pyx_L1_error)
18684 #else
18685 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 496, __pyx_L1_error)
18686 __Pyx_GOTREF(__pyx_t_2);
18687 #endif
18688 } else {
18689 {
18690 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1);
18691 #if !CYTHON_ASSUME_SAFE_MACROS
18692 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 496, __pyx_L1_error)
18693 #endif
18694 if (__pyx_t_4 >= __pyx_temp) break;
18695 }
18696 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
18697 __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 496, __pyx_L1_error)
18698 #else
18699 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 496, __pyx_L1_error)
18700 __Pyx_GOTREF(__pyx_t_2);
18701 #endif
18702 }
18703 } else {
18704 __pyx_t_2 = __pyx_t_5(__pyx_t_1);
18705 if (unlikely(!__pyx_t_2)) {
18706 PyObject* exc_type = PyErr_Occurred();
18707 if (exc_type) {
18708 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
18709 else __PYX_ERR(0, 496, __pyx_L1_error)
18710 }
18711 break;
18712 }
18713 __Pyx_GOTREF(__pyx_t_2);
18714 }
18715 __Pyx_XDECREF_SET(__pyx_v_k, __pyx_t_2);
18716 __pyx_t_2 = 0;
18717
18718 /* "pysam/libcvcf.pyx":497
18719 * # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
18720 * for k in data:
18721 * if k != 'GT': sdata.append( (k,data[k]) ) # <<<<<<<<<<<<<<
18722 * sdata.sort()
18723 * if 'GT' in data:
18724 */
18725 __pyx_t_3 = (__Pyx_PyUnicode_Equals(__pyx_v_k, __pyx_n_u_GT, Py_NE)); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 497, __pyx_L1_error)
18726 if (__pyx_t_3) {
18727 __pyx_t_2 = __Pyx_PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 497, __pyx_L1_error)
18728 __Pyx_GOTREF(__pyx_t_2);
18729 __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 497, __pyx_L1_error)
18730 __Pyx_GOTREF(__pyx_t_7);
18731 __Pyx_INCREF(__pyx_v_k);
18732 __Pyx_GIVEREF(__pyx_v_k);
18733 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_k)) __PYX_ERR(0, 497, __pyx_L1_error);
18734 __Pyx_GIVEREF(__pyx_t_2);
18735 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_2)) __PYX_ERR(0, 497, __pyx_L1_error);
18736 __pyx_t_2 = 0;
18737 __pyx_t_12 = __Pyx_PyList_Append(__pyx_v_sdata, __pyx_t_7); if (unlikely(__pyx_t_12 == ((int)-1))) __PYX_ERR(0, 497, __pyx_L1_error)
18738 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
18739 }
18740
18741 /* "pysam/libcvcf.pyx":496
18742 * if v == format[k].missingvalue: data[k][idx] = "."
18743 * # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
18744 * for k in data: # <<<<<<<<<<<<<<
18745 * if k != 'GT': sdata.append( (k,data[k]) )
18746 * sdata.sort()
18747 */
18748 }
18749 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
18750
18751 /* "pysam/libcvcf.pyx":498
18752 * for k in data:
18753 * if k != 'GT': sdata.append( (k,data[k]) )
18754 * sdata.sort() # <<<<<<<<<<<<<<
18755 * if 'GT' in data:
18756 * sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
18757 */
18758 __pyx_t_12 = PyList_Sort(__pyx_v_sdata); if (unlikely(__pyx_t_12 == ((int)-1))) __PYX_ERR(0, 498, __pyx_L1_error)
18759
18760 /* "pysam/libcvcf.pyx":499
18761 * if k != 'GT': sdata.append( (k,data[k]) )
18762 * sdata.sort()
18763 * if 'GT' in data: # <<<<<<<<<<<<<<
18764 * sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
18765 * for k,v in sdata:
18766 */
18767 __pyx_t_3 = (__Pyx_PySequence_ContainsTF(__pyx_n_u_GT, __pyx_v_data, Py_EQ)); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 499, __pyx_L1_error)
18768 if (__pyx_t_3) {
18769
18770 /* "pysam/libcvcf.pyx":500
18771 * sdata.sort()
18772 * if 'GT' in data:
18773 * sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata # <<<<<<<<<<<<<<
18774 * for k,v in sdata:
18775 * if v == []: v = None
18776 */
18777 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_convertGTback); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 500, __pyx_L1_error)
18778 __Pyx_GOTREF(__pyx_t_1);
18779 __pyx_t_7 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_GT); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 500, __pyx_L1_error)
18780 __Pyx_GOTREF(__pyx_t_7);
18781 __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 500, __pyx_L1_error)
18782 __Pyx_GOTREF(__pyx_t_2);
18783 __Pyx_GIVEREF(__pyx_t_1);
18784 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1)) __PYX_ERR(0, 500, __pyx_L1_error);
18785 __Pyx_GIVEREF(__pyx_t_7);
18786 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_7)) __PYX_ERR(0, 500, __pyx_L1_error);
18787 __pyx_t_1 = 0;
18788 __pyx_t_7 = 0;
18789 __pyx_t_7 = __Pyx_PyObject_Call(__pyx_builtin_map, __pyx_t_2, NULL); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 500, __pyx_L1_error)
18790 __Pyx_GOTREF(__pyx_t_7);
18791 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
18792 __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 500, __pyx_L1_error)
18793 __Pyx_GOTREF(__pyx_t_2);
18794 __Pyx_INCREF(__pyx_n_u_GT);
18795 __Pyx_GIVEREF(__pyx_n_u_GT);
18796 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_n_u_GT)) __PYX_ERR(0, 500, __pyx_L1_error);
18797 __Pyx_GIVEREF(__pyx_t_7);
18798 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_7)) __PYX_ERR(0, 500, __pyx_L1_error);
18799 __pyx_t_7 = 0;
18800 __pyx_t_7 = PyList_New(1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 500, __pyx_L1_error)
18801 __Pyx_GOTREF(__pyx_t_7);
18802 __Pyx_GIVEREF(__pyx_t_2);
18803 if (__Pyx_PyList_SET_ITEM(__pyx_t_7, 0, __pyx_t_2)) __PYX_ERR(0, 500, __pyx_L1_error);
18804 __pyx_t_2 = 0;
18805 __pyx_t_2 = PyNumber_Add(__pyx_t_7, __pyx_v_sdata); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 500, __pyx_L1_error)
18806 __Pyx_GOTREF(__pyx_t_2);
18807 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
18808 __Pyx_DECREF_SET(__pyx_v_sdata, ((PyObject*)__pyx_t_2));
18809 __pyx_t_2 = 0;
18810
18811 /* "pysam/libcvcf.pyx":499
18812 * if k != 'GT': sdata.append( (k,data[k]) )
18813 * sdata.sort()
18814 * if 'GT' in data: # <<<<<<<<<<<<<<
18815 * sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
18816 * for k,v in sdata:
18817 */
18818 }
18819
18820 /* "pysam/libcvcf.pyx":501
18821 * if 'GT' in data:
18822 * sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
18823 * for k,v in sdata: # <<<<<<<<<<<<<<
18824 * if v == []: v = None
18825 * if key and value:
18826 */
18827 __pyx_t_2 = __pyx_v_sdata; __Pyx_INCREF(__pyx_t_2);
18828 __pyx_t_4 = 0;
18829 for (;;) {
18830 {
18831 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2);
18832 #if !CYTHON_ASSUME_SAFE_MACROS
18833 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 501, __pyx_L1_error)
18834 #endif
18835 if (__pyx_t_4 >= __pyx_temp) break;
18836 }
18837 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
18838 __pyx_t_7 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 501, __pyx_L1_error)
18839 #else
18840 __pyx_t_7 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 501, __pyx_L1_error)
18841 __Pyx_GOTREF(__pyx_t_7);
18842 #endif
18843 if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
18844 PyObject* sequence = __pyx_t_7;
18845 Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
18846 if (unlikely(size != 2)) {
18847 if (size > 2) __Pyx_RaiseTooManyValuesError(2);
18848 else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
18849 __PYX_ERR(0, 501, __pyx_L1_error)
18850 }
18851 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
18852 if (likely(PyTuple_CheckExact(sequence))) {
18853 __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
18854 __pyx_t_6 = PyTuple_GET_ITEM(sequence, 1);
18855 } else {
18856 __pyx_t_1 = PyList_GET_ITEM(sequence, 0);
18857 __pyx_t_6 = PyList_GET_ITEM(sequence, 1);
18858 }
18859 __Pyx_INCREF(__pyx_t_1);
18860 __Pyx_INCREF(__pyx_t_6);
18861 #else
18862 __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 501, __pyx_L1_error)
18863 __Pyx_GOTREF(__pyx_t_1);
18864 __pyx_t_6 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 501, __pyx_L1_error)
18865 __Pyx_GOTREF(__pyx_t_6);
18866 #endif
18867 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
18868 } else {
18869 Py_ssize_t index = -1;
18870 __pyx_t_8 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 501, __pyx_L1_error)
18871 __Pyx_GOTREF(__pyx_t_8);
18872 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
18873 __pyx_t_13 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_8);
18874 index = 0; __pyx_t_1 = __pyx_t_13(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L21_unpacking_failed;
18875 __Pyx_GOTREF(__pyx_t_1);
18876 index = 1; __pyx_t_6 = __pyx_t_13(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L21_unpacking_failed;
18877 __Pyx_GOTREF(__pyx_t_6);
18878 if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_8), 2) < 0) __PYX_ERR(0, 501, __pyx_L1_error)
18879 __pyx_t_13 = NULL;
18880 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
18881 goto __pyx_L22_unpacking_done;
18882 __pyx_L21_unpacking_failed:;
18883 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
18884 __pyx_t_13 = NULL;
18885 if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
18886 __PYX_ERR(0, 501, __pyx_L1_error)
18887 __pyx_L22_unpacking_done:;
18888 }
18889 __Pyx_XDECREF_SET(__pyx_v_k, __pyx_t_1);
18890 __pyx_t_1 = 0;
18891 __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_6);
18892 __pyx_t_6 = 0;
18893
18894 /* "pysam/libcvcf.pyx":502
18895 * sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
18896 * for k,v in sdata:
18897 * if v == []: v = None # <<<<<<<<<<<<<<
18898 * if key and value:
18899 * if v != None: output.append( k+"="+','.join(map(str,v)) )
18900 */
18901 __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 502, __pyx_L1_error)
18902 __Pyx_GOTREF(__pyx_t_7);
18903 __pyx_t_6 = PyObject_RichCompare(__pyx_v_v, __pyx_t_7, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 502, __pyx_L1_error)
18904 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
18905 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 502, __pyx_L1_error)
18906 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
18907 if (__pyx_t_3) {
18908 __Pyx_INCREF(Py_None);
18909 __Pyx_DECREF_SET(__pyx_v_v, Py_None);
18910 }
18911
18912 /* "pysam/libcvcf.pyx":503
18913 * for k,v in sdata:
18914 * if v == []: v = None
18915 * if key and value: # <<<<<<<<<<<<<<
18916 * if v != None: output.append( k+"="+','.join(map(str,v)) )
18917 * else: output.append( k )
18918 */
18919 __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_key); if (unlikely((__pyx_t_14 < 0))) __PYX_ERR(0, 503, __pyx_L1_error)
18920 if (__pyx_t_14) {
18921 } else {
18922 __pyx_t_3 = __pyx_t_14;
18923 goto __pyx_L25_bool_binop_done;
18924 }
18925 __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_value); if (unlikely((__pyx_t_14 < 0))) __PYX_ERR(0, 503, __pyx_L1_error)
18926 __pyx_t_3 = __pyx_t_14;
18927 __pyx_L25_bool_binop_done:;
18928 if (__pyx_t_3) {
18929
18930 /* "pysam/libcvcf.pyx":504
18931 * if v == []: v = None
18932 * if key and value:
18933 * if v != None: output.append( k+"="+','.join(map(str,v)) ) # <<<<<<<<<<<<<<
18934 * else: output.append( k )
18935 * elif key: output.append(k)
18936 */
18937 __pyx_t_6 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 504, __pyx_L1_error)
18938 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 504, __pyx_L1_error)
18939 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
18940 if (__pyx_t_3) {
18941 __pyx_t_6 = PyNumber_Add(__pyx_v_k, __pyx_kp_u__7); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 504, __pyx_L1_error)
18942 __Pyx_GOTREF(__pyx_t_6);
18943 __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 504, __pyx_L1_error)
18944 __Pyx_GOTREF(__pyx_t_7);
18945 __Pyx_INCREF((PyObject *)(&PyUnicode_Type));
18946 __Pyx_GIVEREF((PyObject *)(&PyUnicode_Type));
18947 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)(&PyUnicode_Type)))) __PYX_ERR(0, 504, __pyx_L1_error);
18948 __Pyx_INCREF(__pyx_v_v);
18949 __Pyx_GIVEREF(__pyx_v_v);
18950 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_v_v)) __PYX_ERR(0, 504, __pyx_L1_error);
18951 __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_map, __pyx_t_7, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 504, __pyx_L1_error)
18952 __Pyx_GOTREF(__pyx_t_1);
18953 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
18954 __pyx_t_7 = PyUnicode_Join(__pyx_kp_u__2, __pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 504, __pyx_L1_error)
18955 __Pyx_GOTREF(__pyx_t_7);
18956 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
18957 __pyx_t_1 = PyNumber_Add(__pyx_t_6, __pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 504, __pyx_L1_error)
18958 __Pyx_GOTREF(__pyx_t_1);
18959 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
18960 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
18961 __pyx_t_12 = __Pyx_PyList_Append(__pyx_v_output, __pyx_t_1); if (unlikely(__pyx_t_12 == ((int)-1))) __PYX_ERR(0, 504, __pyx_L1_error)
18962 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
18963 goto __pyx_L27;
18964 }
18965
18966 /* "pysam/libcvcf.pyx":505
18967 * if key and value:
18968 * if v != None: output.append( k+"="+','.join(map(str,v)) )
18969 * else: output.append( k ) # <<<<<<<<<<<<<<
18970 * elif key: output.append(k)
18971 * elif value:
18972 */
18973 /*else*/ {
18974 __pyx_t_12 = __Pyx_PyList_Append(__pyx_v_output, __pyx_v_k); if (unlikely(__pyx_t_12 == ((int)-1))) __PYX_ERR(0, 505, __pyx_L1_error)
18975 }
18976 __pyx_L27:;
18977
18978 /* "pysam/libcvcf.pyx":503
18979 * for k,v in sdata:
18980 * if v == []: v = None
18981 * if key and value: # <<<<<<<<<<<<<<
18982 * if v != None: output.append( k+"="+','.join(map(str,v)) )
18983 * else: output.append( k )
18984 */
18985 goto __pyx_L24;
18986 }
18987
18988 /* "pysam/libcvcf.pyx":506
18989 * if v != None: output.append( k+"="+','.join(map(str,v)) )
18990 * else: output.append( k )
18991 * elif key: output.append(k) # <<<<<<<<<<<<<<
18992 * elif value:
18993 * if v != None: output.append( ','.join(map(str,v)) )
18994 */
18995 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_key); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 506, __pyx_L1_error)
18996 if (__pyx_t_3) {
18997 __pyx_t_12 = __Pyx_PyList_Append(__pyx_v_output, __pyx_v_k); if (unlikely(__pyx_t_12 == ((int)-1))) __PYX_ERR(0, 506, __pyx_L1_error)
18998 goto __pyx_L24;
18999 }
19000
19001 /* "pysam/libcvcf.pyx":507
19002 * else: output.append( k )
19003 * elif key: output.append(k)
19004 * elif value: # <<<<<<<<<<<<<<
19005 * if v != None: output.append( ','.join(map(str,v)) )
19006 * else: output.append( "." ) # should not happen
19007 */
19008 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_value); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 507, __pyx_L1_error)
19009 if (__pyx_t_3) {
19010
19011 /* "pysam/libcvcf.pyx":508
19012 * elif key: output.append(k)
19013 * elif value:
19014 * if v != None: output.append( ','.join(map(str,v)) ) # <<<<<<<<<<<<<<
19015 * else: output.append( "." ) # should not happen
19016 * # snip off trailing missing data
19017 */
19018 __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 508, __pyx_L1_error)
19019 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 508, __pyx_L1_error)
19020 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
19021 if (__pyx_t_3) {
19022 __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 508, __pyx_L1_error)
19023 __Pyx_GOTREF(__pyx_t_1);
19024 __Pyx_INCREF((PyObject *)(&PyUnicode_Type));
19025 __Pyx_GIVEREF((PyObject *)(&PyUnicode_Type));
19026 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)(&PyUnicode_Type)))) __PYX_ERR(0, 508, __pyx_L1_error);
19027 __Pyx_INCREF(__pyx_v_v);
19028 __Pyx_GIVEREF(__pyx_v_v);
19029 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_v)) __PYX_ERR(0, 508, __pyx_L1_error);
19030 __pyx_t_7 = __Pyx_PyObject_Call(__pyx_builtin_map, __pyx_t_1, NULL); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 508, __pyx_L1_error)
19031 __Pyx_GOTREF(__pyx_t_7);
19032 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
19033 __pyx_t_1 = PyUnicode_Join(__pyx_kp_u__2, __pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 508, __pyx_L1_error)
19034 __Pyx_GOTREF(__pyx_t_1);
19035 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
19036 __pyx_t_12 = __Pyx_PyList_Append(__pyx_v_output, __pyx_t_1); if (unlikely(__pyx_t_12 == ((int)-1))) __PYX_ERR(0, 508, __pyx_L1_error)
19037 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
19038 goto __pyx_L28;
19039 }
19040
19041 /* "pysam/libcvcf.pyx":509
19042 * elif value:
19043 * if v != None: output.append( ','.join(map(str,v)) )
19044 * else: output.append( "." ) # should not happen # <<<<<<<<<<<<<<
19045 * # snip off trailing missing data
19046 * while len(output) > 1:
19047 */
19048 /*else*/ {
19049 __pyx_t_12 = __Pyx_PyList_Append(__pyx_v_output, __pyx_kp_u__5); if (unlikely(__pyx_t_12 == ((int)-1))) __PYX_ERR(0, 509, __pyx_L1_error)
19050 }
19051 __pyx_L28:;
19052
19053 /* "pysam/libcvcf.pyx":507
19054 * else: output.append( k )
19055 * elif key: output.append(k)
19056 * elif value: # <<<<<<<<<<<<<<
19057 * if v != None: output.append( ','.join(map(str,v)) )
19058 * else: output.append( "." ) # should not happen
19059 */
19060 }
19061 __pyx_L24:;
19062
19063 /* "pysam/libcvcf.pyx":501
19064 * if 'GT' in data:
19065 * sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
19066 * for k,v in sdata: # <<<<<<<<<<<<<<
19067 * if v == []: v = None
19068 * if key and value:
19069 */
19070 }
19071 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
19072
19073 /* "pysam/libcvcf.pyx":511
19074 * else: output.append( "." ) # should not happen
19075 * # snip off trailing missing data
19076 * while len(output) > 1: # <<<<<<<<<<<<<<
19077 * last = output[-1].replace(',','').replace('.','')
19078 * if len(last)>0: break
19079 */
19080 while (1) {
19081 __pyx_t_4 = __Pyx_PyList_GET_SIZE(__pyx_v_output); if (unlikely(__pyx_t_4 == ((Py_ssize_t)-1))) __PYX_ERR(0, 511, __pyx_L1_error)
19082 __pyx_t_3 = (__pyx_t_4 > 1);
19083 if (!__pyx_t_3) break;
19084
19085 /* "pysam/libcvcf.pyx":512
19086 * # snip off trailing missing data
19087 * while len(output) > 1:
19088 * last = output[-1].replace(',','').replace('.','') # <<<<<<<<<<<<<<
19089 * if len(last)>0: break
19090 * output = output[:-1]
19091 */
19092 __pyx_t_2 = __Pyx_GetItemInt_List(__pyx_v_output, -1L, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 512, __pyx_L1_error)
19093 __Pyx_GOTREF(__pyx_t_2);
19094 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_replace); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 512, __pyx_L1_error)
19095 __Pyx_GOTREF(__pyx_t_1);
19096 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
19097 __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_tuple__21, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 512, __pyx_L1_error)
19098 __Pyx_GOTREF(__pyx_t_2);
19099 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
19100 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_replace); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 512, __pyx_L1_error)
19101 __Pyx_GOTREF(__pyx_t_1);
19102 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
19103 __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_tuple__22, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 512, __pyx_L1_error)
19104 __Pyx_GOTREF(__pyx_t_2);
19105 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
19106 __Pyx_XDECREF_SET(__pyx_v_last, __pyx_t_2);
19107 __pyx_t_2 = 0;
19108
19109 /* "pysam/libcvcf.pyx":513
19110 * while len(output) > 1:
19111 * last = output[-1].replace(',','').replace('.','')
19112 * if len(last)>0: break # <<<<<<<<<<<<<<
19113 * output = output[:-1]
19114 * return separator.join(output)
19115 */
19116 __pyx_t_4 = PyObject_Length(__pyx_v_last); if (unlikely(__pyx_t_4 == ((Py_ssize_t)-1))) __PYX_ERR(0, 513, __pyx_L1_error)
19117 __pyx_t_3 = (__pyx_t_4 > 0);
19118 if (__pyx_t_3) {
19119 goto __pyx_L31_break;
19120 }
19121
19122 /* "pysam/libcvcf.pyx":514
19123 * last = output[-1].replace(',','').replace('.','')
19124 * if len(last)>0: break
19125 * output = output[:-1] # <<<<<<<<<<<<<<
19126 * return separator.join(output)
19127 *
19128 */
19129 __pyx_t_2 = __Pyx_PyList_GetSlice(__pyx_v_output, 0, -1L); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 514, __pyx_L1_error)
19130 __Pyx_GOTREF(__pyx_t_2);
19131 __Pyx_DECREF_SET(__pyx_v_output, ((PyObject*)__pyx_t_2));
19132 __pyx_t_2 = 0;
19133 }
19134 __pyx_L31_break:;
19135
19136 /* "pysam/libcvcf.pyx":515
19137 * if len(last)>0: break
19138 * output = output[:-1]
19139 * return separator.join(output) # <<<<<<<<<<<<<<
19140 *
19141 *
19142 */
19143 __Pyx_XDECREF(__pyx_r);
19144 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_separator, __pyx_n_s_join); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 515, __pyx_L1_error)
19145 __Pyx_GOTREF(__pyx_t_1);
19146 __pyx_t_7 = NULL;
19147 __pyx_t_9 = 0;
19148 #if CYTHON_UNPACK_METHODS
19149 if (likely(PyMethod_Check(__pyx_t_1))) {
19150 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_1);
19151 if (likely(__pyx_t_7)) {
19152 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
19153 __Pyx_INCREF(__pyx_t_7);
19154 __Pyx_INCREF(function);
19155 __Pyx_DECREF_SET(__pyx_t_1, function);
19156 __pyx_t_9 = 1;
19157 }
19158 }
19159 #endif
19160 {
19161 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_v_output};
19162 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_9, 1+__pyx_t_9);
19163 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
19164 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 515, __pyx_L1_error)
19165 __Pyx_GOTREF(__pyx_t_2);
19166 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
19167 }
19168 __pyx_r = __pyx_t_2;
19169 __pyx_t_2 = 0;
19170 goto __pyx_L0;
19171
19172 /* "pysam/libcvcf.pyx":484
19173 *
19174 * # todo: trim trailing missing values
19175 * def format_formatdata( self, data, format, key=True, value=True, separator=":" ): # <<<<<<<<<<<<<<
19176 * output, sdata = [], []
19177 * if type(data) == type([]): # for FORMAT field, make data with dummy values
19178 */
19179
19180 /* function exit code */
19181 __pyx_L1_error:;
19182 __Pyx_XDECREF(__pyx_t_1);
19183 __Pyx_XDECREF(__pyx_t_2);
19184 __Pyx_XDECREF(__pyx_t_6);
19185 __Pyx_XDECREF(__pyx_t_7);
19186 __Pyx_XDECREF(__pyx_t_8);
19187 __Pyx_AddTraceback("pysam.libcvcf.VCF.format_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename);
19188 __pyx_r = NULL;
19189 __pyx_L0:;
19190 __Pyx_XDECREF(__pyx_v_output);
19191 __Pyx_XDECREF(__pyx_v_sdata);
19192 __Pyx_XDECREF(__pyx_v_d);
19193 __Pyx_XDECREF(__pyx_v_k);
19194 __Pyx_XDECREF(__pyx_v_idx);
19195 __Pyx_XDECREF(__pyx_v_v);
19196 __Pyx_XDECREF(__pyx_v_last);
19197 __Pyx_XDECREF(__pyx_v_data);
19198 __Pyx_XGIVEREF(__pyx_r);
19199 __Pyx_RefNannyFinishContext();
19200 return __pyx_r;
19201 }
19202
19203 /* "pysam/libcvcf.pyx":518
19204 *
19205 *
19206 * def enter_default_format(self): # <<<<<<<<<<<<<<
19207 * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
19208 * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
19209 */
19210
19211 /* Python wrapper */
19212 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_15enter_default_format(PyObject *__pyx_self,
19213 #if CYTHON_METH_FASTCALL
19214 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
19215 #else
19216 PyObject *__pyx_args, PyObject *__pyx_kwds
19217 #endif
19218 ); /*proto*/
19219 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_14enter_default_format, "VCF.enter_default_format(self)");
19220 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_15enter_default_format = {"enter_default_format", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_15enter_default_format, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_14enter_default_format};
19221 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_15enter_default_format(PyObject *__pyx_self,
19222 #if CYTHON_METH_FASTCALL
19223 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
19224 #else
19225 PyObject *__pyx_args, PyObject *__pyx_kwds
19226 #endif
19227 ) {
19228 PyObject *__pyx_v_self = 0;
19229 #if !CYTHON_METH_FASTCALL
19230 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
19231 #endif
19232 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
19233 PyObject* values[1] = {0};
19234 int __pyx_lineno = 0;
19235 const char *__pyx_filename = NULL;
19236 int __pyx_clineno = 0;
19237 PyObject *__pyx_r = 0;
19238 __Pyx_RefNannyDeclarations
19239 __Pyx_RefNannySetupContext("enter_default_format (wrapper)", 0);
19240 #if !CYTHON_METH_FASTCALL
19241 #if CYTHON_ASSUME_SAFE_MACROS
19242 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
19243 #else
19244 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
19245 #endif
19246 #endif
19247 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
19248 {
19249 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0};
19250 if (__pyx_kwds) {
19251 Py_ssize_t kw_args;
19252 switch (__pyx_nargs) {
19253 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
19254 CYTHON_FALLTHROUGH;
19255 case 0: break;
19256 default: goto __pyx_L5_argtuple_error;
19257 }
19258 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
19259 switch (__pyx_nargs) {
19260 case 0:
19261 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
19262 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
19263 kw_args--;
19264 }
19265 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 518, __pyx_L3_error)
19266 else goto __pyx_L5_argtuple_error;
19267 }
19268 if (unlikely(kw_args > 0)) {
19269 const Py_ssize_t kwd_pos_args = __pyx_nargs;
19270 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "enter_default_format") < 0)) __PYX_ERR(0, 518, __pyx_L3_error)
19271 }
19272 } else if (unlikely(__pyx_nargs != 1)) {
19273 goto __pyx_L5_argtuple_error;
19274 } else {
19275 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
19276 }
19277 __pyx_v_self = values[0];
19278 }
19279 goto __pyx_L6_skip;
19280 __pyx_L5_argtuple_error:;
19281 __Pyx_RaiseArgtupleInvalid("enter_default_format", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 518, __pyx_L3_error)
19282 __pyx_L6_skip:;
19283 goto __pyx_L4_argument_unpacking_done;
19284 __pyx_L3_error:;
19285 {
19286 Py_ssize_t __pyx_temp;
19287 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
19288 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
19289 }
19290 }
19291 __Pyx_AddTraceback("pysam.libcvcf.VCF.enter_default_format", __pyx_clineno, __pyx_lineno, __pyx_filename);
19292 __Pyx_RefNannyFinishContext();
19293 return NULL;
19294 __pyx_L4_argument_unpacking_done:;
19295 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_14enter_default_format(__pyx_self, __pyx_v_self);
19296
19297 /* function exit code */
19298 {
19299 Py_ssize_t __pyx_temp;
19300 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
19301 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
19302 }
19303 }
19304 __Pyx_RefNannyFinishContext();
19305 return __pyx_r;
19306 }
19307
19308 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
19309 PyObject *__pyx_v_f = NULL;
19310 PyObject *__pyx_r = NULL;
19311 __Pyx_RefNannyDeclarations
19312 PyObject *__pyx_t_1 = NULL;
19313 PyObject *__pyx_t_2 = NULL;
19314 PyObject *__pyx_t_3 = NULL;
19315 PyObject *__pyx_t_4 = NULL;
19316 unsigned int __pyx_t_5;
19317 PyObject *__pyx_t_6 = NULL;
19318 PyObject *__pyx_t_7 = NULL;
19319 PyObject *__pyx_t_8 = NULL;
19320 PyObject *__pyx_t_9 = NULL;
19321 PyObject *__pyx_t_10 = NULL;
19322 PyObject *__pyx_t_11 = NULL;
19323 PyObject *__pyx_t_12 = NULL;
19324 PyObject *__pyx_t_13 = NULL;
19325 PyObject *__pyx_t_14 = NULL;
19326 PyObject *__pyx_t_15 = NULL;
19327 PyObject *__pyx_t_16 = NULL;
19328 PyObject *__pyx_t_17 = NULL;
19329 PyObject *__pyx_t_18 = NULL;
19330 Py_ssize_t __pyx_t_19;
19331 int __pyx_t_20;
19332 int __pyx_lineno = 0;
19333 const char *__pyx_filename = NULL;
19334 int __pyx_clineno = 0;
19335 __Pyx_RefNannySetupContext("enter_default_format", 1);
19336
19337 /* "pysam/libcvcf.pyx":519
19338 *
19339 * def enter_default_format(self):
19340 * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), # <<<<<<<<<<<<<<
19341 * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
19342 * FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
19343 */
19344 __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 519, __pyx_L1_error)
19345 __Pyx_GOTREF(__pyx_t_2);
19346 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NUMBER); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 519, __pyx_L1_error)
19347 __Pyx_GOTREF(__pyx_t_3);
19348 __pyx_t_4 = NULL;
19349 __pyx_t_5 = 0;
19350 #if CYTHON_UNPACK_METHODS
19351 if (unlikely(PyMethod_Check(__pyx_t_2))) {
19352 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_2);
19353 if (likely(__pyx_t_4)) {
19354 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
19355 __Pyx_INCREF(__pyx_t_4);
19356 __Pyx_INCREF(function);
19357 __Pyx_DECREF_SET(__pyx_t_2, function);
19358 __pyx_t_5 = 1;
19359 }
19360 }
19361 #endif
19362 {
19363 PyObject *__pyx_callargs[7] = {__pyx_t_4, __pyx_n_u_GT, __pyx_t_3, __pyx_int_1, __pyx_n_u_String, __pyx_n_u_Genotype, __pyx_kp_u__5};
19364 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19365 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
19366 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
19367 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 519, __pyx_L1_error)
19368 __Pyx_GOTREF(__pyx_t_1);
19369 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
19370 }
19371
19372 /* "pysam/libcvcf.pyx":520
19373 * def enter_default_format(self):
19374 * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
19375 * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1), # <<<<<<<<<<<<<<
19376 * FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
19377 * FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
19378 */
19379 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 520, __pyx_L1_error)
19380 __Pyx_GOTREF(__pyx_t_3);
19381 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NUMBER); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 520, __pyx_L1_error)
19382 __Pyx_GOTREF(__pyx_t_4);
19383 __pyx_t_6 = NULL;
19384 __pyx_t_5 = 0;
19385 #if CYTHON_UNPACK_METHODS
19386 if (unlikely(PyMethod_Check(__pyx_t_3))) {
19387 __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_3);
19388 if (likely(__pyx_t_6)) {
19389 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
19390 __Pyx_INCREF(__pyx_t_6);
19391 __Pyx_INCREF(function);
19392 __Pyx_DECREF_SET(__pyx_t_3, function);
19393 __pyx_t_5 = 1;
19394 }
19395 }
19396 #endif
19397 {
19398 PyObject *__pyx_callargs[7] = {__pyx_t_6, __pyx_n_u_DP, __pyx_t_4, __pyx_int_1, __pyx_n_u_Integer, __pyx_kp_u_Read_depth_at_this_position_for, __pyx_int_neg_1};
19399 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19400 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
19401 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
19402 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 520, __pyx_L1_error)
19403 __Pyx_GOTREF(__pyx_t_2);
19404 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
19405 }
19406
19407 /* "pysam/libcvcf.pyx":521
19408 * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
19409 * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
19410 * FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'), # <<<<<<<<<<<<<<
19411 * FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
19412 * FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
19413 */
19414 __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 521, __pyx_L1_error)
19415 __Pyx_GOTREF(__pyx_t_4);
19416 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NUMBER); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 521, __pyx_L1_error)
19417 __Pyx_GOTREF(__pyx_t_6);
19418 __pyx_t_7 = NULL;
19419 __pyx_t_5 = 0;
19420 #if CYTHON_UNPACK_METHODS
19421 if (unlikely(PyMethod_Check(__pyx_t_4))) {
19422 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_4);
19423 if (likely(__pyx_t_7)) {
19424 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
19425 __Pyx_INCREF(__pyx_t_7);
19426 __Pyx_INCREF(function);
19427 __Pyx_DECREF_SET(__pyx_t_4, function);
19428 __pyx_t_5 = 1;
19429 }
19430 }
19431 #endif
19432 {
19433 PyObject *__pyx_callargs[7] = {__pyx_t_7, __pyx_n_u_FT, __pyx_t_6, __pyx_int_1, __pyx_n_u_String, __pyx_kp_u_Sample_Genotype_Filter, __pyx_kp_u__5};
19434 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19435 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
19436 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
19437 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 521, __pyx_L1_error)
19438 __Pyx_GOTREF(__pyx_t_3);
19439 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
19440 }
19441
19442 /* "pysam/libcvcf.pyx":522
19443 * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
19444 * FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
19445 * FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), # <<<<<<<<<<<<<<
19446 * FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
19447 * FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
19448 */
19449 __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 522, __pyx_L1_error)
19450 __Pyx_GOTREF(__pyx_t_6);
19451 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_UNKNOWN); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 522, __pyx_L1_error)
19452 __Pyx_GOTREF(__pyx_t_7);
19453 __pyx_t_8 = NULL;
19454 __pyx_t_5 = 0;
19455 #if CYTHON_UNPACK_METHODS
19456 if (unlikely(PyMethod_Check(__pyx_t_6))) {
19457 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_6);
19458 if (likely(__pyx_t_8)) {
19459 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
19460 __Pyx_INCREF(__pyx_t_8);
19461 __Pyx_INCREF(function);
19462 __Pyx_DECREF_SET(__pyx_t_6, function);
19463 __pyx_t_5 = 1;
19464 }
19465 }
19466 #endif
19467 {
19468 PyObject *__pyx_callargs[7] = {__pyx_t_8, __pyx_n_u_GL, __pyx_t_7, __pyx_int_neg_1, __pyx_n_u_Float, __pyx_kp_u_Genotype_likelihoods, __pyx_kp_u__5};
19469 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19470 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
19471 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
19472 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 522, __pyx_L1_error)
19473 __Pyx_GOTREF(__pyx_t_4);
19474 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
19475 }
19476
19477 /* "pysam/libcvcf.pyx":523
19478 * FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
19479 * FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
19480 * FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), # <<<<<<<<<<<<<<
19481 * FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
19482 * FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'),
19483 */
19484 __Pyx_GetModuleGlobalName(__pyx_t_7, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 523, __pyx_L1_error)
19485 __Pyx_GOTREF(__pyx_t_7);
19486 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_UNKNOWN); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 523, __pyx_L1_error)
19487 __Pyx_GOTREF(__pyx_t_8);
19488 __pyx_t_9 = NULL;
19489 __pyx_t_5 = 0;
19490 #if CYTHON_UNPACK_METHODS
19491 if (unlikely(PyMethod_Check(__pyx_t_7))) {
19492 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_7);
19493 if (likely(__pyx_t_9)) {
19494 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7);
19495 __Pyx_INCREF(__pyx_t_9);
19496 __Pyx_INCREF(function);
19497 __Pyx_DECREF_SET(__pyx_t_7, function);
19498 __pyx_t_5 = 1;
19499 }
19500 }
19501 #endif
19502 {
19503 PyObject *__pyx_callargs[7] = {__pyx_t_9, __pyx_n_u_GLE, __pyx_t_8, __pyx_int_neg_1, __pyx_n_u_Float, __pyx_kp_u_Genotype_likelihoods, __pyx_kp_u__5};
19504 __pyx_t_6 = __Pyx_PyObject_FastCall(__pyx_t_7, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19505 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
19506 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
19507 if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 523, __pyx_L1_error)
19508 __Pyx_GOTREF(__pyx_t_6);
19509 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
19510 }
19511
19512 /* "pysam/libcvcf.pyx":524
19513 * FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
19514 * FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
19515 * FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1), # <<<<<<<<<<<<<<
19516 * FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'),
19517 * FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'),
19518 */
19519 __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 524, __pyx_L1_error)
19520 __Pyx_GOTREF(__pyx_t_8);
19521 __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NUMBER); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 524, __pyx_L1_error)
19522 __Pyx_GOTREF(__pyx_t_9);
19523 __pyx_t_10 = NULL;
19524 __pyx_t_5 = 0;
19525 #if CYTHON_UNPACK_METHODS
19526 if (unlikely(PyMethod_Check(__pyx_t_8))) {
19527 __pyx_t_10 = PyMethod_GET_SELF(__pyx_t_8);
19528 if (likely(__pyx_t_10)) {
19529 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_8);
19530 __Pyx_INCREF(__pyx_t_10);
19531 __Pyx_INCREF(function);
19532 __Pyx_DECREF_SET(__pyx_t_8, function);
19533 __pyx_t_5 = 1;
19534 }
19535 }
19536 #endif
19537 {
19538 PyObject *__pyx_callargs[7] = {__pyx_t_10, __pyx_n_u_GQ, __pyx_t_9, __pyx_int_1, __pyx_n_u_Integer, __pyx_kp_u_Genotype_Quality, __pyx_int_neg_1};
19539 __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19540 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
19541 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
19542 if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 524, __pyx_L1_error)
19543 __Pyx_GOTREF(__pyx_t_7);
19544 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
19545 }
19546
19547 /* "pysam/libcvcf.pyx":525
19548 * FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
19549 * FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
19550 * FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'), # <<<<<<<<<<<<<<
19551 * FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'),
19552 * FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'),
19553 */
19554 __Pyx_GetModuleGlobalName(__pyx_t_9, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 525, __pyx_L1_error)
19555 __Pyx_GOTREF(__pyx_t_9);
19556 __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_GENOTYPES); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 525, __pyx_L1_error)
19557 __Pyx_GOTREF(__pyx_t_10);
19558 __pyx_t_11 = NULL;
19559 __pyx_t_5 = 0;
19560 #if CYTHON_UNPACK_METHODS
19561 if (unlikely(PyMethod_Check(__pyx_t_9))) {
19562 __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_9);
19563 if (likely(__pyx_t_11)) {
19564 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_9);
19565 __Pyx_INCREF(__pyx_t_11);
19566 __Pyx_INCREF(function);
19567 __Pyx_DECREF_SET(__pyx_t_9, function);
19568 __pyx_t_5 = 1;
19569 }
19570 }
19571 #endif
19572 {
19573 PyObject *__pyx_callargs[7] = {__pyx_t_11, __pyx_n_u_PL, __pyx_t_10, __pyx_int_neg_1, __pyx_n_u_Integer, __pyx_kp_u_Phred_scaled_genotype_likelihood, __pyx_kp_u__5};
19574 __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19575 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
19576 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
19577 if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 525, __pyx_L1_error)
19578 __Pyx_GOTREF(__pyx_t_8);
19579 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
19580 }
19581
19582 /* "pysam/libcvcf.pyx":526
19583 * FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
19584 * FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'),
19585 * FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'), # <<<<<<<<<<<<<<
19586 * FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'),
19587 * FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
19588 */
19589 __Pyx_GetModuleGlobalName(__pyx_t_10, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 526, __pyx_L1_error)
19590 __Pyx_GOTREF(__pyx_t_10);
19591 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_GENOTYPES); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 526, __pyx_L1_error)
19592 __Pyx_GOTREF(__pyx_t_11);
19593 __pyx_t_12 = NULL;
19594 __pyx_t_5 = 0;
19595 #if CYTHON_UNPACK_METHODS
19596 if (unlikely(PyMethod_Check(__pyx_t_10))) {
19597 __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_10);
19598 if (likely(__pyx_t_12)) {
19599 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_10);
19600 __Pyx_INCREF(__pyx_t_12);
19601 __Pyx_INCREF(function);
19602 __Pyx_DECREF_SET(__pyx_t_10, function);
19603 __pyx_t_5 = 1;
19604 }
19605 }
19606 #endif
19607 {
19608 PyObject *__pyx_callargs[7] = {__pyx_t_12, __pyx_n_u_GP, __pyx_t_11, __pyx_int_neg_1, __pyx_n_u_Float, __pyx_kp_u_Genotype_posterior_probabilities, __pyx_kp_u__5};
19609 __pyx_t_9 = __Pyx_PyObject_FastCall(__pyx_t_10, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19610 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
19611 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
19612 if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 526, __pyx_L1_error)
19613 __Pyx_GOTREF(__pyx_t_9);
19614 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
19615 }
19616
19617 /* "pysam/libcvcf.pyx":527
19618 * FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'),
19619 * FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'),
19620 * FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'), # <<<<<<<<<<<<<<
19621 * FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
19622 * FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'),
19623 */
19624 __Pyx_GetModuleGlobalName(__pyx_t_11, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 527, __pyx_L1_error)
19625 __Pyx_GOTREF(__pyx_t_11);
19626 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_GENOTYPES); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 527, __pyx_L1_error)
19627 __Pyx_GOTREF(__pyx_t_12);
19628 __pyx_t_13 = NULL;
19629 __pyx_t_5 = 0;
19630 #if CYTHON_UNPACK_METHODS
19631 if (unlikely(PyMethod_Check(__pyx_t_11))) {
19632 __pyx_t_13 = PyMethod_GET_SELF(__pyx_t_11);
19633 if (likely(__pyx_t_13)) {
19634 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
19635 __Pyx_INCREF(__pyx_t_13);
19636 __Pyx_INCREF(function);
19637 __Pyx_DECREF_SET(__pyx_t_11, function);
19638 __pyx_t_5 = 1;
19639 }
19640 }
19641 #endif
19642 {
19643 PyObject *__pyx_callargs[7] = {__pyx_t_13, __pyx_n_u_GQ, __pyx_t_12, __pyx_int_neg_1, __pyx_n_u_Integer, __pyx_kp_u_Conditional_genotype_quality, __pyx_kp_u__5};
19644 __pyx_t_10 = __Pyx_PyObject_FastCall(__pyx_t_11, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19645 __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
19646 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
19647 if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 527, __pyx_L1_error)
19648 __Pyx_GOTREF(__pyx_t_10);
19649 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
19650 }
19651
19652 /* "pysam/libcvcf.pyx":528
19653 * FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'),
19654 * FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'),
19655 * FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid # <<<<<<<<<<<<<<
19656 * FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'),
19657 * FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1),
19658 */
19659 __Pyx_GetModuleGlobalName(__pyx_t_12, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 528, __pyx_L1_error)
19660 __Pyx_GOTREF(__pyx_t_12);
19661 __pyx_t_13 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_UNKNOWN); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 528, __pyx_L1_error)
19662 __Pyx_GOTREF(__pyx_t_13);
19663 __pyx_t_14 = NULL;
19664 __pyx_t_5 = 0;
19665 #if CYTHON_UNPACK_METHODS
19666 if (unlikely(PyMethod_Check(__pyx_t_12))) {
19667 __pyx_t_14 = PyMethod_GET_SELF(__pyx_t_12);
19668 if (likely(__pyx_t_14)) {
19669 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_12);
19670 __Pyx_INCREF(__pyx_t_14);
19671 __Pyx_INCREF(function);
19672 __Pyx_DECREF_SET(__pyx_t_12, function);
19673 __pyx_t_5 = 1;
19674 }
19675 }
19676 #endif
19677 {
19678 PyObject *__pyx_callargs[7] = {__pyx_t_14, __pyx_n_u_HQ, __pyx_t_13, __pyx_int_neg_1, __pyx_n_u_Integer, __pyx_kp_u_Haplotype_Quality, __pyx_int_neg_1};
19679 __pyx_t_11 = __Pyx_PyObject_FastCall(__pyx_t_12, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19680 __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
19681 __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
19682 if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 528, __pyx_L1_error)
19683 __Pyx_GOTREF(__pyx_t_11);
19684 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
19685 }
19686
19687 /* "pysam/libcvcf.pyx":529
19688 * FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'),
19689 * FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
19690 * FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'), # <<<<<<<<<<<<<<
19691 * FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1),
19692 * FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1),
19693 */
19694 __Pyx_GetModuleGlobalName(__pyx_t_13, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 529, __pyx_L1_error)
19695 __Pyx_GOTREF(__pyx_t_13);
19696 __pyx_t_14 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_UNKNOWN); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 529, __pyx_L1_error)
19697 __Pyx_GOTREF(__pyx_t_14);
19698 __pyx_t_15 = NULL;
19699 __pyx_t_5 = 0;
19700 #if CYTHON_UNPACK_METHODS
19701 if (unlikely(PyMethod_Check(__pyx_t_13))) {
19702 __pyx_t_15 = PyMethod_GET_SELF(__pyx_t_13);
19703 if (likely(__pyx_t_15)) {
19704 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_13);
19705 __Pyx_INCREF(__pyx_t_15);
19706 __Pyx_INCREF(function);
19707 __Pyx_DECREF_SET(__pyx_t_13, function);
19708 __pyx_t_5 = 1;
19709 }
19710 }
19711 #endif
19712 {
19713 PyObject *__pyx_callargs[7] = {__pyx_t_15, __pyx_n_u_PS, __pyx_t_14, __pyx_int_neg_1, __pyx_n_u_Integer, __pyx_kp_u_Phase_set, __pyx_kp_u__5};
19714 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_13, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19715 __Pyx_XDECREF(__pyx_t_15); __pyx_t_15 = 0;
19716 __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
19717 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 529, __pyx_L1_error)
19718 __Pyx_GOTREF(__pyx_t_12);
19719 __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
19720 }
19721
19722 /* "pysam/libcvcf.pyx":530
19723 * FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
19724 * FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'),
19725 * FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1), # <<<<<<<<<<<<<<
19726 * FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1),
19727 * FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1),
19728 */
19729 __Pyx_GetModuleGlobalName(__pyx_t_14, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 530, __pyx_L1_error)
19730 __Pyx_GOTREF(__pyx_t_14);
19731 __pyx_t_15 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NUMBER); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 530, __pyx_L1_error)
19732 __Pyx_GOTREF(__pyx_t_15);
19733 __pyx_t_16 = NULL;
19734 __pyx_t_5 = 0;
19735 #if CYTHON_UNPACK_METHODS
19736 if (unlikely(PyMethod_Check(__pyx_t_14))) {
19737 __pyx_t_16 = PyMethod_GET_SELF(__pyx_t_14);
19738 if (likely(__pyx_t_16)) {
19739 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_14);
19740 __Pyx_INCREF(__pyx_t_16);
19741 __Pyx_INCREF(function);
19742 __Pyx_DECREF_SET(__pyx_t_14, function);
19743 __pyx_t_5 = 1;
19744 }
19745 }
19746 #endif
19747 {
19748 PyObject *__pyx_callargs[7] = {__pyx_t_16, __pyx_n_u_PQ, __pyx_t_15, __pyx_int_1, __pyx_n_u_Integer, __pyx_kp_u_Phasing_quality, __pyx_int_neg_1};
19749 __pyx_t_13 = __Pyx_PyObject_FastCall(__pyx_t_14, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19750 __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
19751 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
19752 if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 530, __pyx_L1_error)
19753 __Pyx_GOTREF(__pyx_t_13);
19754 __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
19755 }
19756
19757 /* "pysam/libcvcf.pyx":531
19758 * FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'),
19759 * FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1),
19760 * FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1), # <<<<<<<<<<<<<<
19761 * FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1),
19762 * ]:
19763 */
19764 __Pyx_GetModuleGlobalName(__pyx_t_15, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 531, __pyx_L1_error)
19765 __Pyx_GOTREF(__pyx_t_15);
19766 __pyx_t_16 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_ALLELES); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 531, __pyx_L1_error)
19767 __Pyx_GOTREF(__pyx_t_16);
19768 __pyx_t_17 = NULL;
19769 __pyx_t_5 = 0;
19770 #if CYTHON_UNPACK_METHODS
19771 if (unlikely(PyMethod_Check(__pyx_t_15))) {
19772 __pyx_t_17 = PyMethod_GET_SELF(__pyx_t_15);
19773 if (likely(__pyx_t_17)) {
19774 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_15);
19775 __Pyx_INCREF(__pyx_t_17);
19776 __Pyx_INCREF(function);
19777 __Pyx_DECREF_SET(__pyx_t_15, function);
19778 __pyx_t_5 = 1;
19779 }
19780 }
19781 #endif
19782 {
19783 PyObject *__pyx_callargs[7] = {__pyx_t_17, __pyx_n_u_EC, __pyx_t_16, __pyx_int_1, __pyx_n_u_Integer, __pyx_kp_u_Expected_alternate_allel_counts, __pyx_int_neg_1};
19784 __pyx_t_14 = __Pyx_PyObject_FastCall(__pyx_t_15, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19785 __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
19786 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
19787 if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 531, __pyx_L1_error)
19788 __Pyx_GOTREF(__pyx_t_14);
19789 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
19790 }
19791
19792 /* "pysam/libcvcf.pyx":532
19793 * FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1),
19794 * FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1),
19795 * FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1), # <<<<<<<<<<<<<<
19796 * ]:
19797 * if f.id not in self._format:
19798 */
19799 __Pyx_GetModuleGlobalName(__pyx_t_16, __pyx_n_s_FORMAT); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 532, __pyx_L1_error)
19800 __Pyx_GOTREF(__pyx_t_16);
19801 __pyx_t_17 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_NT_NUMBER); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 532, __pyx_L1_error)
19802 __Pyx_GOTREF(__pyx_t_17);
19803 __pyx_t_18 = NULL;
19804 __pyx_t_5 = 0;
19805 #if CYTHON_UNPACK_METHODS
19806 if (unlikely(PyMethod_Check(__pyx_t_16))) {
19807 __pyx_t_18 = PyMethod_GET_SELF(__pyx_t_16);
19808 if (likely(__pyx_t_18)) {
19809 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_16);
19810 __Pyx_INCREF(__pyx_t_18);
19811 __Pyx_INCREF(function);
19812 __Pyx_DECREF_SET(__pyx_t_16, function);
19813 __pyx_t_5 = 1;
19814 }
19815 }
19816 #endif
19817 {
19818 PyObject *__pyx_callargs[7] = {__pyx_t_18, __pyx_n_u_MQ, __pyx_t_17, __pyx_int_1, __pyx_n_u_Integer, __pyx_kp_u_RMS_mapping_quality, __pyx_int_neg_1};
19819 __pyx_t_15 = __Pyx_PyObject_FastCall(__pyx_t_16, __pyx_callargs+1-__pyx_t_5, 6+__pyx_t_5);
19820 __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
19821 __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
19822 if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 532, __pyx_L1_error)
19823 __Pyx_GOTREF(__pyx_t_15);
19824 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
19825 }
19826
19827 /* "pysam/libcvcf.pyx":519
19828 *
19829 * def enter_default_format(self):
19830 * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), # <<<<<<<<<<<<<<
19831 * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
19832 * FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
19833 */
19834 __pyx_t_16 = PyTuple_New(14); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 519, __pyx_L1_error)
19835 __Pyx_GOTREF(__pyx_t_16);
19836 __Pyx_GIVEREF(__pyx_t_1);
19837 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 0, __pyx_t_1)) __PYX_ERR(0, 519, __pyx_L1_error);
19838 __Pyx_GIVEREF(__pyx_t_2);
19839 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 1, __pyx_t_2)) __PYX_ERR(0, 519, __pyx_L1_error);
19840 __Pyx_GIVEREF(__pyx_t_3);
19841 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 2, __pyx_t_3)) __PYX_ERR(0, 519, __pyx_L1_error);
19842 __Pyx_GIVEREF(__pyx_t_4);
19843 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 3, __pyx_t_4)) __PYX_ERR(0, 519, __pyx_L1_error);
19844 __Pyx_GIVEREF(__pyx_t_6);
19845 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 4, __pyx_t_6)) __PYX_ERR(0, 519, __pyx_L1_error);
19846 __Pyx_GIVEREF(__pyx_t_7);
19847 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 5, __pyx_t_7)) __PYX_ERR(0, 519, __pyx_L1_error);
19848 __Pyx_GIVEREF(__pyx_t_8);
19849 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 6, __pyx_t_8)) __PYX_ERR(0, 519, __pyx_L1_error);
19850 __Pyx_GIVEREF(__pyx_t_9);
19851 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 7, __pyx_t_9)) __PYX_ERR(0, 519, __pyx_L1_error);
19852 __Pyx_GIVEREF(__pyx_t_10);
19853 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 8, __pyx_t_10)) __PYX_ERR(0, 519, __pyx_L1_error);
19854 __Pyx_GIVEREF(__pyx_t_11);
19855 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 9, __pyx_t_11)) __PYX_ERR(0, 519, __pyx_L1_error);
19856 __Pyx_GIVEREF(__pyx_t_12);
19857 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 10, __pyx_t_12)) __PYX_ERR(0, 519, __pyx_L1_error);
19858 __Pyx_GIVEREF(__pyx_t_13);
19859 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 11, __pyx_t_13)) __PYX_ERR(0, 519, __pyx_L1_error);
19860 __Pyx_GIVEREF(__pyx_t_14);
19861 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 12, __pyx_t_14)) __PYX_ERR(0, 519, __pyx_L1_error);
19862 __Pyx_GIVEREF(__pyx_t_15);
19863 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_16, 13, __pyx_t_15)) __PYX_ERR(0, 519, __pyx_L1_error);
19864 __pyx_t_1 = 0;
19865 __pyx_t_2 = 0;
19866 __pyx_t_3 = 0;
19867 __pyx_t_4 = 0;
19868 __pyx_t_6 = 0;
19869 __pyx_t_7 = 0;
19870 __pyx_t_8 = 0;
19871 __pyx_t_9 = 0;
19872 __pyx_t_10 = 0;
19873 __pyx_t_11 = 0;
19874 __pyx_t_12 = 0;
19875 __pyx_t_13 = 0;
19876 __pyx_t_14 = 0;
19877 __pyx_t_15 = 0;
19878 __pyx_t_15 = __pyx_t_16; __Pyx_INCREF(__pyx_t_15);
19879 __pyx_t_19 = 0;
19880 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
19881 for (;;) {
19882 if (__pyx_t_19 >= 14) break;
19883 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
19884 __pyx_t_16 = PyTuple_GET_ITEM(__pyx_t_15, __pyx_t_19); __Pyx_INCREF(__pyx_t_16); __pyx_t_19++; if (unlikely((0 < 0))) __PYX_ERR(0, 519, __pyx_L1_error)
19885 #else
19886 __pyx_t_16 = __Pyx_PySequence_ITEM(__pyx_t_15, __pyx_t_19); __pyx_t_19++; if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 519, __pyx_L1_error)
19887 __Pyx_GOTREF(__pyx_t_16);
19888 #endif
19889 __Pyx_XDECREF_SET(__pyx_v_f, __pyx_t_16);
19890 __pyx_t_16 = 0;
19891
19892 /* "pysam/libcvcf.pyx":534
19893 * FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1),
19894 * ]:
19895 * if f.id not in self._format: # <<<<<<<<<<<<<<
19896 * self._format[f.id] = f
19897 *
19898 */
19899 __pyx_t_16 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_id_2); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 534, __pyx_L1_error)
19900 __Pyx_GOTREF(__pyx_t_16);
19901 __pyx_t_14 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_2); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 534, __pyx_L1_error)
19902 __Pyx_GOTREF(__pyx_t_14);
19903 __pyx_t_20 = (__Pyx_PySequence_ContainsTF(__pyx_t_16, __pyx_t_14, Py_NE)); if (unlikely((__pyx_t_20 < 0))) __PYX_ERR(0, 534, __pyx_L1_error)
19904 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
19905 __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
19906 if (__pyx_t_20) {
19907
19908 /* "pysam/libcvcf.pyx":535
19909 * ]:
19910 * if f.id not in self._format:
19911 * self._format[f.id] = f # <<<<<<<<<<<<<<
19912 *
19913 * def parse_header(self, line):
19914 */
19915 __pyx_t_14 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_2); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 535, __pyx_L1_error)
19916 __Pyx_GOTREF(__pyx_t_14);
19917 __pyx_t_16 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_id_2); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 535, __pyx_L1_error)
19918 __Pyx_GOTREF(__pyx_t_16);
19919 if (unlikely((PyObject_SetItem(__pyx_t_14, __pyx_t_16, __pyx_v_f) < 0))) __PYX_ERR(0, 535, __pyx_L1_error)
19920 __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
19921 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
19922
19923 /* "pysam/libcvcf.pyx":534
19924 * FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1),
19925 * ]:
19926 * if f.id not in self._format: # <<<<<<<<<<<<<<
19927 * self._format[f.id] = f
19928 *
19929 */
19930 }
19931
19932 /* "pysam/libcvcf.pyx":519
19933 *
19934 * def enter_default_format(self):
19935 * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), # <<<<<<<<<<<<<<
19936 * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
19937 * FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
19938 */
19939 }
19940 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
19941
19942 /* "pysam/libcvcf.pyx":518
19943 *
19944 *
19945 * def enter_default_format(self): # <<<<<<<<<<<<<<
19946 * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
19947 * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
19948 */
19949
19950 /* function exit code */
19951 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
19952 goto __pyx_L0;
19953 __pyx_L1_error:;
19954 __Pyx_XDECREF(__pyx_t_1);
19955 __Pyx_XDECREF(__pyx_t_2);
19956 __Pyx_XDECREF(__pyx_t_3);
19957 __Pyx_XDECREF(__pyx_t_4);
19958 __Pyx_XDECREF(__pyx_t_6);
19959 __Pyx_XDECREF(__pyx_t_7);
19960 __Pyx_XDECREF(__pyx_t_8);
19961 __Pyx_XDECREF(__pyx_t_9);
19962 __Pyx_XDECREF(__pyx_t_10);
19963 __Pyx_XDECREF(__pyx_t_11);
19964 __Pyx_XDECREF(__pyx_t_12);
19965 __Pyx_XDECREF(__pyx_t_13);
19966 __Pyx_XDECREF(__pyx_t_14);
19967 __Pyx_XDECREF(__pyx_t_15);
19968 __Pyx_XDECREF(__pyx_t_16);
19969 __Pyx_XDECREF(__pyx_t_17);
19970 __Pyx_XDECREF(__pyx_t_18);
19971 __Pyx_AddTraceback("pysam.libcvcf.VCF.enter_default_format", __pyx_clineno, __pyx_lineno, __pyx_filename);
19972 __pyx_r = NULL;
19973 __pyx_L0:;
19974 __Pyx_XDECREF(__pyx_v_f);
19975 __Pyx_XGIVEREF(__pyx_r);
19976 __Pyx_RefNannyFinishContext();
19977 return __pyx_r;
19978 }
19979
19980 /* "pysam/libcvcf.pyx":537
19981 * self._format[f.id] = f
19982 *
19983 * def parse_header(self, line): # <<<<<<<<<<<<<<
19984 *
19985 * assert line.startswith('##')
19986 */
19987
19988 /* Python wrapper */
19989 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_17parse_header(PyObject *__pyx_self,
19990 #if CYTHON_METH_FASTCALL
19991 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
19992 #else
19993 PyObject *__pyx_args, PyObject *__pyx_kwds
19994 #endif
19995 ); /*proto*/
19996 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_16parse_header, "VCF.parse_header(self, line)");
19997 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_17parse_header = {"parse_header", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_17parse_header, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_16parse_header};
19998 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_17parse_header(PyObject *__pyx_self,
19999 #if CYTHON_METH_FASTCALL
20000 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
20001 #else
20002 PyObject *__pyx_args, PyObject *__pyx_kwds
20003 #endif
20004 ) {
20005 PyObject *__pyx_v_self = 0;
20006 PyObject *__pyx_v_line = 0;
20007 #if !CYTHON_METH_FASTCALL
20008 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
20009 #endif
20010 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
20011 PyObject* values[2] = {0,0};
20012 int __pyx_lineno = 0;
20013 const char *__pyx_filename = NULL;
20014 int __pyx_clineno = 0;
20015 PyObject *__pyx_r = 0;
20016 __Pyx_RefNannyDeclarations
20017 __Pyx_RefNannySetupContext("parse_header (wrapper)", 0);
20018 #if !CYTHON_METH_FASTCALL
20019 #if CYTHON_ASSUME_SAFE_MACROS
20020 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
20021 #else
20022 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
20023 #endif
20024 #endif
20025 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
20026 {
20027 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_line,0};
20028 if (__pyx_kwds) {
20029 Py_ssize_t kw_args;
20030 switch (__pyx_nargs) {
20031 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
20032 CYTHON_FALLTHROUGH;
20033 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
20034 CYTHON_FALLTHROUGH;
20035 case 0: break;
20036 default: goto __pyx_L5_argtuple_error;
20037 }
20038 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
20039 switch (__pyx_nargs) {
20040 case 0:
20041 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
20042 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
20043 kw_args--;
20044 }
20045 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 537, __pyx_L3_error)
20046 else goto __pyx_L5_argtuple_error;
20047 CYTHON_FALLTHROUGH;
20048 case 1:
20049 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_line)) != 0)) {
20050 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
20051 kw_args--;
20052 }
20053 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 537, __pyx_L3_error)
20054 else {
20055 __Pyx_RaiseArgtupleInvalid("parse_header", 1, 2, 2, 1); __PYX_ERR(0, 537, __pyx_L3_error)
20056 }
20057 }
20058 if (unlikely(kw_args > 0)) {
20059 const Py_ssize_t kwd_pos_args = __pyx_nargs;
20060 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "parse_header") < 0)) __PYX_ERR(0, 537, __pyx_L3_error)
20061 }
20062 } else if (unlikely(__pyx_nargs != 2)) {
20063 goto __pyx_L5_argtuple_error;
20064 } else {
20065 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
20066 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
20067 }
20068 __pyx_v_self = values[0];
20069 __pyx_v_line = values[1];
20070 }
20071 goto __pyx_L6_skip;
20072 __pyx_L5_argtuple_error:;
20073 __Pyx_RaiseArgtupleInvalid("parse_header", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 537, __pyx_L3_error)
20074 __pyx_L6_skip:;
20075 goto __pyx_L4_argument_unpacking_done;
20076 __pyx_L3_error:;
20077 {
20078 Py_ssize_t __pyx_temp;
20079 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
20080 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
20081 }
20082 }
20083 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename);
20084 __Pyx_RefNannyFinishContext();
20085 return NULL;
20086 __pyx_L4_argument_unpacking_done:;
20087 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_16parse_header(__pyx_self, __pyx_v_self, __pyx_v_line);
20088
20089 /* function exit code */
20090 {
20091 Py_ssize_t __pyx_temp;
20092 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
20093 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
20094 }
20095 }
20096 __Pyx_RefNannyFinishContext();
20097 return __pyx_r;
20098 }
20099
20100 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line) {
20101 PyObject *__pyx_v_elts = NULL;
20102 PyObject *__pyx_v_key = NULL;
20103 PyObject *__pyx_v_value = NULL;
20104 PyObject *__pyx_v_f = NULL;
20105 PyObject *__pyx_r = NULL;
20106 __Pyx_RefNannyDeclarations
20107 PyObject *__pyx_t_1 = NULL;
20108 PyObject *__pyx_t_2 = NULL;
20109 PyObject *__pyx_t_3 = NULL;
20110 unsigned int __pyx_t_4;
20111 int __pyx_t_5;
20112 PyObject *__pyx_t_6 = NULL;
20113 int __pyx_t_7;
20114 int __pyx_lineno = 0;
20115 const char *__pyx_filename = NULL;
20116 int __pyx_clineno = 0;
20117 __Pyx_RefNannySetupContext("parse_header", 1);
20118
20119 /* "pysam/libcvcf.pyx":539
20120 * def parse_header(self, line):
20121 *
20122 * assert line.startswith('##') # <<<<<<<<<<<<<<
20123 * elts = line[2:].split('=')
20124 * key = elts[0].strip()
20125 */
20126 #ifndef CYTHON_WITHOUT_ASSERTIONS
20127 if (unlikely(__pyx_assertions_enabled())) {
20128 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_startswith); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 539, __pyx_L1_error)
20129 __Pyx_GOTREF(__pyx_t_2);
20130 __pyx_t_3 = NULL;
20131 __pyx_t_4 = 0;
20132 #if CYTHON_UNPACK_METHODS
20133 if (likely(PyMethod_Check(__pyx_t_2))) {
20134 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
20135 if (likely(__pyx_t_3)) {
20136 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
20137 __Pyx_INCREF(__pyx_t_3);
20138 __Pyx_INCREF(function);
20139 __Pyx_DECREF_SET(__pyx_t_2, function);
20140 __pyx_t_4 = 1;
20141 }
20142 }
20143 #endif
20144 {
20145 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_kp_u__23};
20146 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
20147 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
20148 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 539, __pyx_L1_error)
20149 __Pyx_GOTREF(__pyx_t_1);
20150 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
20151 }
20152 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 539, __pyx_L1_error)
20153 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
20154 if (unlikely(!__pyx_t_5)) {
20155 __Pyx_Raise(__pyx_builtin_AssertionError, 0, 0, 0);
20156 __PYX_ERR(0, 539, __pyx_L1_error)
20157 }
20158 }
20159 #else
20160 if ((1)); else __PYX_ERR(0, 539, __pyx_L1_error)
20161 #endif
20162
20163 /* "pysam/libcvcf.pyx":540
20164 *
20165 * assert line.startswith('##')
20166 * elts = line[2:].split('=') # <<<<<<<<<<<<<<
20167 * key = elts[0].strip()
20168 * value = '='.join(elts[1:]).strip()
20169 */
20170 __pyx_t_2 = __Pyx_PyObject_GetSlice(__pyx_v_line, 2, 0, NULL, NULL, &__pyx_slice__20, 1, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 540, __pyx_L1_error)
20171 __Pyx_GOTREF(__pyx_t_2);
20172 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_split); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 540, __pyx_L1_error)
20173 __Pyx_GOTREF(__pyx_t_3);
20174 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
20175 __pyx_t_2 = NULL;
20176 __pyx_t_4 = 0;
20177 #if CYTHON_UNPACK_METHODS
20178 if (likely(PyMethod_Check(__pyx_t_3))) {
20179 __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_3);
20180 if (likely(__pyx_t_2)) {
20181 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
20182 __Pyx_INCREF(__pyx_t_2);
20183 __Pyx_INCREF(function);
20184 __Pyx_DECREF_SET(__pyx_t_3, function);
20185 __pyx_t_4 = 1;
20186 }
20187 }
20188 #endif
20189 {
20190 PyObject *__pyx_callargs[2] = {__pyx_t_2, __pyx_kp_u__7};
20191 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
20192 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
20193 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 540, __pyx_L1_error)
20194 __Pyx_GOTREF(__pyx_t_1);
20195 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
20196 }
20197 __pyx_v_elts = __pyx_t_1;
20198 __pyx_t_1 = 0;
20199
20200 /* "pysam/libcvcf.pyx":541
20201 * assert line.startswith('##')
20202 * elts = line[2:].split('=')
20203 * key = elts[0].strip() # <<<<<<<<<<<<<<
20204 * value = '='.join(elts[1:]).strip()
20205 * if key == "fileformat":
20206 */
20207 __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_elts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 541, __pyx_L1_error)
20208 __Pyx_GOTREF(__pyx_t_3);
20209 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_strip); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 541, __pyx_L1_error)
20210 __Pyx_GOTREF(__pyx_t_2);
20211 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
20212 __pyx_t_3 = NULL;
20213 __pyx_t_4 = 0;
20214 #if CYTHON_UNPACK_METHODS
20215 if (likely(PyMethod_Check(__pyx_t_2))) {
20216 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
20217 if (likely(__pyx_t_3)) {
20218 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
20219 __Pyx_INCREF(__pyx_t_3);
20220 __Pyx_INCREF(function);
20221 __Pyx_DECREF_SET(__pyx_t_2, function);
20222 __pyx_t_4 = 1;
20223 }
20224 }
20225 #endif
20226 {
20227 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
20228 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
20229 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
20230 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 541, __pyx_L1_error)
20231 __Pyx_GOTREF(__pyx_t_1);
20232 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
20233 }
20234 __pyx_v_key = __pyx_t_1;
20235 __pyx_t_1 = 0;
20236
20237 /* "pysam/libcvcf.pyx":542
20238 * elts = line[2:].split('=')
20239 * key = elts[0].strip()
20240 * value = '='.join(elts[1:]).strip() # <<<<<<<<<<<<<<
20241 * if key == "fileformat":
20242 * if value == "VCFv3.3":
20243 */
20244 __pyx_t_2 = __Pyx_PyObject_GetSlice(__pyx_v_elts, 1, 0, NULL, NULL, &__pyx_slice__18, 1, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 542, __pyx_L1_error)
20245 __Pyx_GOTREF(__pyx_t_2);
20246 __pyx_t_3 = PyUnicode_Join(__pyx_kp_u__7, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 542, __pyx_L1_error)
20247 __Pyx_GOTREF(__pyx_t_3);
20248 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
20249 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_strip); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 542, __pyx_L1_error)
20250 __Pyx_GOTREF(__pyx_t_2);
20251 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
20252 __pyx_t_3 = NULL;
20253 __pyx_t_4 = 0;
20254 #if CYTHON_UNPACK_METHODS
20255 if (likely(PyMethod_Check(__pyx_t_2))) {
20256 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
20257 if (likely(__pyx_t_3)) {
20258 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
20259 __Pyx_INCREF(__pyx_t_3);
20260 __Pyx_INCREF(function);
20261 __Pyx_DECREF_SET(__pyx_t_2, function);
20262 __pyx_t_4 = 1;
20263 }
20264 }
20265 #endif
20266 {
20267 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
20268 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
20269 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
20270 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 542, __pyx_L1_error)
20271 __Pyx_GOTREF(__pyx_t_1);
20272 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
20273 }
20274 __pyx_v_value = __pyx_t_1;
20275 __pyx_t_1 = 0;
20276
20277 /* "pysam/libcvcf.pyx":543
20278 * key = elts[0].strip()
20279 * value = '='.join(elts[1:]).strip()
20280 * if key == "fileformat": # <<<<<<<<<<<<<<
20281 * if value == "VCFv3.3":
20282 * self._version = 33
20283 */
20284 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_v_key, __pyx_n_u_fileformat, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 543, __pyx_L1_error)
20285 if (__pyx_t_5) {
20286
20287 /* "pysam/libcvcf.pyx":544
20288 * value = '='.join(elts[1:]).strip()
20289 * if key == "fileformat":
20290 * if value == "VCFv3.3": # <<<<<<<<<<<<<<
20291 * self._version = 33
20292 * elif value == "VCFv4.0":
20293 */
20294 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_v_value, __pyx_kp_u_VCFv3_3, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 544, __pyx_L1_error)
20295 if (__pyx_t_5) {
20296
20297 /* "pysam/libcvcf.pyx":545
20298 * if key == "fileformat":
20299 * if value == "VCFv3.3":
20300 * self._version = 33 # <<<<<<<<<<<<<<
20301 * elif value == "VCFv4.0":
20302 * self._version = 40
20303 */
20304 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_version, __pyx_int_33) < 0) __PYX_ERR(0, 545, __pyx_L1_error)
20305
20306 /* "pysam/libcvcf.pyx":544
20307 * value = '='.join(elts[1:]).strip()
20308 * if key == "fileformat":
20309 * if value == "VCFv3.3": # <<<<<<<<<<<<<<
20310 * self._version = 33
20311 * elif value == "VCFv4.0":
20312 */
20313 goto __pyx_L4;
20314 }
20315
20316 /* "pysam/libcvcf.pyx":546
20317 * if value == "VCFv3.3":
20318 * self._version = 33
20319 * elif value == "VCFv4.0": # <<<<<<<<<<<<<<
20320 * self._version = 40
20321 * elif value == "VCFv4.1":
20322 */
20323 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_v_value, __pyx_kp_u_VCFv4_0, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 546, __pyx_L1_error)
20324 if (__pyx_t_5) {
20325
20326 /* "pysam/libcvcf.pyx":547
20327 * self._version = 33
20328 * elif value == "VCFv4.0":
20329 * self._version = 40 # <<<<<<<<<<<<<<
20330 * elif value == "VCFv4.1":
20331 * # AH - for testing
20332 */
20333 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_version, __pyx_int_40) < 0) __PYX_ERR(0, 547, __pyx_L1_error)
20334
20335 /* "pysam/libcvcf.pyx":546
20336 * if value == "VCFv3.3":
20337 * self._version = 33
20338 * elif value == "VCFv4.0": # <<<<<<<<<<<<<<
20339 * self._version = 40
20340 * elif value == "VCFv4.1":
20341 */
20342 goto __pyx_L4;
20343 }
20344
20345 /* "pysam/libcvcf.pyx":548
20346 * elif value == "VCFv4.0":
20347 * self._version = 40
20348 * elif value == "VCFv4.1": # <<<<<<<<<<<<<<
20349 * # AH - for testing
20350 * self._version = 40
20351 */
20352 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_v_value, __pyx_kp_u_VCFv4_1, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 548, __pyx_L1_error)
20353 if (__pyx_t_5) {
20354
20355 /* "pysam/libcvcf.pyx":550
20356 * elif value == "VCFv4.1":
20357 * # AH - for testing
20358 * self._version = 40 # <<<<<<<<<<<<<<
20359 * elif value == "VCFv4.2":
20360 * # AH - for testing
20361 */
20362 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_version, __pyx_int_40) < 0) __PYX_ERR(0, 550, __pyx_L1_error)
20363
20364 /* "pysam/libcvcf.pyx":548
20365 * elif value == "VCFv4.0":
20366 * self._version = 40
20367 * elif value == "VCFv4.1": # <<<<<<<<<<<<<<
20368 * # AH - for testing
20369 * self._version = 40
20370 */
20371 goto __pyx_L4;
20372 }
20373
20374 /* "pysam/libcvcf.pyx":551
20375 * # AH - for testing
20376 * self._version = 40
20377 * elif value == "VCFv4.2": # <<<<<<<<<<<<<<
20378 * # AH - for testing
20379 * self._version = 40
20380 */
20381 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_v_value, __pyx_kp_u_VCFv4_2, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 551, __pyx_L1_error)
20382 if (__pyx_t_5) {
20383
20384 /* "pysam/libcvcf.pyx":553
20385 * elif value == "VCFv4.2":
20386 * # AH - for testing
20387 * self._version = 40 # <<<<<<<<<<<<<<
20388 * else:
20389 * self.error(line,self.UNKNOWN_FORMAT_STRING)
20390 */
20391 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_version, __pyx_int_40) < 0) __PYX_ERR(0, 553, __pyx_L1_error)
20392
20393 /* "pysam/libcvcf.pyx":551
20394 * # AH - for testing
20395 * self._version = 40
20396 * elif value == "VCFv4.2": # <<<<<<<<<<<<<<
20397 * # AH - for testing
20398 * self._version = 40
20399 */
20400 goto __pyx_L4;
20401 }
20402
20403 /* "pysam/libcvcf.pyx":555
20404 * self._version = 40
20405 * else:
20406 * self.error(line,self.UNKNOWN_FORMAT_STRING) # <<<<<<<<<<<<<<
20407 * elif key == "INFO":
20408 * f = self.parse_format(line, value)
20409 */
20410 /*else*/ {
20411 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 555, __pyx_L1_error)
20412 __Pyx_GOTREF(__pyx_t_2);
20413 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_UNKNOWN_FORMAT_STRING); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 555, __pyx_L1_error)
20414 __Pyx_GOTREF(__pyx_t_3);
20415 __pyx_t_6 = NULL;
20416 __pyx_t_4 = 0;
20417 #if CYTHON_UNPACK_METHODS
20418 if (likely(PyMethod_Check(__pyx_t_2))) {
20419 __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_2);
20420 if (likely(__pyx_t_6)) {
20421 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
20422 __Pyx_INCREF(__pyx_t_6);
20423 __Pyx_INCREF(function);
20424 __Pyx_DECREF_SET(__pyx_t_2, function);
20425 __pyx_t_4 = 1;
20426 }
20427 }
20428 #endif
20429 {
20430 PyObject *__pyx_callargs[3] = {__pyx_t_6, __pyx_v_line, __pyx_t_3};
20431 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
20432 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
20433 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
20434 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 555, __pyx_L1_error)
20435 __Pyx_GOTREF(__pyx_t_1);
20436 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
20437 }
20438 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
20439 }
20440 __pyx_L4:;
20441
20442 /* "pysam/libcvcf.pyx":543
20443 * key = elts[0].strip()
20444 * value = '='.join(elts[1:]).strip()
20445 * if key == "fileformat": # <<<<<<<<<<<<<<
20446 * if value == "VCFv3.3":
20447 * self._version = 33
20448 */
20449 goto __pyx_L3;
20450 }
20451
20452 /* "pysam/libcvcf.pyx":556
20453 * else:
20454 * self.error(line,self.UNKNOWN_FORMAT_STRING)
20455 * elif key == "INFO": # <<<<<<<<<<<<<<
20456 * f = self.parse_format(line, value)
20457 * self._info[ f.id ] = f
20458 */
20459 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_v_key, __pyx_n_u_INFO, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 556, __pyx_L1_error)
20460 if (__pyx_t_5) {
20461
20462 /* "pysam/libcvcf.pyx":557
20463 * self.error(line,self.UNKNOWN_FORMAT_STRING)
20464 * elif key == "INFO":
20465 * f = self.parse_format(line, value) # <<<<<<<<<<<<<<
20466 * self._info[ f.id ] = f
20467 * elif key == "FILTER":
20468 */
20469 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parse_format); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 557, __pyx_L1_error)
20470 __Pyx_GOTREF(__pyx_t_2);
20471 __pyx_t_3 = NULL;
20472 __pyx_t_4 = 0;
20473 #if CYTHON_UNPACK_METHODS
20474 if (likely(PyMethod_Check(__pyx_t_2))) {
20475 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
20476 if (likely(__pyx_t_3)) {
20477 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
20478 __Pyx_INCREF(__pyx_t_3);
20479 __Pyx_INCREF(function);
20480 __Pyx_DECREF_SET(__pyx_t_2, function);
20481 __pyx_t_4 = 1;
20482 }
20483 }
20484 #endif
20485 {
20486 PyObject *__pyx_callargs[3] = {__pyx_t_3, __pyx_v_line, __pyx_v_value};
20487 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
20488 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
20489 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 557, __pyx_L1_error)
20490 __Pyx_GOTREF(__pyx_t_1);
20491 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
20492 }
20493 __pyx_v_f = __pyx_t_1;
20494 __pyx_t_1 = 0;
20495
20496 /* "pysam/libcvcf.pyx":558
20497 * elif key == "INFO":
20498 * f = self.parse_format(line, value)
20499 * self._info[ f.id ] = f # <<<<<<<<<<<<<<
20500 * elif key == "FILTER":
20501 * f = self.parse_format(line, value, filter=True)
20502 */
20503 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_info); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 558, __pyx_L1_error)
20504 __Pyx_GOTREF(__pyx_t_1);
20505 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_id_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 558, __pyx_L1_error)
20506 __Pyx_GOTREF(__pyx_t_2);
20507 if (unlikely((PyObject_SetItem(__pyx_t_1, __pyx_t_2, __pyx_v_f) < 0))) __PYX_ERR(0, 558, __pyx_L1_error)
20508 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
20509 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
20510
20511 /* "pysam/libcvcf.pyx":556
20512 * else:
20513 * self.error(line,self.UNKNOWN_FORMAT_STRING)
20514 * elif key == "INFO": # <<<<<<<<<<<<<<
20515 * f = self.parse_format(line, value)
20516 * self._info[ f.id ] = f
20517 */
20518 goto __pyx_L3;
20519 }
20520
20521 /* "pysam/libcvcf.pyx":559
20522 * f = self.parse_format(line, value)
20523 * self._info[ f.id ] = f
20524 * elif key == "FILTER": # <<<<<<<<<<<<<<
20525 * f = self.parse_format(line, value, filter=True)
20526 * self._filter[ f.id ] = f
20527 */
20528 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_v_key, __pyx_n_u_FILTER, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 559, __pyx_L1_error)
20529 if (__pyx_t_5) {
20530
20531 /* "pysam/libcvcf.pyx":560
20532 * self._info[ f.id ] = f
20533 * elif key == "FILTER":
20534 * f = self.parse_format(line, value, filter=True) # <<<<<<<<<<<<<<
20535 * self._filter[ f.id ] = f
20536 * elif key == "FORMAT":
20537 */
20538 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parse_format); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 560, __pyx_L1_error)
20539 __Pyx_GOTREF(__pyx_t_2);
20540 __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 560, __pyx_L1_error)
20541 __Pyx_GOTREF(__pyx_t_1);
20542 __Pyx_INCREF(__pyx_v_line);
20543 __Pyx_GIVEREF(__pyx_v_line);
20544 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_line)) __PYX_ERR(0, 560, __pyx_L1_error);
20545 __Pyx_INCREF(__pyx_v_value);
20546 __Pyx_GIVEREF(__pyx_v_value);
20547 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_value)) __PYX_ERR(0, 560, __pyx_L1_error);
20548 __pyx_t_3 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 560, __pyx_L1_error)
20549 __Pyx_GOTREF(__pyx_t_3);
20550 if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_filter_2, Py_True) < 0) __PYX_ERR(0, 560, __pyx_L1_error)
20551 __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_1, __pyx_t_3); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 560, __pyx_L1_error)
20552 __Pyx_GOTREF(__pyx_t_6);
20553 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
20554 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
20555 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
20556 __pyx_v_f = __pyx_t_6;
20557 __pyx_t_6 = 0;
20558
20559 /* "pysam/libcvcf.pyx":561
20560 * elif key == "FILTER":
20561 * f = self.parse_format(line, value, filter=True)
20562 * self._filter[ f.id ] = f # <<<<<<<<<<<<<<
20563 * elif key == "FORMAT":
20564 * f = self.parse_format(line, value)
20565 */
20566 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_filter); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 561, __pyx_L1_error)
20567 __Pyx_GOTREF(__pyx_t_6);
20568 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_id_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 561, __pyx_L1_error)
20569 __Pyx_GOTREF(__pyx_t_3);
20570 if (unlikely((PyObject_SetItem(__pyx_t_6, __pyx_t_3, __pyx_v_f) < 0))) __PYX_ERR(0, 561, __pyx_L1_error)
20571 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
20572 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
20573
20574 /* "pysam/libcvcf.pyx":559
20575 * f = self.parse_format(line, value)
20576 * self._info[ f.id ] = f
20577 * elif key == "FILTER": # <<<<<<<<<<<<<<
20578 * f = self.parse_format(line, value, filter=True)
20579 * self._filter[ f.id ] = f
20580 */
20581 goto __pyx_L3;
20582 }
20583
20584 /* "pysam/libcvcf.pyx":562
20585 * f = self.parse_format(line, value, filter=True)
20586 * self._filter[ f.id ] = f
20587 * elif key == "FORMAT": # <<<<<<<<<<<<<<
20588 * f = self.parse_format(line, value)
20589 * self._format[ f.id ] = f
20590 */
20591 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_v_key, __pyx_n_u_FORMAT, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 562, __pyx_L1_error)
20592 if (__pyx_t_5) {
20593
20594 /* "pysam/libcvcf.pyx":563
20595 * self._filter[ f.id ] = f
20596 * elif key == "FORMAT":
20597 * f = self.parse_format(line, value) # <<<<<<<<<<<<<<
20598 * self._format[ f.id ] = f
20599 * else:
20600 */
20601 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parse_format); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 563, __pyx_L1_error)
20602 __Pyx_GOTREF(__pyx_t_6);
20603 __pyx_t_1 = NULL;
20604 __pyx_t_4 = 0;
20605 #if CYTHON_UNPACK_METHODS
20606 if (likely(PyMethod_Check(__pyx_t_6))) {
20607 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_6);
20608 if (likely(__pyx_t_1)) {
20609 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
20610 __Pyx_INCREF(__pyx_t_1);
20611 __Pyx_INCREF(function);
20612 __Pyx_DECREF_SET(__pyx_t_6, function);
20613 __pyx_t_4 = 1;
20614 }
20615 }
20616 #endif
20617 {
20618 PyObject *__pyx_callargs[3] = {__pyx_t_1, __pyx_v_line, __pyx_v_value};
20619 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
20620 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
20621 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 563, __pyx_L1_error)
20622 __Pyx_GOTREF(__pyx_t_3);
20623 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
20624 }
20625 __pyx_v_f = __pyx_t_3;
20626 __pyx_t_3 = 0;
20627
20628 /* "pysam/libcvcf.pyx":564
20629 * elif key == "FORMAT":
20630 * f = self.parse_format(line, value)
20631 * self._format[ f.id ] = f # <<<<<<<<<<<<<<
20632 * else:
20633 * # keep other keys in the header field
20634 */
20635 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 564, __pyx_L1_error)
20636 __Pyx_GOTREF(__pyx_t_3);
20637 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_id_2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 564, __pyx_L1_error)
20638 __Pyx_GOTREF(__pyx_t_6);
20639 if (unlikely((PyObject_SetItem(__pyx_t_3, __pyx_t_6, __pyx_v_f) < 0))) __PYX_ERR(0, 564, __pyx_L1_error)
20640 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
20641 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
20642
20643 /* "pysam/libcvcf.pyx":562
20644 * f = self.parse_format(line, value, filter=True)
20645 * self._filter[ f.id ] = f
20646 * elif key == "FORMAT": # <<<<<<<<<<<<<<
20647 * f = self.parse_format(line, value)
20648 * self._format[ f.id ] = f
20649 */
20650 goto __pyx_L3;
20651 }
20652
20653 /* "pysam/libcvcf.pyx":567
20654 * else:
20655 * # keep other keys in the header field
20656 * self._header.append( (key,value) ) # <<<<<<<<<<<<<<
20657 *
20658 *
20659 */
20660 /*else*/ {
20661 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_header); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 567, __pyx_L1_error)
20662 __Pyx_GOTREF(__pyx_t_6);
20663 __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 567, __pyx_L1_error)
20664 __Pyx_GOTREF(__pyx_t_3);
20665 __Pyx_INCREF(__pyx_v_key);
20666 __Pyx_GIVEREF(__pyx_v_key);
20667 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_key)) __PYX_ERR(0, 567, __pyx_L1_error);
20668 __Pyx_INCREF(__pyx_v_value);
20669 __Pyx_GIVEREF(__pyx_v_value);
20670 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_value)) __PYX_ERR(0, 567, __pyx_L1_error);
20671 __pyx_t_7 = __Pyx_PyObject_Append(__pyx_t_6, __pyx_t_3); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 567, __pyx_L1_error)
20672 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
20673 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
20674 }
20675 __pyx_L3:;
20676
20677 /* "pysam/libcvcf.pyx":537
20678 * self._format[f.id] = f
20679 *
20680 * def parse_header(self, line): # <<<<<<<<<<<<<<
20681 *
20682 * assert line.startswith('##')
20683 */
20684
20685 /* function exit code */
20686 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
20687 goto __pyx_L0;
20688 __pyx_L1_error:;
20689 __Pyx_XDECREF(__pyx_t_1);
20690 __Pyx_XDECREF(__pyx_t_2);
20691 __Pyx_XDECREF(__pyx_t_3);
20692 __Pyx_XDECREF(__pyx_t_6);
20693 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename);
20694 __pyx_r = NULL;
20695 __pyx_L0:;
20696 __Pyx_XDECREF(__pyx_v_elts);
20697 __Pyx_XDECREF(__pyx_v_key);
20698 __Pyx_XDECREF(__pyx_v_value);
20699 __Pyx_XDECREF(__pyx_v_f);
20700 __Pyx_XGIVEREF(__pyx_r);
20701 __Pyx_RefNannyFinishContext();
20702 return __pyx_r;
20703 }
20704
20705 /* "pysam/libcvcf.pyx":570
20706 *
20707 *
20708 * def write_header( self, stream ): # <<<<<<<<<<<<<<
20709 * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
20710 * for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
20711 */
20712
20713 /* Python wrapper */
20714 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_19write_header(PyObject *__pyx_self,
20715 #if CYTHON_METH_FASTCALL
20716 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
20717 #else
20718 PyObject *__pyx_args, PyObject *__pyx_kwds
20719 #endif
20720 ); /*proto*/
20721 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_18write_header, "VCF.write_header(self, stream)");
20722 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_19write_header = {"write_header", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_19write_header, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_18write_header};
20723 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_19write_header(PyObject *__pyx_self,
20724 #if CYTHON_METH_FASTCALL
20725 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
20726 #else
20727 PyObject *__pyx_args, PyObject *__pyx_kwds
20728 #endif
20729 ) {
20730 PyObject *__pyx_v_self = 0;
20731 PyObject *__pyx_v_stream = 0;
20732 #if !CYTHON_METH_FASTCALL
20733 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
20734 #endif
20735 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
20736 PyObject* values[2] = {0,0};
20737 int __pyx_lineno = 0;
20738 const char *__pyx_filename = NULL;
20739 int __pyx_clineno = 0;
20740 PyObject *__pyx_r = 0;
20741 __Pyx_RefNannyDeclarations
20742 __Pyx_RefNannySetupContext("write_header (wrapper)", 0);
20743 #if !CYTHON_METH_FASTCALL
20744 #if CYTHON_ASSUME_SAFE_MACROS
20745 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
20746 #else
20747 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
20748 #endif
20749 #endif
20750 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
20751 {
20752 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_stream,0};
20753 if (__pyx_kwds) {
20754 Py_ssize_t kw_args;
20755 switch (__pyx_nargs) {
20756 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
20757 CYTHON_FALLTHROUGH;
20758 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
20759 CYTHON_FALLTHROUGH;
20760 case 0: break;
20761 default: goto __pyx_L5_argtuple_error;
20762 }
20763 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
20764 switch (__pyx_nargs) {
20765 case 0:
20766 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
20767 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
20768 kw_args--;
20769 }
20770 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 570, __pyx_L3_error)
20771 else goto __pyx_L5_argtuple_error;
20772 CYTHON_FALLTHROUGH;
20773 case 1:
20774 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_stream)) != 0)) {
20775 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
20776 kw_args--;
20777 }
20778 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 570, __pyx_L3_error)
20779 else {
20780 __Pyx_RaiseArgtupleInvalid("write_header", 1, 2, 2, 1); __PYX_ERR(0, 570, __pyx_L3_error)
20781 }
20782 }
20783 if (unlikely(kw_args > 0)) {
20784 const Py_ssize_t kwd_pos_args = __pyx_nargs;
20785 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "write_header") < 0)) __PYX_ERR(0, 570, __pyx_L3_error)
20786 }
20787 } else if (unlikely(__pyx_nargs != 2)) {
20788 goto __pyx_L5_argtuple_error;
20789 } else {
20790 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
20791 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
20792 }
20793 __pyx_v_self = values[0];
20794 __pyx_v_stream = values[1];
20795 }
20796 goto __pyx_L6_skip;
20797 __pyx_L5_argtuple_error:;
20798 __Pyx_RaiseArgtupleInvalid("write_header", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 570, __pyx_L3_error)
20799 __pyx_L6_skip:;
20800 goto __pyx_L4_argument_unpacking_done;
20801 __pyx_L3_error:;
20802 {
20803 Py_ssize_t __pyx_temp;
20804 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
20805 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
20806 }
20807 }
20808 __Pyx_AddTraceback("pysam.libcvcf.VCF.write_header", __pyx_clineno, __pyx_lineno, __pyx_filename);
20809 __Pyx_RefNannyFinishContext();
20810 return NULL;
20811 __pyx_L4_argument_unpacking_done:;
20812 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_18write_header(__pyx_self, __pyx_v_self, __pyx_v_stream);
20813
20814 /* function exit code */
20815 {
20816 Py_ssize_t __pyx_temp;
20817 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
20818 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
20819 }
20820 }
20821 __Pyx_RefNannyFinishContext();
20822 return __pyx_r;
20823 }
20824
20825 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) {
20826 PyObject *__pyx_v_key = NULL;
20827 PyObject *__pyx_v_value = NULL;
20828 PyObject *__pyx_v_var = NULL;
20829 PyObject *__pyx_v_label = NULL;
20830 PyObject *__pyx_v_f = NULL;
20831 PyObject *__pyx_r = NULL;
20832 __Pyx_RefNannyDeclarations
20833 PyObject *__pyx_t_1 = NULL;
20834 PyObject *__pyx_t_2 = NULL;
20835 PyObject *__pyx_t_3 = NULL;
20836 Py_ssize_t __pyx_t_4;
20837 Py_UCS4 __pyx_t_5;
20838 PyObject *__pyx_t_6 = NULL;
20839 PyObject *__pyx_t_7 = NULL;
20840 unsigned int __pyx_t_8;
20841 PyObject *(*__pyx_t_9)(PyObject *);
20842 PyObject *(*__pyx_t_10)(PyObject *);
20843 Py_ssize_t __pyx_t_11;
20844 Py_ssize_t __pyx_t_12;
20845 int __pyx_t_13;
20846 int __pyx_t_14;
20847 Py_ssize_t __pyx_t_15;
20848 PyObject *__pyx_t_16 = NULL;
20849 PyObject *__pyx_t_17 = NULL;
20850 PyObject *__pyx_t_18 = NULL;
20851 PyObject *__pyx_t_19 = NULL;
20852 int __pyx_lineno = 0;
20853 const char *__pyx_filename = NULL;
20854 int __pyx_clineno = 0;
20855 __Pyx_RefNannySetupContext("write_header", 1);
20856
20857 /* "pysam/libcvcf.pyx":571
20858 *
20859 * def write_header( self, stream ):
20860 * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10)) # <<<<<<<<<<<<<<
20861 * for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
20862 * for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]:
20863 */
20864 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_stream, __pyx_n_s_write); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 571, __pyx_L1_error)
20865 __Pyx_GOTREF(__pyx_t_2);
20866 __pyx_t_3 = PyTuple_New(5); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 571, __pyx_L1_error)
20867 __Pyx_GOTREF(__pyx_t_3);
20868 __pyx_t_4 = 0;
20869 __pyx_t_5 = 127;
20870 __Pyx_INCREF(__pyx_kp_u_fileformat_VCFv);
20871 __pyx_t_4 += 17;
20872 __Pyx_GIVEREF(__pyx_kp_u_fileformat_VCFv);
20873 PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_kp_u_fileformat_VCFv);
20874 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_version); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 571, __pyx_L1_error)
20875 __Pyx_GOTREF(__pyx_t_6);
20876 __pyx_t_7 = __Pyx_PyInt_FloorDivideObjC(__pyx_t_6, __pyx_int_10, 10, 0, 0); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 571, __pyx_L1_error)
20877 __Pyx_GOTREF(__pyx_t_7);
20878 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
20879 __pyx_t_6 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_7), __pyx_empty_unicode); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 571, __pyx_L1_error)
20880 __Pyx_GOTREF(__pyx_t_6);
20881 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
20882 __pyx_t_5 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_6) > __pyx_t_5) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_6) : __pyx_t_5;
20883 __pyx_t_4 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_6);
20884 __Pyx_GIVEREF(__pyx_t_6);
20885 PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_6);
20886 __pyx_t_6 = 0;
20887 __Pyx_INCREF(__pyx_kp_u__5);
20888 __pyx_t_4 += 1;
20889 __Pyx_GIVEREF(__pyx_kp_u__5);
20890 PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_kp_u__5);
20891 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_version); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 571, __pyx_L1_error)
20892 __Pyx_GOTREF(__pyx_t_6);
20893 __pyx_t_7 = __Pyx_PyInt_RemainderObjC(__pyx_t_6, __pyx_int_10, 10, 0, 0); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 571, __pyx_L1_error)
20894 __Pyx_GOTREF(__pyx_t_7);
20895 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
20896 __pyx_t_6 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_7), __pyx_empty_unicode); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 571, __pyx_L1_error)
20897 __Pyx_GOTREF(__pyx_t_6);
20898 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
20899 __pyx_t_5 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_6) > __pyx_t_5) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_6) : __pyx_t_5;
20900 __pyx_t_4 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_6);
20901 __Pyx_GIVEREF(__pyx_t_6);
20902 PyTuple_SET_ITEM(__pyx_t_3, 3, __pyx_t_6);
20903 __pyx_t_6 = 0;
20904 __Pyx_INCREF(__pyx_kp_u__14);
20905 __pyx_t_4 += 1;
20906 __Pyx_GIVEREF(__pyx_kp_u__14);
20907 PyTuple_SET_ITEM(__pyx_t_3, 4, __pyx_kp_u__14);
20908 __pyx_t_6 = __Pyx_PyUnicode_Join(__pyx_t_3, 5, __pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 571, __pyx_L1_error)
20909 __Pyx_GOTREF(__pyx_t_6);
20910 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
20911 __pyx_t_3 = NULL;
20912 __pyx_t_8 = 0;
20913 #if CYTHON_UNPACK_METHODS
20914 if (likely(PyMethod_Check(__pyx_t_2))) {
20915 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
20916 if (likely(__pyx_t_3)) {
20917 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
20918 __Pyx_INCREF(__pyx_t_3);
20919 __Pyx_INCREF(function);
20920 __Pyx_DECREF_SET(__pyx_t_2, function);
20921 __pyx_t_8 = 1;
20922 }
20923 }
20924 #endif
20925 {
20926 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_t_6};
20927 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
20928 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
20929 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
20930 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 571, __pyx_L1_error)
20931 __Pyx_GOTREF(__pyx_t_1);
20932 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
20933 }
20934 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
20935
20936 /* "pysam/libcvcf.pyx":572
20937 * def write_header( self, stream ):
20938 * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
20939 * for key,value in self._header: stream.write("##%s=%s\n" % (key,value)) # <<<<<<<<<<<<<<
20940 * for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]:
20941 * for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER"))))
20942 */
20943 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_header); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 572, __pyx_L1_error)
20944 __Pyx_GOTREF(__pyx_t_1);
20945 if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) {
20946 __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2);
20947 __pyx_t_4 = 0;
20948 __pyx_t_9 = NULL;
20949 } else {
20950 __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 572, __pyx_L1_error)
20951 __Pyx_GOTREF(__pyx_t_2);
20952 __pyx_t_9 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 572, __pyx_L1_error)
20953 }
20954 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
20955 for (;;) {
20956 if (likely(!__pyx_t_9)) {
20957 if (likely(PyList_CheckExact(__pyx_t_2))) {
20958 {
20959 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2);
20960 #if !CYTHON_ASSUME_SAFE_MACROS
20961 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 572, __pyx_L1_error)
20962 #endif
20963 if (__pyx_t_4 >= __pyx_temp) break;
20964 }
20965 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
20966 __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 572, __pyx_L1_error)
20967 #else
20968 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 572, __pyx_L1_error)
20969 __Pyx_GOTREF(__pyx_t_1);
20970 #endif
20971 } else {
20972 {
20973 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_2);
20974 #if !CYTHON_ASSUME_SAFE_MACROS
20975 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 572, __pyx_L1_error)
20976 #endif
20977 if (__pyx_t_4 >= __pyx_temp) break;
20978 }
20979 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
20980 __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 572, __pyx_L1_error)
20981 #else
20982 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 572, __pyx_L1_error)
20983 __Pyx_GOTREF(__pyx_t_1);
20984 #endif
20985 }
20986 } else {
20987 __pyx_t_1 = __pyx_t_9(__pyx_t_2);
20988 if (unlikely(!__pyx_t_1)) {
20989 PyObject* exc_type = PyErr_Occurred();
20990 if (exc_type) {
20991 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
20992 else __PYX_ERR(0, 572, __pyx_L1_error)
20993 }
20994 break;
20995 }
20996 __Pyx_GOTREF(__pyx_t_1);
20997 }
20998 if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
20999 PyObject* sequence = __pyx_t_1;
21000 Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
21001 if (unlikely(size != 2)) {
21002 if (size > 2) __Pyx_RaiseTooManyValuesError(2);
21003 else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
21004 __PYX_ERR(0, 572, __pyx_L1_error)
21005 }
21006 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
21007 if (likely(PyTuple_CheckExact(sequence))) {
21008 __pyx_t_6 = PyTuple_GET_ITEM(sequence, 0);
21009 __pyx_t_3 = PyTuple_GET_ITEM(sequence, 1);
21010 } else {
21011 __pyx_t_6 = PyList_GET_ITEM(sequence, 0);
21012 __pyx_t_3 = PyList_GET_ITEM(sequence, 1);
21013 }
21014 __Pyx_INCREF(__pyx_t_6);
21015 __Pyx_INCREF(__pyx_t_3);
21016 #else
21017 __pyx_t_6 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 572, __pyx_L1_error)
21018 __Pyx_GOTREF(__pyx_t_6);
21019 __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 572, __pyx_L1_error)
21020 __Pyx_GOTREF(__pyx_t_3);
21021 #endif
21022 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
21023 } else {
21024 Py_ssize_t index = -1;
21025 __pyx_t_7 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 572, __pyx_L1_error)
21026 __Pyx_GOTREF(__pyx_t_7);
21027 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
21028 __pyx_t_10 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_7);
21029 index = 0; __pyx_t_6 = __pyx_t_10(__pyx_t_7); if (unlikely(!__pyx_t_6)) goto __pyx_L5_unpacking_failed;
21030 __Pyx_GOTREF(__pyx_t_6);
21031 index = 1; __pyx_t_3 = __pyx_t_10(__pyx_t_7); if (unlikely(!__pyx_t_3)) goto __pyx_L5_unpacking_failed;
21032 __Pyx_GOTREF(__pyx_t_3);
21033 if (__Pyx_IternextUnpackEndCheck(__pyx_t_10(__pyx_t_7), 2) < 0) __PYX_ERR(0, 572, __pyx_L1_error)
21034 __pyx_t_10 = NULL;
21035 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
21036 goto __pyx_L6_unpacking_done;
21037 __pyx_L5_unpacking_failed:;
21038 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
21039 __pyx_t_10 = NULL;
21040 if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
21041 __PYX_ERR(0, 572, __pyx_L1_error)
21042 __pyx_L6_unpacking_done:;
21043 }
21044 __Pyx_XDECREF_SET(__pyx_v_key, __pyx_t_6);
21045 __pyx_t_6 = 0;
21046 __Pyx_XDECREF_SET(__pyx_v_value, __pyx_t_3);
21047 __pyx_t_3 = 0;
21048 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_stream, __pyx_n_s_write); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 572, __pyx_L1_error)
21049 __Pyx_GOTREF(__pyx_t_3);
21050 __pyx_t_6 = PyTuple_New(5); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 572, __pyx_L1_error)
21051 __Pyx_GOTREF(__pyx_t_6);
21052 __pyx_t_11 = 0;
21053 __pyx_t_5 = 127;
21054 __Pyx_INCREF(__pyx_kp_u__23);
21055 __pyx_t_11 += 2;
21056 __Pyx_GIVEREF(__pyx_kp_u__23);
21057 PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_kp_u__23);
21058 __pyx_t_7 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_key), __pyx_empty_unicode); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 572, __pyx_L1_error)
21059 __Pyx_GOTREF(__pyx_t_7);
21060 __pyx_t_5 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) > __pyx_t_5) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) : __pyx_t_5;
21061 __pyx_t_11 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_7);
21062 __Pyx_GIVEREF(__pyx_t_7);
21063 PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_7);
21064 __pyx_t_7 = 0;
21065 __Pyx_INCREF(__pyx_kp_u__7);
21066 __pyx_t_11 += 1;
21067 __Pyx_GIVEREF(__pyx_kp_u__7);
21068 PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_kp_u__7);
21069 __pyx_t_7 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_value), __pyx_empty_unicode); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 572, __pyx_L1_error)
21070 __Pyx_GOTREF(__pyx_t_7);
21071 __pyx_t_5 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) > __pyx_t_5) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) : __pyx_t_5;
21072 __pyx_t_11 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_7);
21073 __Pyx_GIVEREF(__pyx_t_7);
21074 PyTuple_SET_ITEM(__pyx_t_6, 3, __pyx_t_7);
21075 __pyx_t_7 = 0;
21076 __Pyx_INCREF(__pyx_kp_u__14);
21077 __pyx_t_11 += 1;
21078 __Pyx_GIVEREF(__pyx_kp_u__14);
21079 PyTuple_SET_ITEM(__pyx_t_6, 4, __pyx_kp_u__14);
21080 __pyx_t_7 = __Pyx_PyUnicode_Join(__pyx_t_6, 5, __pyx_t_11, __pyx_t_5); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 572, __pyx_L1_error)
21081 __Pyx_GOTREF(__pyx_t_7);
21082 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
21083 __pyx_t_6 = NULL;
21084 __pyx_t_8 = 0;
21085 #if CYTHON_UNPACK_METHODS
21086 if (likely(PyMethod_Check(__pyx_t_3))) {
21087 __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_3);
21088 if (likely(__pyx_t_6)) {
21089 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
21090 __Pyx_INCREF(__pyx_t_6);
21091 __Pyx_INCREF(function);
21092 __Pyx_DECREF_SET(__pyx_t_3, function);
21093 __pyx_t_8 = 1;
21094 }
21095 }
21096 #endif
21097 {
21098 PyObject *__pyx_callargs[2] = {__pyx_t_6, __pyx_t_7};
21099 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
21100 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
21101 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
21102 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 572, __pyx_L1_error)
21103 __Pyx_GOTREF(__pyx_t_1);
21104 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
21105 }
21106 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
21107 }
21108 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
21109
21110 /* "pysam/libcvcf.pyx":573
21111 * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
21112 * for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
21113 * for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]: # <<<<<<<<<<<<<<
21114 * for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER"))))
21115 *
21116 */
21117 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 573, __pyx_L1_error)
21118 __Pyx_GOTREF(__pyx_t_2);
21119 __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 573, __pyx_L1_error)
21120 __Pyx_GOTREF(__pyx_t_1);
21121 __Pyx_GIVEREF(__pyx_t_2);
21122 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2)) __PYX_ERR(0, 573, __pyx_L1_error);
21123 __Pyx_INCREF(__pyx_n_u_INFO);
21124 __Pyx_GIVEREF(__pyx_n_u_INFO);
21125 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_n_u_INFO)) __PYX_ERR(0, 573, __pyx_L1_error);
21126 __pyx_t_2 = 0;
21127 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_filter); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 573, __pyx_L1_error)
21128 __Pyx_GOTREF(__pyx_t_2);
21129 __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 573, __pyx_L1_error)
21130 __Pyx_GOTREF(__pyx_t_3);
21131 __Pyx_GIVEREF(__pyx_t_2);
21132 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2)) __PYX_ERR(0, 573, __pyx_L1_error);
21133 __Pyx_INCREF(__pyx_n_u_FILTER);
21134 __Pyx_GIVEREF(__pyx_n_u_FILTER);
21135 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_n_u_FILTER)) __PYX_ERR(0, 573, __pyx_L1_error);
21136 __pyx_t_2 = 0;
21137 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 573, __pyx_L1_error)
21138 __Pyx_GOTREF(__pyx_t_2);
21139 __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 573, __pyx_L1_error)
21140 __Pyx_GOTREF(__pyx_t_7);
21141 __Pyx_GIVEREF(__pyx_t_2);
21142 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2)) __PYX_ERR(0, 573, __pyx_L1_error);
21143 __Pyx_INCREF(__pyx_n_u_FORMAT);
21144 __Pyx_GIVEREF(__pyx_n_u_FORMAT);
21145 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_n_u_FORMAT)) __PYX_ERR(0, 573, __pyx_L1_error);
21146 __pyx_t_2 = 0;
21147 __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 573, __pyx_L1_error)
21148 __Pyx_GOTREF(__pyx_t_2);
21149 __Pyx_GIVEREF(__pyx_t_1);
21150 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1)) __PYX_ERR(0, 573, __pyx_L1_error);
21151 __Pyx_GIVEREF(__pyx_t_3);
21152 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_3)) __PYX_ERR(0, 573, __pyx_L1_error);
21153 __Pyx_GIVEREF(__pyx_t_7);
21154 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_7)) __PYX_ERR(0, 573, __pyx_L1_error);
21155 __pyx_t_1 = 0;
21156 __pyx_t_3 = 0;
21157 __pyx_t_7 = 0;
21158 __pyx_t_7 = __pyx_t_2; __Pyx_INCREF(__pyx_t_7);
21159 __pyx_t_4 = 0;
21160 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
21161 for (;;) {
21162 if (__pyx_t_4 >= 3) break;
21163 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
21164 __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_7, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 573, __pyx_L1_error)
21165 #else
21166 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_7, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 573, __pyx_L1_error)
21167 __Pyx_GOTREF(__pyx_t_2);
21168 #endif
21169 if (likely(__pyx_t_2 != Py_None)) {
21170 PyObject* sequence = __pyx_t_2;
21171 Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
21172 if (unlikely(size != 2)) {
21173 if (size > 2) __Pyx_RaiseTooManyValuesError(2);
21174 else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
21175 __PYX_ERR(0, 573, __pyx_L1_error)
21176 }
21177 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
21178 __pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
21179 __pyx_t_1 = PyTuple_GET_ITEM(sequence, 1);
21180 __Pyx_INCREF(__pyx_t_3);
21181 __Pyx_INCREF(__pyx_t_1);
21182 #else
21183 __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 573, __pyx_L1_error)
21184 __Pyx_GOTREF(__pyx_t_3);
21185 __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 573, __pyx_L1_error)
21186 __Pyx_GOTREF(__pyx_t_1);
21187 #endif
21188 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
21189 } else {
21190 __Pyx_RaiseNoneNotIterableError(); __PYX_ERR(0, 573, __pyx_L1_error)
21191 }
21192 __Pyx_XDECREF_SET(__pyx_v_var, __pyx_t_3);
21193 __pyx_t_3 = 0;
21194 __Pyx_XDECREF_SET(__pyx_v_label, __pyx_t_1);
21195 __pyx_t_1 = 0;
21196
21197 /* "pysam/libcvcf.pyx":574
21198 * for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
21199 * for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]:
21200 * for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER")))) # <<<<<<<<<<<<<<
21201 *
21202 *
21203 */
21204 __pyx_t_11 = 0;
21205 if (unlikely(__pyx_v_var == Py_None)) {
21206 PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%.30s'", "itervalues");
21207 __PYX_ERR(0, 574, __pyx_L1_error)
21208 }
21209 __pyx_t_1 = __Pyx_dict_iterator(__pyx_v_var, 0, __pyx_n_s_itervalues, (&__pyx_t_12), (&__pyx_t_13)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 574, __pyx_L1_error)
21210 __Pyx_GOTREF(__pyx_t_1);
21211 __Pyx_XDECREF(__pyx_t_2);
21212 __pyx_t_2 = __pyx_t_1;
21213 __pyx_t_1 = 0;
21214 while (1) {
21215 __pyx_t_14 = __Pyx_dict_iter_next(__pyx_t_2, __pyx_t_12, &__pyx_t_11, NULL, &__pyx_t_1, NULL, __pyx_t_13);
21216 if (unlikely(__pyx_t_14 == 0)) break;
21217 if (unlikely(__pyx_t_14 == -1)) __PYX_ERR(0, 574, __pyx_L1_error)
21218 __Pyx_GOTREF(__pyx_t_1);
21219 __Pyx_XDECREF_SET(__pyx_v_f, __pyx_t_1);
21220 __pyx_t_1 = 0;
21221 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_stream, __pyx_n_s_write); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 574, __pyx_L1_error)
21222 __Pyx_GOTREF(__pyx_t_3);
21223 __pyx_t_6 = PyTuple_New(5); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 574, __pyx_L1_error)
21224 __Pyx_GOTREF(__pyx_t_6);
21225 __pyx_t_15 = 0;
21226 __pyx_t_5 = 127;
21227 __Pyx_INCREF(__pyx_kp_u__23);
21228 __pyx_t_15 += 2;
21229 __Pyx_GIVEREF(__pyx_kp_u__23);
21230 PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_kp_u__23);
21231 __pyx_t_16 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_label), __pyx_empty_unicode); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 574, __pyx_L1_error)
21232 __Pyx_GOTREF(__pyx_t_16);
21233 __pyx_t_5 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_16) > __pyx_t_5) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_16) : __pyx_t_5;
21234 __pyx_t_15 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_16);
21235 __Pyx_GIVEREF(__pyx_t_16);
21236 PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_16);
21237 __pyx_t_16 = 0;
21238 __Pyx_INCREF(__pyx_kp_u__7);
21239 __pyx_t_15 += 1;
21240 __Pyx_GIVEREF(__pyx_kp_u__7);
21241 PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_kp_u__7);
21242 __pyx_t_16 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_format); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 574, __pyx_L1_error)
21243 __Pyx_GOTREF(__pyx_t_16);
21244 __pyx_t_17 = PyTuple_New(1); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 574, __pyx_L1_error)
21245 __Pyx_GOTREF(__pyx_t_17);
21246 __Pyx_INCREF(__pyx_v_f);
21247 __Pyx_GIVEREF(__pyx_v_f);
21248 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_17, 0, __pyx_v_f)) __PYX_ERR(0, 574, __pyx_L1_error);
21249 __pyx_t_18 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 574, __pyx_L1_error)
21250 __Pyx_GOTREF(__pyx_t_18);
21251 __pyx_t_19 = PyObject_RichCompare(__pyx_v_label, __pyx_n_u_FILTER, Py_EQ); __Pyx_XGOTREF(__pyx_t_19); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 574, __pyx_L1_error)
21252 if (PyDict_SetItem(__pyx_t_18, __pyx_n_s_filter_2, __pyx_t_19) < 0) __PYX_ERR(0, 574, __pyx_L1_error)
21253 __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
21254 __pyx_t_19 = __Pyx_PyObject_Call(__pyx_t_16, __pyx_t_17, __pyx_t_18); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 574, __pyx_L1_error)
21255 __Pyx_GOTREF(__pyx_t_19);
21256 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
21257 __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
21258 __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
21259 __pyx_t_18 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_19), __pyx_empty_unicode); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 574, __pyx_L1_error)
21260 __Pyx_GOTREF(__pyx_t_18);
21261 __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
21262 __pyx_t_5 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_18) > __pyx_t_5) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_18) : __pyx_t_5;
21263 __pyx_t_15 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_18);
21264 __Pyx_GIVEREF(__pyx_t_18);
21265 PyTuple_SET_ITEM(__pyx_t_6, 3, __pyx_t_18);
21266 __pyx_t_18 = 0;
21267 __Pyx_INCREF(__pyx_kp_u__14);
21268 __pyx_t_15 += 1;
21269 __Pyx_GIVEREF(__pyx_kp_u__14);
21270 PyTuple_SET_ITEM(__pyx_t_6, 4, __pyx_kp_u__14);
21271 __pyx_t_18 = __Pyx_PyUnicode_Join(__pyx_t_6, 5, __pyx_t_15, __pyx_t_5); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 574, __pyx_L1_error)
21272 __Pyx_GOTREF(__pyx_t_18);
21273 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
21274 __pyx_t_6 = NULL;
21275 __pyx_t_8 = 0;
21276 #if CYTHON_UNPACK_METHODS
21277 if (likely(PyMethod_Check(__pyx_t_3))) {
21278 __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_3);
21279 if (likely(__pyx_t_6)) {
21280 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
21281 __Pyx_INCREF(__pyx_t_6);
21282 __Pyx_INCREF(function);
21283 __Pyx_DECREF_SET(__pyx_t_3, function);
21284 __pyx_t_8 = 1;
21285 }
21286 }
21287 #endif
21288 {
21289 PyObject *__pyx_callargs[2] = {__pyx_t_6, __pyx_t_18};
21290 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
21291 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
21292 __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
21293 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 574, __pyx_L1_error)
21294 __Pyx_GOTREF(__pyx_t_1);
21295 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
21296 }
21297 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
21298 }
21299 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
21300
21301 /* "pysam/libcvcf.pyx":573
21302 * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
21303 * for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
21304 * for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]: # <<<<<<<<<<<<<<
21305 * for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER"))))
21306 *
21307 */
21308 }
21309 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
21310
21311 /* "pysam/libcvcf.pyx":570
21312 *
21313 *
21314 * def write_header( self, stream ): # <<<<<<<<<<<<<<
21315 * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
21316 * for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
21317 */
21318
21319 /* function exit code */
21320 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
21321 goto __pyx_L0;
21322 __pyx_L1_error:;
21323 __Pyx_XDECREF(__pyx_t_1);
21324 __Pyx_XDECREF(__pyx_t_2);
21325 __Pyx_XDECREF(__pyx_t_3);
21326 __Pyx_XDECREF(__pyx_t_6);
21327 __Pyx_XDECREF(__pyx_t_7);
21328 __Pyx_XDECREF(__pyx_t_16);
21329 __Pyx_XDECREF(__pyx_t_17);
21330 __Pyx_XDECREF(__pyx_t_18);
21331 __Pyx_XDECREF(__pyx_t_19);
21332 __Pyx_AddTraceback("pysam.libcvcf.VCF.write_header", __pyx_clineno, __pyx_lineno, __pyx_filename);
21333 __pyx_r = NULL;
21334 __pyx_L0:;
21335 __Pyx_XDECREF(__pyx_v_key);
21336 __Pyx_XDECREF(__pyx_v_value);
21337 __Pyx_XDECREF(__pyx_v_var);
21338 __Pyx_XDECREF(__pyx_v_label);
21339 __Pyx_XDECREF(__pyx_v_f);
21340 __Pyx_XGIVEREF(__pyx_r);
21341 __Pyx_RefNannyFinishContext();
21342 return __pyx_r;
21343 }
21344
21345 /* "pysam/libcvcf.pyx":577
21346 *
21347 *
21348 * def parse_heading( self, line ): # <<<<<<<<<<<<<<
21349 * assert line.startswith('#')
21350 * assert not line.startswith('##')
21351 */
21352
21353 /* Python wrapper */
21354 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_21parse_heading(PyObject *__pyx_self,
21355 #if CYTHON_METH_FASTCALL
21356 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
21357 #else
21358 PyObject *__pyx_args, PyObject *__pyx_kwds
21359 #endif
21360 ); /*proto*/
21361 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_20parse_heading, "VCF.parse_heading(self, line)");
21362 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_21parse_heading = {"parse_heading", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_21parse_heading, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_20parse_heading};
21363 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_21parse_heading(PyObject *__pyx_self,
21364 #if CYTHON_METH_FASTCALL
21365 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
21366 #else
21367 PyObject *__pyx_args, PyObject *__pyx_kwds
21368 #endif
21369 ) {
21370 PyObject *__pyx_v_self = 0;
21371 PyObject *__pyx_v_line = 0;
21372 #if !CYTHON_METH_FASTCALL
21373 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
21374 #endif
21375 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
21376 PyObject* values[2] = {0,0};
21377 int __pyx_lineno = 0;
21378 const char *__pyx_filename = NULL;
21379 int __pyx_clineno = 0;
21380 PyObject *__pyx_r = 0;
21381 __Pyx_RefNannyDeclarations
21382 __Pyx_RefNannySetupContext("parse_heading (wrapper)", 0);
21383 #if !CYTHON_METH_FASTCALL
21384 #if CYTHON_ASSUME_SAFE_MACROS
21385 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
21386 #else
21387 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
21388 #endif
21389 #endif
21390 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
21391 {
21392 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_line,0};
21393 if (__pyx_kwds) {
21394 Py_ssize_t kw_args;
21395 switch (__pyx_nargs) {
21396 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
21397 CYTHON_FALLTHROUGH;
21398 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
21399 CYTHON_FALLTHROUGH;
21400 case 0: break;
21401 default: goto __pyx_L5_argtuple_error;
21402 }
21403 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
21404 switch (__pyx_nargs) {
21405 case 0:
21406 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
21407 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
21408 kw_args--;
21409 }
21410 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 577, __pyx_L3_error)
21411 else goto __pyx_L5_argtuple_error;
21412 CYTHON_FALLTHROUGH;
21413 case 1:
21414 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_line)) != 0)) {
21415 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
21416 kw_args--;
21417 }
21418 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 577, __pyx_L3_error)
21419 else {
21420 __Pyx_RaiseArgtupleInvalid("parse_heading", 1, 2, 2, 1); __PYX_ERR(0, 577, __pyx_L3_error)
21421 }
21422 }
21423 if (unlikely(kw_args > 0)) {
21424 const Py_ssize_t kwd_pos_args = __pyx_nargs;
21425 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "parse_heading") < 0)) __PYX_ERR(0, 577, __pyx_L3_error)
21426 }
21427 } else if (unlikely(__pyx_nargs != 2)) {
21428 goto __pyx_L5_argtuple_error;
21429 } else {
21430 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
21431 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
21432 }
21433 __pyx_v_self = values[0];
21434 __pyx_v_line = values[1];
21435 }
21436 goto __pyx_L6_skip;
21437 __pyx_L5_argtuple_error:;
21438 __Pyx_RaiseArgtupleInvalid("parse_heading", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 577, __pyx_L3_error)
21439 __pyx_L6_skip:;
21440 goto __pyx_L4_argument_unpacking_done;
21441 __pyx_L3_error:;
21442 {
21443 Py_ssize_t __pyx_temp;
21444 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
21445 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
21446 }
21447 }
21448 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_heading", __pyx_clineno, __pyx_lineno, __pyx_filename);
21449 __Pyx_RefNannyFinishContext();
21450 return NULL;
21451 __pyx_L4_argument_unpacking_done:;
21452 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_20parse_heading(__pyx_self, __pyx_v_self, __pyx_v_line);
21453
21454 /* function exit code */
21455 {
21456 Py_ssize_t __pyx_temp;
21457 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
21458 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
21459 }
21460 }
21461 __Pyx_RefNannyFinishContext();
21462 return __pyx_r;
21463 }
21464
21465 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line) {
21466 PyObject *__pyx_v_headings = NULL;
21467 PyObject *__pyx_v_i = NULL;
21468 PyObject *__pyx_v_s = NULL;
21469 PyObject *__pyx_v_err = NULL;
21470 PyObject *__pyx_8genexpr2__pyx_v_x = NULL;
21471 PyObject *__pyx_8genexpr2__pyx_v_y = NULL;
21472 PyObject *__pyx_r = NULL;
21473 __Pyx_RefNannyDeclarations
21474 PyObject *__pyx_t_1 = NULL;
21475 PyObject *__pyx_t_2 = NULL;
21476 PyObject *__pyx_t_3 = NULL;
21477 unsigned int __pyx_t_4;
21478 int __pyx_t_5;
21479 int __pyx_t_6;
21480 Py_ssize_t __pyx_t_7;
21481 PyObject *__pyx_t_8 = NULL;
21482 PyObject *(*__pyx_t_9)(PyObject *);
21483 Py_ssize_t __pyx_t_10;
21484 Py_UCS4 __pyx_t_11;
21485 PyObject *__pyx_t_12 = NULL;
21486 int __pyx_t_13;
21487 PyObject *__pyx_t_14 = NULL;
21488 int __pyx_lineno = 0;
21489 const char *__pyx_filename = NULL;
21490 int __pyx_clineno = 0;
21491 __Pyx_RefNannySetupContext("parse_heading", 1);
21492
21493 /* "pysam/libcvcf.pyx":578
21494 *
21495 * def parse_heading( self, line ):
21496 * assert line.startswith('#') # <<<<<<<<<<<<<<
21497 * assert not line.startswith('##')
21498 * headings = line[1:].split('\t')
21499 */
21500 #ifndef CYTHON_WITHOUT_ASSERTIONS
21501 if (unlikely(__pyx_assertions_enabled())) {
21502 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_startswith); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 578, __pyx_L1_error)
21503 __Pyx_GOTREF(__pyx_t_2);
21504 __pyx_t_3 = NULL;
21505 __pyx_t_4 = 0;
21506 #if CYTHON_UNPACK_METHODS
21507 if (likely(PyMethod_Check(__pyx_t_2))) {
21508 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
21509 if (likely(__pyx_t_3)) {
21510 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
21511 __Pyx_INCREF(__pyx_t_3);
21512 __Pyx_INCREF(function);
21513 __Pyx_DECREF_SET(__pyx_t_2, function);
21514 __pyx_t_4 = 1;
21515 }
21516 }
21517 #endif
21518 {
21519 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_kp_u__24};
21520 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
21521 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
21522 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 578, __pyx_L1_error)
21523 __Pyx_GOTREF(__pyx_t_1);
21524 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
21525 }
21526 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 578, __pyx_L1_error)
21527 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
21528 if (unlikely(!__pyx_t_5)) {
21529 __Pyx_Raise(__pyx_builtin_AssertionError, 0, 0, 0);
21530 __PYX_ERR(0, 578, __pyx_L1_error)
21531 }
21532 }
21533 #else
21534 if ((1)); else __PYX_ERR(0, 578, __pyx_L1_error)
21535 #endif
21536
21537 /* "pysam/libcvcf.pyx":579
21538 * def parse_heading( self, line ):
21539 * assert line.startswith('#')
21540 * assert not line.startswith('##') # <<<<<<<<<<<<<<
21541 * headings = line[1:].split('\t')
21542 * # test for 8, as FORMAT field might be missing
21543 */
21544 #ifndef CYTHON_WITHOUT_ASSERTIONS
21545 if (unlikely(__pyx_assertions_enabled())) {
21546 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_startswith); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 579, __pyx_L1_error)
21547 __Pyx_GOTREF(__pyx_t_2);
21548 __pyx_t_3 = NULL;
21549 __pyx_t_4 = 0;
21550 #if CYTHON_UNPACK_METHODS
21551 if (likely(PyMethod_Check(__pyx_t_2))) {
21552 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
21553 if (likely(__pyx_t_3)) {
21554 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
21555 __Pyx_INCREF(__pyx_t_3);
21556 __Pyx_INCREF(function);
21557 __Pyx_DECREF_SET(__pyx_t_2, function);
21558 __pyx_t_4 = 1;
21559 }
21560 }
21561 #endif
21562 {
21563 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_kp_u__23};
21564 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
21565 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
21566 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 579, __pyx_L1_error)
21567 __Pyx_GOTREF(__pyx_t_1);
21568 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
21569 }
21570 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 579, __pyx_L1_error)
21571 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
21572 __pyx_t_6 = (!__pyx_t_5);
21573 if (unlikely(!__pyx_t_6)) {
21574 __Pyx_Raise(__pyx_builtin_AssertionError, 0, 0, 0);
21575 __PYX_ERR(0, 579, __pyx_L1_error)
21576 }
21577 }
21578 #else
21579 if ((1)); else __PYX_ERR(0, 579, __pyx_L1_error)
21580 #endif
21581
21582 /* "pysam/libcvcf.pyx":580
21583 * assert line.startswith('#')
21584 * assert not line.startswith('##')
21585 * headings = line[1:].split('\t') # <<<<<<<<<<<<<<
21586 * # test for 8, as FORMAT field might be missing
21587 * if len(headings)==1 and len(line[1:].split()) >= 8:
21588 */
21589 __pyx_t_2 = __Pyx_PyObject_GetSlice(__pyx_v_line, 1, 0, NULL, NULL, &__pyx_slice__18, 1, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 580, __pyx_L1_error)
21590 __Pyx_GOTREF(__pyx_t_2);
21591 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_split); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 580, __pyx_L1_error)
21592 __Pyx_GOTREF(__pyx_t_3);
21593 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
21594 __pyx_t_2 = NULL;
21595 __pyx_t_4 = 0;
21596 #if CYTHON_UNPACK_METHODS
21597 if (likely(PyMethod_Check(__pyx_t_3))) {
21598 __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_3);
21599 if (likely(__pyx_t_2)) {
21600 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
21601 __Pyx_INCREF(__pyx_t_2);
21602 __Pyx_INCREF(function);
21603 __Pyx_DECREF_SET(__pyx_t_3, function);
21604 __pyx_t_4 = 1;
21605 }
21606 }
21607 #endif
21608 {
21609 PyObject *__pyx_callargs[2] = {__pyx_t_2, __pyx_kp_u__25};
21610 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
21611 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
21612 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 580, __pyx_L1_error)
21613 __Pyx_GOTREF(__pyx_t_1);
21614 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
21615 }
21616 __pyx_v_headings = __pyx_t_1;
21617 __pyx_t_1 = 0;
21618
21619 /* "pysam/libcvcf.pyx":582
21620 * headings = line[1:].split('\t')
21621 * # test for 8, as FORMAT field might be missing
21622 * if len(headings)==1 and len(line[1:].split()) >= 8: # <<<<<<<<<<<<<<
21623 * self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS)
21624 * headings = line[1:].split()
21625 */
21626 __pyx_t_7 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_7 == ((Py_ssize_t)-1))) __PYX_ERR(0, 582, __pyx_L1_error)
21627 __pyx_t_5 = (__pyx_t_7 == 1);
21628 if (__pyx_t_5) {
21629 } else {
21630 __pyx_t_6 = __pyx_t_5;
21631 goto __pyx_L4_bool_binop_done;
21632 }
21633 __pyx_t_3 = __Pyx_PyObject_GetSlice(__pyx_v_line, 1, 0, NULL, NULL, &__pyx_slice__18, 1, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 582, __pyx_L1_error)
21634 __Pyx_GOTREF(__pyx_t_3);
21635 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_split); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 582, __pyx_L1_error)
21636 __Pyx_GOTREF(__pyx_t_2);
21637 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
21638 __pyx_t_3 = NULL;
21639 __pyx_t_4 = 0;
21640 #if CYTHON_UNPACK_METHODS
21641 if (likely(PyMethod_Check(__pyx_t_2))) {
21642 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
21643 if (likely(__pyx_t_3)) {
21644 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
21645 __Pyx_INCREF(__pyx_t_3);
21646 __Pyx_INCREF(function);
21647 __Pyx_DECREF_SET(__pyx_t_2, function);
21648 __pyx_t_4 = 1;
21649 }
21650 }
21651 #endif
21652 {
21653 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
21654 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
21655 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
21656 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 582, __pyx_L1_error)
21657 __Pyx_GOTREF(__pyx_t_1);
21658 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
21659 }
21660 __pyx_t_7 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_7 == ((Py_ssize_t)-1))) __PYX_ERR(0, 582, __pyx_L1_error)
21661 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
21662 __pyx_t_5 = (__pyx_t_7 >= 8);
21663 __pyx_t_6 = __pyx_t_5;
21664 __pyx_L4_bool_binop_done:;
21665 if (__pyx_t_6) {
21666
21667 /* "pysam/libcvcf.pyx":583
21668 * # test for 8, as FORMAT field might be missing
21669 * if len(headings)==1 and len(line[1:].split()) >= 8:
21670 * self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS) # <<<<<<<<<<<<<<
21671 * headings = line[1:].split()
21672 *
21673 */
21674 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 583, __pyx_L1_error)
21675 __Pyx_GOTREF(__pyx_t_2);
21676 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_HEADING_NOT_SEPARATED_BY_TABS); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 583, __pyx_L1_error)
21677 __Pyx_GOTREF(__pyx_t_3);
21678 __pyx_t_8 = NULL;
21679 __pyx_t_4 = 0;
21680 #if CYTHON_UNPACK_METHODS
21681 if (likely(PyMethod_Check(__pyx_t_2))) {
21682 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_2);
21683 if (likely(__pyx_t_8)) {
21684 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
21685 __Pyx_INCREF(__pyx_t_8);
21686 __Pyx_INCREF(function);
21687 __Pyx_DECREF_SET(__pyx_t_2, function);
21688 __pyx_t_4 = 1;
21689 }
21690 }
21691 #endif
21692 {
21693 PyObject *__pyx_callargs[3] = {__pyx_t_8, __pyx_v_line, __pyx_t_3};
21694 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
21695 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
21696 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
21697 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 583, __pyx_L1_error)
21698 __Pyx_GOTREF(__pyx_t_1);
21699 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
21700 }
21701 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
21702
21703 /* "pysam/libcvcf.pyx":584
21704 * if len(headings)==1 and len(line[1:].split()) >= 8:
21705 * self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS)
21706 * headings = line[1:].split() # <<<<<<<<<<<<<<
21707 *
21708 * for i,s in enumerate(self._required):
21709 */
21710 __pyx_t_2 = __Pyx_PyObject_GetSlice(__pyx_v_line, 1, 0, NULL, NULL, &__pyx_slice__18, 1, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 584, __pyx_L1_error)
21711 __Pyx_GOTREF(__pyx_t_2);
21712 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_split); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 584, __pyx_L1_error)
21713 __Pyx_GOTREF(__pyx_t_3);
21714 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
21715 __pyx_t_2 = NULL;
21716 __pyx_t_4 = 0;
21717 #if CYTHON_UNPACK_METHODS
21718 if (likely(PyMethod_Check(__pyx_t_3))) {
21719 __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_3);
21720 if (likely(__pyx_t_2)) {
21721 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
21722 __Pyx_INCREF(__pyx_t_2);
21723 __Pyx_INCREF(function);
21724 __Pyx_DECREF_SET(__pyx_t_3, function);
21725 __pyx_t_4 = 1;
21726 }
21727 }
21728 #endif
21729 {
21730 PyObject *__pyx_callargs[2] = {__pyx_t_2, NULL};
21731 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
21732 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
21733 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 584, __pyx_L1_error)
21734 __Pyx_GOTREF(__pyx_t_1);
21735 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
21736 }
21737 __Pyx_DECREF_SET(__pyx_v_headings, __pyx_t_1);
21738 __pyx_t_1 = 0;
21739
21740 /* "pysam/libcvcf.pyx":582
21741 * headings = line[1:].split('\t')
21742 * # test for 8, as FORMAT field might be missing
21743 * if len(headings)==1 and len(line[1:].split()) >= 8: # <<<<<<<<<<<<<<
21744 * self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS)
21745 * headings = line[1:].split()
21746 */
21747 }
21748
21749 /* "pysam/libcvcf.pyx":586
21750 * headings = line[1:].split()
21751 *
21752 * for i,s in enumerate(self._required): # <<<<<<<<<<<<<<
21753 *
21754 * if len(headings)<=i or headings[i] != s:
21755 */
21756 __Pyx_INCREF(__pyx_int_0);
21757 __pyx_t_1 = __pyx_int_0;
21758 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_required); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 586, __pyx_L1_error)
21759 __Pyx_GOTREF(__pyx_t_3);
21760 if (likely(PyList_CheckExact(__pyx_t_3)) || PyTuple_CheckExact(__pyx_t_3)) {
21761 __pyx_t_2 = __pyx_t_3; __Pyx_INCREF(__pyx_t_2);
21762 __pyx_t_7 = 0;
21763 __pyx_t_9 = NULL;
21764 } else {
21765 __pyx_t_7 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 586, __pyx_L1_error)
21766 __Pyx_GOTREF(__pyx_t_2);
21767 __pyx_t_9 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 586, __pyx_L1_error)
21768 }
21769 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
21770 for (;;) {
21771 if (likely(!__pyx_t_9)) {
21772 if (likely(PyList_CheckExact(__pyx_t_2))) {
21773 {
21774 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2);
21775 #if !CYTHON_ASSUME_SAFE_MACROS
21776 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 586, __pyx_L1_error)
21777 #endif
21778 if (__pyx_t_7 >= __pyx_temp) break;
21779 }
21780 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
21781 __pyx_t_3 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_7); __Pyx_INCREF(__pyx_t_3); __pyx_t_7++; if (unlikely((0 < 0))) __PYX_ERR(0, 586, __pyx_L1_error)
21782 #else
21783 __pyx_t_3 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 586, __pyx_L1_error)
21784 __Pyx_GOTREF(__pyx_t_3);
21785 #endif
21786 } else {
21787 {
21788 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_2);
21789 #if !CYTHON_ASSUME_SAFE_MACROS
21790 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 586, __pyx_L1_error)
21791 #endif
21792 if (__pyx_t_7 >= __pyx_temp) break;
21793 }
21794 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
21795 __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_7); __Pyx_INCREF(__pyx_t_3); __pyx_t_7++; if (unlikely((0 < 0))) __PYX_ERR(0, 586, __pyx_L1_error)
21796 #else
21797 __pyx_t_3 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 586, __pyx_L1_error)
21798 __Pyx_GOTREF(__pyx_t_3);
21799 #endif
21800 }
21801 } else {
21802 __pyx_t_3 = __pyx_t_9(__pyx_t_2);
21803 if (unlikely(!__pyx_t_3)) {
21804 PyObject* exc_type = PyErr_Occurred();
21805 if (exc_type) {
21806 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
21807 else __PYX_ERR(0, 586, __pyx_L1_error)
21808 }
21809 break;
21810 }
21811 __Pyx_GOTREF(__pyx_t_3);
21812 }
21813 __Pyx_XDECREF_SET(__pyx_v_s, __pyx_t_3);
21814 __pyx_t_3 = 0;
21815 __Pyx_INCREF(__pyx_t_1);
21816 __Pyx_XDECREF_SET(__pyx_v_i, __pyx_t_1);
21817 __pyx_t_3 = __Pyx_PyInt_AddObjC(__pyx_t_1, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 586, __pyx_L1_error)
21818 __Pyx_GOTREF(__pyx_t_3);
21819 __Pyx_DECREF(__pyx_t_1);
21820 __pyx_t_1 = __pyx_t_3;
21821 __pyx_t_3 = 0;
21822
21823 /* "pysam/libcvcf.pyx":588
21824 * for i,s in enumerate(self._required):
21825 *
21826 * if len(headings)<=i or headings[i] != s: # <<<<<<<<<<<<<<
21827 *
21828 * if len(headings) <= i:
21829 */
21830 __pyx_t_10 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_10 == ((Py_ssize_t)-1))) __PYX_ERR(0, 588, __pyx_L1_error)
21831 __pyx_t_3 = PyInt_FromSsize_t(__pyx_t_10); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 588, __pyx_L1_error)
21832 __Pyx_GOTREF(__pyx_t_3);
21833 __pyx_t_8 = PyObject_RichCompare(__pyx_t_3, __pyx_v_i, Py_LE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 588, __pyx_L1_error)
21834 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
21835 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 588, __pyx_L1_error)
21836 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
21837 if (!__pyx_t_5) {
21838 } else {
21839 __pyx_t_6 = __pyx_t_5;
21840 goto __pyx_L9_bool_binop_done;
21841 }
21842 __pyx_t_8 = __Pyx_PyObject_GetItem(__pyx_v_headings, __pyx_v_i); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 588, __pyx_L1_error)
21843 __Pyx_GOTREF(__pyx_t_8);
21844 __pyx_t_3 = PyObject_RichCompare(__pyx_t_8, __pyx_v_s, Py_NE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 588, __pyx_L1_error)
21845 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
21846 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 588, __pyx_L1_error)
21847 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
21848 __pyx_t_6 = __pyx_t_5;
21849 __pyx_L9_bool_binop_done:;
21850 if (__pyx_t_6) {
21851
21852 /* "pysam/libcvcf.pyx":590
21853 * if len(headings)<=i or headings[i] != s:
21854 *
21855 * if len(headings) <= i: # <<<<<<<<<<<<<<
21856 * err = "(%sth entry not found)" % (i+1)
21857 * else:
21858 */
21859 __pyx_t_10 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_10 == ((Py_ssize_t)-1))) __PYX_ERR(0, 590, __pyx_L1_error)
21860 __pyx_t_3 = PyInt_FromSsize_t(__pyx_t_10); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 590, __pyx_L1_error)
21861 __Pyx_GOTREF(__pyx_t_3);
21862 __pyx_t_8 = PyObject_RichCompare(__pyx_t_3, __pyx_v_i, Py_LE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 590, __pyx_L1_error)
21863 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
21864 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 590, __pyx_L1_error)
21865 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
21866 if (__pyx_t_6) {
21867
21868 /* "pysam/libcvcf.pyx":591
21869 *
21870 * if len(headings) <= i:
21871 * err = "(%sth entry not found)" % (i+1) # <<<<<<<<<<<<<<
21872 * else:
21873 * err = "(found %s, expected %s)" % (headings[i],s)
21874 */
21875 __pyx_t_8 = __Pyx_PyInt_AddObjC(__pyx_v_i, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 591, __pyx_L1_error)
21876 __Pyx_GOTREF(__pyx_t_8);
21877 __pyx_t_3 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_sth_entry_not_found, __pyx_t_8); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 591, __pyx_L1_error)
21878 __Pyx_GOTREF(__pyx_t_3);
21879 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
21880 __Pyx_XDECREF_SET(__pyx_v_err, ((PyObject*)__pyx_t_3));
21881 __pyx_t_3 = 0;
21882
21883 /* "pysam/libcvcf.pyx":590
21884 * if len(headings)<=i or headings[i] != s:
21885 *
21886 * if len(headings) <= i: # <<<<<<<<<<<<<<
21887 * err = "(%sth entry not found)" % (i+1)
21888 * else:
21889 */
21890 goto __pyx_L11;
21891 }
21892
21893 /* "pysam/libcvcf.pyx":593
21894 * err = "(%sth entry not found)" % (i+1)
21895 * else:
21896 * err = "(found %s, expected %s)" % (headings[i],s) # <<<<<<<<<<<<<<
21897 *
21898 * #self.error(line,self.BADLY_FORMATTED_HEADING,err)
21899 */
21900 /*else*/ {
21901 __pyx_t_3 = PyTuple_New(5); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 593, __pyx_L1_error)
21902 __Pyx_GOTREF(__pyx_t_3);
21903 __pyx_t_10 = 0;
21904 __pyx_t_11 = 127;
21905 __Pyx_INCREF(__pyx_kp_u_found);
21906 __pyx_t_10 += 7;
21907 __Pyx_GIVEREF(__pyx_kp_u_found);
21908 PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_kp_u_found);
21909 __pyx_t_8 = __Pyx_PyObject_GetItem(__pyx_v_headings, __pyx_v_i); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 593, __pyx_L1_error)
21910 __Pyx_GOTREF(__pyx_t_8);
21911 __pyx_t_12 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_8), __pyx_empty_unicode); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 593, __pyx_L1_error)
21912 __Pyx_GOTREF(__pyx_t_12);
21913 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
21914 __pyx_t_11 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_12) > __pyx_t_11) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_12) : __pyx_t_11;
21915 __pyx_t_10 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_12);
21916 __Pyx_GIVEREF(__pyx_t_12);
21917 PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_12);
21918 __pyx_t_12 = 0;
21919 __Pyx_INCREF(__pyx_kp_u_expected_2);
21920 __pyx_t_10 += 11;
21921 __Pyx_GIVEREF(__pyx_kp_u_expected_2);
21922 PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_kp_u_expected_2);
21923 __pyx_t_12 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_s), __pyx_empty_unicode); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 593, __pyx_L1_error)
21924 __Pyx_GOTREF(__pyx_t_12);
21925 __pyx_t_11 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_12) > __pyx_t_11) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_12) : __pyx_t_11;
21926 __pyx_t_10 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_12);
21927 __Pyx_GIVEREF(__pyx_t_12);
21928 PyTuple_SET_ITEM(__pyx_t_3, 3, __pyx_t_12);
21929 __pyx_t_12 = 0;
21930 __Pyx_INCREF(__pyx_kp_u__8);
21931 __pyx_t_10 += 1;
21932 __Pyx_GIVEREF(__pyx_kp_u__8);
21933 PyTuple_SET_ITEM(__pyx_t_3, 4, __pyx_kp_u__8);
21934 __pyx_t_12 = __Pyx_PyUnicode_Join(__pyx_t_3, 5, __pyx_t_10, __pyx_t_11); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 593, __pyx_L1_error)
21935 __Pyx_GOTREF(__pyx_t_12);
21936 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
21937 __Pyx_XDECREF_SET(__pyx_v_err, ((PyObject*)__pyx_t_12));
21938 __pyx_t_12 = 0;
21939 }
21940 __pyx_L11:;
21941
21942 /* "pysam/libcvcf.pyx":597
21943 * #self.error(line,self.BADLY_FORMATTED_HEADING,err)
21944 * # allow FORMAT column to be absent
21945 * if len(headings) == 8: # <<<<<<<<<<<<<<
21946 * headings.append("FORMAT")
21947 * else:
21948 */
21949 __pyx_t_10 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_10 == ((Py_ssize_t)-1))) __PYX_ERR(0, 597, __pyx_L1_error)
21950 __pyx_t_6 = (__pyx_t_10 == 8);
21951 if (__pyx_t_6) {
21952
21953 /* "pysam/libcvcf.pyx":598
21954 * # allow FORMAT column to be absent
21955 * if len(headings) == 8:
21956 * headings.append("FORMAT") # <<<<<<<<<<<<<<
21957 * else:
21958 * self.error(line,self.BADLY_FORMATTED_HEADING,err)
21959 */
21960 __pyx_t_13 = __Pyx_PyObject_Append(__pyx_v_headings, __pyx_n_u_FORMAT); if (unlikely(__pyx_t_13 == ((int)-1))) __PYX_ERR(0, 598, __pyx_L1_error)
21961
21962 /* "pysam/libcvcf.pyx":597
21963 * #self.error(line,self.BADLY_FORMATTED_HEADING,err)
21964 * # allow FORMAT column to be absent
21965 * if len(headings) == 8: # <<<<<<<<<<<<<<
21966 * headings.append("FORMAT")
21967 * else:
21968 */
21969 goto __pyx_L12;
21970 }
21971
21972 /* "pysam/libcvcf.pyx":600
21973 * headings.append("FORMAT")
21974 * else:
21975 * self.error(line,self.BADLY_FORMATTED_HEADING,err) # <<<<<<<<<<<<<<
21976 *
21977 * self._samples = headings[9:]
21978 */
21979 /*else*/ {
21980 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 600, __pyx_L1_error)
21981 __Pyx_GOTREF(__pyx_t_3);
21982 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_BADLY_FORMATTED_HEADING); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 600, __pyx_L1_error)
21983 __Pyx_GOTREF(__pyx_t_8);
21984 __pyx_t_14 = NULL;
21985 __pyx_t_4 = 0;
21986 #if CYTHON_UNPACK_METHODS
21987 if (likely(PyMethod_Check(__pyx_t_3))) {
21988 __pyx_t_14 = PyMethod_GET_SELF(__pyx_t_3);
21989 if (likely(__pyx_t_14)) {
21990 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
21991 __Pyx_INCREF(__pyx_t_14);
21992 __Pyx_INCREF(function);
21993 __Pyx_DECREF_SET(__pyx_t_3, function);
21994 __pyx_t_4 = 1;
21995 }
21996 }
21997 #endif
21998 {
21999 PyObject *__pyx_callargs[4] = {__pyx_t_14, __pyx_v_line, __pyx_t_8, __pyx_v_err};
22000 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
22001 __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
22002 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
22003 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 600, __pyx_L1_error)
22004 __Pyx_GOTREF(__pyx_t_12);
22005 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
22006 }
22007 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
22008 }
22009 __pyx_L12:;
22010
22011 /* "pysam/libcvcf.pyx":588
22012 * for i,s in enumerate(self._required):
22013 *
22014 * if len(headings)<=i or headings[i] != s: # <<<<<<<<<<<<<<
22015 *
22016 * if len(headings) <= i:
22017 */
22018 }
22019
22020 /* "pysam/libcvcf.pyx":586
22021 * headings = line[1:].split()
22022 *
22023 * for i,s in enumerate(self._required): # <<<<<<<<<<<<<<
22024 *
22025 * if len(headings)<=i or headings[i] != s:
22026 */
22027 }
22028 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
22029 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
22030
22031 /* "pysam/libcvcf.pyx":602
22032 * self.error(line,self.BADLY_FORMATTED_HEADING,err)
22033 *
22034 * self._samples = headings[9:] # <<<<<<<<<<<<<<
22035 * self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] )
22036 *
22037 */
22038 __pyx_t_1 = __Pyx_PyObject_GetSlice(__pyx_v_headings, 9, 0, NULL, NULL, &__pyx_slice__26, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 602, __pyx_L1_error)
22039 __Pyx_GOTREF(__pyx_t_1);
22040 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_samples, __pyx_t_1) < 0) __PYX_ERR(0, 602, __pyx_L1_error)
22041 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
22042
22043 /* "pysam/libcvcf.pyx":603
22044 *
22045 * self._samples = headings[9:]
22046 * self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] ) # <<<<<<<<<<<<<<
22047 *
22048 * def write_heading( self, stream ):
22049 */
22050 { /* enter inner scope */
22051 __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 603, __pyx_L16_error)
22052 __Pyx_GOTREF(__pyx_t_1);
22053 __Pyx_INCREF(__pyx_int_0);
22054 __pyx_t_2 = __pyx_int_0;
22055 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_samples); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 603, __pyx_L16_error)
22056 __Pyx_GOTREF(__pyx_t_12);
22057 if (likely(PyList_CheckExact(__pyx_t_12)) || PyTuple_CheckExact(__pyx_t_12)) {
22058 __pyx_t_3 = __pyx_t_12; __Pyx_INCREF(__pyx_t_3);
22059 __pyx_t_7 = 0;
22060 __pyx_t_9 = NULL;
22061 } else {
22062 __pyx_t_7 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_t_12); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 603, __pyx_L16_error)
22063 __Pyx_GOTREF(__pyx_t_3);
22064 __pyx_t_9 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_3); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 603, __pyx_L16_error)
22065 }
22066 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
22067 for (;;) {
22068 if (likely(!__pyx_t_9)) {
22069 if (likely(PyList_CheckExact(__pyx_t_3))) {
22070 {
22071 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_3);
22072 #if !CYTHON_ASSUME_SAFE_MACROS
22073 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 603, __pyx_L16_error)
22074 #endif
22075 if (__pyx_t_7 >= __pyx_temp) break;
22076 }
22077 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
22078 __pyx_t_12 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_7); __Pyx_INCREF(__pyx_t_12); __pyx_t_7++; if (unlikely((0 < 0))) __PYX_ERR(0, 603, __pyx_L16_error)
22079 #else
22080 __pyx_t_12 = __Pyx_PySequence_ITEM(__pyx_t_3, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 603, __pyx_L16_error)
22081 __Pyx_GOTREF(__pyx_t_12);
22082 #endif
22083 } else {
22084 {
22085 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_3);
22086 #if !CYTHON_ASSUME_SAFE_MACROS
22087 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 603, __pyx_L16_error)
22088 #endif
22089 if (__pyx_t_7 >= __pyx_temp) break;
22090 }
22091 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
22092 __pyx_t_12 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_7); __Pyx_INCREF(__pyx_t_12); __pyx_t_7++; if (unlikely((0 < 0))) __PYX_ERR(0, 603, __pyx_L16_error)
22093 #else
22094 __pyx_t_12 = __Pyx_PySequence_ITEM(__pyx_t_3, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 603, __pyx_L16_error)
22095 __Pyx_GOTREF(__pyx_t_12);
22096 #endif
22097 }
22098 } else {
22099 __pyx_t_12 = __pyx_t_9(__pyx_t_3);
22100 if (unlikely(!__pyx_t_12)) {
22101 PyObject* exc_type = PyErr_Occurred();
22102 if (exc_type) {
22103 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
22104 else __PYX_ERR(0, 603, __pyx_L16_error)
22105 }
22106 break;
22107 }
22108 __Pyx_GOTREF(__pyx_t_12);
22109 }
22110 __Pyx_XDECREF_SET(__pyx_8genexpr2__pyx_v_y, __pyx_t_12);
22111 __pyx_t_12 = 0;
22112 __Pyx_INCREF(__pyx_t_2);
22113 __Pyx_XDECREF_SET(__pyx_8genexpr2__pyx_v_x, __pyx_t_2);
22114 __pyx_t_12 = __Pyx_PyInt_AddObjC(__pyx_t_2, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 603, __pyx_L16_error)
22115 __Pyx_GOTREF(__pyx_t_12);
22116 __Pyx_DECREF(__pyx_t_2);
22117 __pyx_t_2 = __pyx_t_12;
22118 __pyx_t_12 = 0;
22119 __pyx_t_12 = __Pyx_PyInt_AddObjC(__pyx_8genexpr2__pyx_v_x, __pyx_int_9, 9, 0, 0); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 603, __pyx_L16_error)
22120 __Pyx_GOTREF(__pyx_t_12);
22121 __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 603, __pyx_L16_error)
22122 __Pyx_GOTREF(__pyx_t_8);
22123 __Pyx_INCREF(__pyx_8genexpr2__pyx_v_y);
22124 __Pyx_GIVEREF(__pyx_8genexpr2__pyx_v_y);
22125 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_8genexpr2__pyx_v_y)) __PYX_ERR(0, 603, __pyx_L16_error);
22126 __Pyx_GIVEREF(__pyx_t_12);
22127 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_12)) __PYX_ERR(0, 603, __pyx_L16_error);
22128 __pyx_t_12 = 0;
22129 if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_8))) __PYX_ERR(0, 603, __pyx_L16_error)
22130 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
22131 }
22132 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
22133 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
22134 __Pyx_XDECREF(__pyx_8genexpr2__pyx_v_x); __pyx_8genexpr2__pyx_v_x = 0;
22135 __Pyx_XDECREF(__pyx_8genexpr2__pyx_v_y); __pyx_8genexpr2__pyx_v_y = 0;
22136 goto __pyx_L20_exit_scope;
22137 __pyx_L16_error:;
22138 __Pyx_XDECREF(__pyx_8genexpr2__pyx_v_x); __pyx_8genexpr2__pyx_v_x = 0;
22139 __Pyx_XDECREF(__pyx_8genexpr2__pyx_v_y); __pyx_8genexpr2__pyx_v_y = 0;
22140 goto __pyx_L1_error;
22141 __pyx_L20_exit_scope:;
22142 } /* exit inner scope */
22143 __pyx_t_2 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyDict_Type)), __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 603, __pyx_L1_error)
22144 __Pyx_GOTREF(__pyx_t_2);
22145 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
22146 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_sample2column, __pyx_t_2) < 0) __PYX_ERR(0, 603, __pyx_L1_error)
22147 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
22148
22149 /* "pysam/libcvcf.pyx":577
22150 *
22151 *
22152 * def parse_heading( self, line ): # <<<<<<<<<<<<<<
22153 * assert line.startswith('#')
22154 * assert not line.startswith('##')
22155 */
22156
22157 /* function exit code */
22158 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
22159 goto __pyx_L0;
22160 __pyx_L1_error:;
22161 __Pyx_XDECREF(__pyx_t_1);
22162 __Pyx_XDECREF(__pyx_t_2);
22163 __Pyx_XDECREF(__pyx_t_3);
22164 __Pyx_XDECREF(__pyx_t_8);
22165 __Pyx_XDECREF(__pyx_t_12);
22166 __Pyx_XDECREF(__pyx_t_14);
22167 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_heading", __pyx_clineno, __pyx_lineno, __pyx_filename);
22168 __pyx_r = NULL;
22169 __pyx_L0:;
22170 __Pyx_XDECREF(__pyx_v_headings);
22171 __Pyx_XDECREF(__pyx_v_i);
22172 __Pyx_XDECREF(__pyx_v_s);
22173 __Pyx_XDECREF(__pyx_v_err);
22174 __Pyx_XDECREF(__pyx_8genexpr2__pyx_v_x);
22175 __Pyx_XDECREF(__pyx_8genexpr2__pyx_v_y);
22176 __Pyx_XGIVEREF(__pyx_r);
22177 __Pyx_RefNannyFinishContext();
22178 return __pyx_r;
22179 }
22180
22181 /* "pysam/libcvcf.pyx":605
22182 * self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] )
22183 *
22184 * def write_heading( self, stream ): # <<<<<<<<<<<<<<
22185 * stream.write("#" + "\t".join(self._required + self._samples) + "\n")
22186 *
22187 */
22188
22189 /* Python wrapper */
22190 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_23write_heading(PyObject *__pyx_self,
22191 #if CYTHON_METH_FASTCALL
22192 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
22193 #else
22194 PyObject *__pyx_args, PyObject *__pyx_kwds
22195 #endif
22196 ); /*proto*/
22197 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_22write_heading, "VCF.write_heading(self, stream)");
22198 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_23write_heading = {"write_heading", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_23write_heading, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_22write_heading};
22199 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_23write_heading(PyObject *__pyx_self,
22200 #if CYTHON_METH_FASTCALL
22201 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
22202 #else
22203 PyObject *__pyx_args, PyObject *__pyx_kwds
22204 #endif
22205 ) {
22206 PyObject *__pyx_v_self = 0;
22207 PyObject *__pyx_v_stream = 0;
22208 #if !CYTHON_METH_FASTCALL
22209 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
22210 #endif
22211 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
22212 PyObject* values[2] = {0,0};
22213 int __pyx_lineno = 0;
22214 const char *__pyx_filename = NULL;
22215 int __pyx_clineno = 0;
22216 PyObject *__pyx_r = 0;
22217 __Pyx_RefNannyDeclarations
22218 __Pyx_RefNannySetupContext("write_heading (wrapper)", 0);
22219 #if !CYTHON_METH_FASTCALL
22220 #if CYTHON_ASSUME_SAFE_MACROS
22221 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
22222 #else
22223 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
22224 #endif
22225 #endif
22226 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
22227 {
22228 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_stream,0};
22229 if (__pyx_kwds) {
22230 Py_ssize_t kw_args;
22231 switch (__pyx_nargs) {
22232 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
22233 CYTHON_FALLTHROUGH;
22234 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
22235 CYTHON_FALLTHROUGH;
22236 case 0: break;
22237 default: goto __pyx_L5_argtuple_error;
22238 }
22239 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
22240 switch (__pyx_nargs) {
22241 case 0:
22242 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
22243 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
22244 kw_args--;
22245 }
22246 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 605, __pyx_L3_error)
22247 else goto __pyx_L5_argtuple_error;
22248 CYTHON_FALLTHROUGH;
22249 case 1:
22250 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_stream)) != 0)) {
22251 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
22252 kw_args--;
22253 }
22254 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 605, __pyx_L3_error)
22255 else {
22256 __Pyx_RaiseArgtupleInvalid("write_heading", 1, 2, 2, 1); __PYX_ERR(0, 605, __pyx_L3_error)
22257 }
22258 }
22259 if (unlikely(kw_args > 0)) {
22260 const Py_ssize_t kwd_pos_args = __pyx_nargs;
22261 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "write_heading") < 0)) __PYX_ERR(0, 605, __pyx_L3_error)
22262 }
22263 } else if (unlikely(__pyx_nargs != 2)) {
22264 goto __pyx_L5_argtuple_error;
22265 } else {
22266 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
22267 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
22268 }
22269 __pyx_v_self = values[0];
22270 __pyx_v_stream = values[1];
22271 }
22272 goto __pyx_L6_skip;
22273 __pyx_L5_argtuple_error:;
22274 __Pyx_RaiseArgtupleInvalid("write_heading", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 605, __pyx_L3_error)
22275 __pyx_L6_skip:;
22276 goto __pyx_L4_argument_unpacking_done;
22277 __pyx_L3_error:;
22278 {
22279 Py_ssize_t __pyx_temp;
22280 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
22281 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
22282 }
22283 }
22284 __Pyx_AddTraceback("pysam.libcvcf.VCF.write_heading", __pyx_clineno, __pyx_lineno, __pyx_filename);
22285 __Pyx_RefNannyFinishContext();
22286 return NULL;
22287 __pyx_L4_argument_unpacking_done:;
22288 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_22write_heading(__pyx_self, __pyx_v_self, __pyx_v_stream);
22289
22290 /* function exit code */
22291 {
22292 Py_ssize_t __pyx_temp;
22293 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
22294 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
22295 }
22296 }
22297 __Pyx_RefNannyFinishContext();
22298 return __pyx_r;
22299 }
22300
22301 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) {
22302 PyObject *__pyx_r = NULL;
22303 __Pyx_RefNannyDeclarations
22304 PyObject *__pyx_t_1 = NULL;
22305 PyObject *__pyx_t_2 = NULL;
22306 PyObject *__pyx_t_3 = NULL;
22307 PyObject *__pyx_t_4 = NULL;
22308 PyObject *__pyx_t_5 = NULL;
22309 unsigned int __pyx_t_6;
22310 int __pyx_lineno = 0;
22311 const char *__pyx_filename = NULL;
22312 int __pyx_clineno = 0;
22313 __Pyx_RefNannySetupContext("write_heading", 1);
22314
22315 /* "pysam/libcvcf.pyx":606
22316 *
22317 * def write_heading( self, stream ):
22318 * stream.write("#" + "\t".join(self._required + self._samples) + "\n") # <<<<<<<<<<<<<<
22319 *
22320 * def convertGT(self, GTstring):
22321 */
22322 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_stream, __pyx_n_s_write); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 606, __pyx_L1_error)
22323 __Pyx_GOTREF(__pyx_t_2);
22324 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_required); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 606, __pyx_L1_error)
22325 __Pyx_GOTREF(__pyx_t_3);
22326 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_samples); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 606, __pyx_L1_error)
22327 __Pyx_GOTREF(__pyx_t_4);
22328 __pyx_t_5 = PyNumber_Add(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 606, __pyx_L1_error)
22329 __Pyx_GOTREF(__pyx_t_5);
22330 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
22331 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
22332 __pyx_t_4 = PyUnicode_Join(__pyx_kp_u__25, __pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 606, __pyx_L1_error)
22333 __Pyx_GOTREF(__pyx_t_4);
22334 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
22335 __pyx_t_5 = __Pyx_PyUnicode_Concat(__pyx_kp_u__24, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 606, __pyx_L1_error)
22336 __Pyx_GOTREF(__pyx_t_5);
22337 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
22338 __pyx_t_4 = __Pyx_PyUnicode_ConcatInPlace(__pyx_t_5, __pyx_kp_u__14); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 606, __pyx_L1_error)
22339 __Pyx_GOTREF(__pyx_t_4);
22340 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
22341 __pyx_t_5 = NULL;
22342 __pyx_t_6 = 0;
22343 #if CYTHON_UNPACK_METHODS
22344 if (likely(PyMethod_Check(__pyx_t_2))) {
22345 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_2);
22346 if (likely(__pyx_t_5)) {
22347 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
22348 __Pyx_INCREF(__pyx_t_5);
22349 __Pyx_INCREF(function);
22350 __Pyx_DECREF_SET(__pyx_t_2, function);
22351 __pyx_t_6 = 1;
22352 }
22353 }
22354 #endif
22355 {
22356 PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_t_4};
22357 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_6, 1+__pyx_t_6);
22358 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
22359 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
22360 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 606, __pyx_L1_error)
22361 __Pyx_GOTREF(__pyx_t_1);
22362 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
22363 }
22364 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
22365
22366 /* "pysam/libcvcf.pyx":605
22367 * self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] )
22368 *
22369 * def write_heading( self, stream ): # <<<<<<<<<<<<<<
22370 * stream.write("#" + "\t".join(self._required + self._samples) + "\n")
22371 *
22372 */
22373
22374 /* function exit code */
22375 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
22376 goto __pyx_L0;
22377 __pyx_L1_error:;
22378 __Pyx_XDECREF(__pyx_t_1);
22379 __Pyx_XDECREF(__pyx_t_2);
22380 __Pyx_XDECREF(__pyx_t_3);
22381 __Pyx_XDECREF(__pyx_t_4);
22382 __Pyx_XDECREF(__pyx_t_5);
22383 __Pyx_AddTraceback("pysam.libcvcf.VCF.write_heading", __pyx_clineno, __pyx_lineno, __pyx_filename);
22384 __pyx_r = NULL;
22385 __pyx_L0:;
22386 __Pyx_XGIVEREF(__pyx_r);
22387 __Pyx_RefNannyFinishContext();
22388 return __pyx_r;
22389 }
22390
22391 /* "pysam/libcvcf.pyx":608
22392 * stream.write("#" + "\t".join(self._required + self._samples) + "\n")
22393 *
22394 * def convertGT(self, GTstring): # <<<<<<<<<<<<<<
22395 * if GTstring == ".": return ["."]
22396 * try:
22397 */
22398
22399 /* Python wrapper */
22400 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_25convertGT(PyObject *__pyx_self,
22401 #if CYTHON_METH_FASTCALL
22402 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
22403 #else
22404 PyObject *__pyx_args, PyObject *__pyx_kwds
22405 #endif
22406 ); /*proto*/
22407 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_24convertGT, "VCF.convertGT(self, GTstring)");
22408 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_25convertGT = {"convertGT", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_25convertGT, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_24convertGT};
22409 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_25convertGT(PyObject *__pyx_self,
22410 #if CYTHON_METH_FASTCALL
22411 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
22412 #else
22413 PyObject *__pyx_args, PyObject *__pyx_kwds
22414 #endif
22415 ) {
22416 PyObject *__pyx_v_self = 0;
22417 PyObject *__pyx_v_GTstring = 0;
22418 #if !CYTHON_METH_FASTCALL
22419 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
22420 #endif
22421 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
22422 PyObject* values[2] = {0,0};
22423 int __pyx_lineno = 0;
22424 const char *__pyx_filename = NULL;
22425 int __pyx_clineno = 0;
22426 PyObject *__pyx_r = 0;
22427 __Pyx_RefNannyDeclarations
22428 __Pyx_RefNannySetupContext("convertGT (wrapper)", 0);
22429 #if !CYTHON_METH_FASTCALL
22430 #if CYTHON_ASSUME_SAFE_MACROS
22431 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
22432 #else
22433 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
22434 #endif
22435 #endif
22436 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
22437 {
22438 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_GTstring,0};
22439 if (__pyx_kwds) {
22440 Py_ssize_t kw_args;
22441 switch (__pyx_nargs) {
22442 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
22443 CYTHON_FALLTHROUGH;
22444 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
22445 CYTHON_FALLTHROUGH;
22446 case 0: break;
22447 default: goto __pyx_L5_argtuple_error;
22448 }
22449 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
22450 switch (__pyx_nargs) {
22451 case 0:
22452 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
22453 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
22454 kw_args--;
22455 }
22456 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 608, __pyx_L3_error)
22457 else goto __pyx_L5_argtuple_error;
22458 CYTHON_FALLTHROUGH;
22459 case 1:
22460 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_GTstring)) != 0)) {
22461 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
22462 kw_args--;
22463 }
22464 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 608, __pyx_L3_error)
22465 else {
22466 __Pyx_RaiseArgtupleInvalid("convertGT", 1, 2, 2, 1); __PYX_ERR(0, 608, __pyx_L3_error)
22467 }
22468 }
22469 if (unlikely(kw_args > 0)) {
22470 const Py_ssize_t kwd_pos_args = __pyx_nargs;
22471 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "convertGT") < 0)) __PYX_ERR(0, 608, __pyx_L3_error)
22472 }
22473 } else if (unlikely(__pyx_nargs != 2)) {
22474 goto __pyx_L5_argtuple_error;
22475 } else {
22476 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
22477 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
22478 }
22479 __pyx_v_self = values[0];
22480 __pyx_v_GTstring = values[1];
22481 }
22482 goto __pyx_L6_skip;
22483 __pyx_L5_argtuple_error:;
22484 __Pyx_RaiseArgtupleInvalid("convertGT", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 608, __pyx_L3_error)
22485 __pyx_L6_skip:;
22486 goto __pyx_L4_argument_unpacking_done;
22487 __pyx_L3_error:;
22488 {
22489 Py_ssize_t __pyx_temp;
22490 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
22491 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
22492 }
22493 }
22494 __Pyx_AddTraceback("pysam.libcvcf.VCF.convertGT", __pyx_clineno, __pyx_lineno, __pyx_filename);
22495 __Pyx_RefNannyFinishContext();
22496 return NULL;
22497 __pyx_L4_argument_unpacking_done:;
22498 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_24convertGT(__pyx_self, __pyx_v_self, __pyx_v_GTstring);
22499
22500 /* function exit code */
22501 {
22502 Py_ssize_t __pyx_temp;
22503 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
22504 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
22505 }
22506 }
22507 __Pyx_RefNannyFinishContext();
22508 return __pyx_r;
22509 }
22510
22511 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_GTstring) {
22512 PyObject *__pyx_v_gts = NULL;
22513 PyObject *__pyx_r = NULL;
22514 __Pyx_RefNannyDeclarations
22515 int __pyx_t_1;
22516 PyObject *__pyx_t_2 = NULL;
22517 PyObject *__pyx_t_3 = NULL;
22518 PyObject *__pyx_t_4 = NULL;
22519 PyObject *__pyx_t_5 = NULL;
22520 PyObject *__pyx_t_6 = NULL;
22521 PyObject *__pyx_t_7 = NULL;
22522 unsigned int __pyx_t_8;
22523 Py_ssize_t __pyx_t_9;
22524 int __pyx_t_10;
22525 Py_ssize_t __pyx_t_11;
22526 PyObject *__pyx_t_12 = NULL;
22527 int __pyx_t_13;
22528 PyObject *__pyx_t_14 = NULL;
22529 PyObject *__pyx_t_15 = NULL;
22530 PyObject *__pyx_t_16 = NULL;
22531 PyObject *__pyx_t_17 = NULL;
22532 int __pyx_lineno = 0;
22533 const char *__pyx_filename = NULL;
22534 int __pyx_clineno = 0;
22535 __Pyx_RefNannySetupContext("convertGT", 1);
22536
22537 /* "pysam/libcvcf.pyx":609
22538 *
22539 * def convertGT(self, GTstring):
22540 * if GTstring == ".": return ["."] # <<<<<<<<<<<<<<
22541 * try:
22542 * gts = gtsRegEx.split(GTstring)
22543 */
22544 __pyx_t_1 = (__Pyx_PyUnicode_Equals(__pyx_v_GTstring, __pyx_kp_u__5, Py_EQ)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 609, __pyx_L1_error)
22545 if (__pyx_t_1) {
22546 __Pyx_XDECREF(__pyx_r);
22547 __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 609, __pyx_L1_error)
22548 __Pyx_GOTREF(__pyx_t_2);
22549 __Pyx_INCREF(__pyx_kp_u__5);
22550 __Pyx_GIVEREF(__pyx_kp_u__5);
22551 if (__Pyx_PyList_SET_ITEM(__pyx_t_2, 0, __pyx_kp_u__5)) __PYX_ERR(0, 609, __pyx_L1_error);
22552 __pyx_r = __pyx_t_2;
22553 __pyx_t_2 = 0;
22554 goto __pyx_L0;
22555 }
22556
22557 /* "pysam/libcvcf.pyx":610
22558 * def convertGT(self, GTstring):
22559 * if GTstring == ".": return ["."]
22560 * try: # <<<<<<<<<<<<<<
22561 * gts = gtsRegEx.split(GTstring)
22562 * if len(gts) == 1: return [int(gts[0])]
22563 */
22564 {
22565 __Pyx_PyThreadState_declare
22566 __Pyx_PyThreadState_assign
22567 __Pyx_ExceptionSave(&__pyx_t_3, &__pyx_t_4, &__pyx_t_5);
22568 __Pyx_XGOTREF(__pyx_t_3);
22569 __Pyx_XGOTREF(__pyx_t_4);
22570 __Pyx_XGOTREF(__pyx_t_5);
22571 /*try:*/ {
22572
22573 /* "pysam/libcvcf.pyx":611
22574 * if GTstring == ".": return ["."]
22575 * try:
22576 * gts = gtsRegEx.split(GTstring) # <<<<<<<<<<<<<<
22577 * if len(gts) == 1: return [int(gts[0])]
22578 * if len(gts) != 2: raise ValueError()
22579 */
22580 __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_gtsRegEx); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 611, __pyx_L4_error)
22581 __Pyx_GOTREF(__pyx_t_6);
22582 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_split); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 611, __pyx_L4_error)
22583 __Pyx_GOTREF(__pyx_t_7);
22584 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
22585 __pyx_t_6 = NULL;
22586 __pyx_t_8 = 0;
22587 #if CYTHON_UNPACK_METHODS
22588 if (unlikely(PyMethod_Check(__pyx_t_7))) {
22589 __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_7);
22590 if (likely(__pyx_t_6)) {
22591 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7);
22592 __Pyx_INCREF(__pyx_t_6);
22593 __Pyx_INCREF(function);
22594 __Pyx_DECREF_SET(__pyx_t_7, function);
22595 __pyx_t_8 = 1;
22596 }
22597 }
22598 #endif
22599 {
22600 PyObject *__pyx_callargs[2] = {__pyx_t_6, __pyx_v_GTstring};
22601 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_7, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
22602 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
22603 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 611, __pyx_L4_error)
22604 __Pyx_GOTREF(__pyx_t_2);
22605 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
22606 }
22607 __pyx_v_gts = __pyx_t_2;
22608 __pyx_t_2 = 0;
22609
22610 /* "pysam/libcvcf.pyx":612
22611 * try:
22612 * gts = gtsRegEx.split(GTstring)
22613 * if len(gts) == 1: return [int(gts[0])] # <<<<<<<<<<<<<<
22614 * if len(gts) != 2: raise ValueError()
22615 * if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
22616 */
22617 __pyx_t_9 = PyObject_Length(__pyx_v_gts); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 612, __pyx_L4_error)
22618 __pyx_t_1 = (__pyx_t_9 == 1);
22619 if (__pyx_t_1) {
22620 __Pyx_XDECREF(__pyx_r);
22621 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 612, __pyx_L4_error)
22622 __Pyx_GOTREF(__pyx_t_2);
22623 __pyx_t_7 = __Pyx_PyNumber_Int(__pyx_t_2); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 612, __pyx_L4_error)
22624 __Pyx_GOTREF(__pyx_t_7);
22625 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
22626 __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 612, __pyx_L4_error)
22627 __Pyx_GOTREF(__pyx_t_2);
22628 __Pyx_GIVEREF(__pyx_t_7);
22629 if (__Pyx_PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_7)) __PYX_ERR(0, 612, __pyx_L4_error);
22630 __pyx_t_7 = 0;
22631 __pyx_r = __pyx_t_2;
22632 __pyx_t_2 = 0;
22633 goto __pyx_L8_try_return;
22634 }
22635
22636 /* "pysam/libcvcf.pyx":613
22637 * gts = gtsRegEx.split(GTstring)
22638 * if len(gts) == 1: return [int(gts[0])]
22639 * if len(gts) != 2: raise ValueError() # <<<<<<<<<<<<<<
22640 * if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
22641 * return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
22642 */
22643 __pyx_t_9 = PyObject_Length(__pyx_v_gts); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 613, __pyx_L4_error)
22644 __pyx_t_1 = (__pyx_t_9 != 2);
22645 if (unlikely(__pyx_t_1)) {
22646 __pyx_t_2 = __Pyx_PyObject_CallNoArg(__pyx_builtin_ValueError); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 613, __pyx_L4_error)
22647 __Pyx_GOTREF(__pyx_t_2);
22648 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
22649 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
22650 __PYX_ERR(0, 613, __pyx_L4_error)
22651 }
22652
22653 /* "pysam/libcvcf.pyx":614
22654 * if len(gts) == 1: return [int(gts[0])]
22655 * if len(gts) != 2: raise ValueError()
22656 * if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]] # <<<<<<<<<<<<<<
22657 * return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
22658 * except ValueError:
22659 */
22660 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 614, __pyx_L4_error)
22661 __Pyx_GOTREF(__pyx_t_2);
22662 __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_2, __pyx_kp_u__5, Py_EQ)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 614, __pyx_L4_error)
22663 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
22664 if (__pyx_t_10) {
22665 } else {
22666 __pyx_t_1 = __pyx_t_10;
22667 goto __pyx_L13_bool_binop_done;
22668 }
22669 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 614, __pyx_L4_error)
22670 __Pyx_GOTREF(__pyx_t_2);
22671 __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_2, __pyx_kp_u__5, Py_EQ)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 614, __pyx_L4_error)
22672 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
22673 __pyx_t_1 = __pyx_t_10;
22674 __pyx_L13_bool_binop_done:;
22675 if (__pyx_t_1) {
22676 __Pyx_XDECREF(__pyx_r);
22677 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 614, __pyx_L4_error)
22678 __Pyx_GOTREF(__pyx_t_2);
22679 __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 614, __pyx_L4_error)
22680 __Pyx_GOTREF(__pyx_t_7);
22681 __pyx_t_9 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 614, __pyx_L4_error)
22682 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
22683 __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 614, __pyx_L4_error)
22684 __Pyx_GOTREF(__pyx_t_7);
22685 __pyx_t_11 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_11 == ((Py_ssize_t)-1))) __PYX_ERR(0, 614, __pyx_L4_error)
22686 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
22687 __pyx_t_7 = __Pyx_PyObject_GetSlice(__pyx_v_GTstring, __pyx_t_9, (-__pyx_t_11), NULL, NULL, NULL, 1, 1, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 614, __pyx_L4_error)
22688 __Pyx_GOTREF(__pyx_t_7);
22689 __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_gts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 614, __pyx_L4_error)
22690 __Pyx_GOTREF(__pyx_t_6);
22691 __pyx_t_12 = PyList_New(3); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 614, __pyx_L4_error)
22692 __Pyx_GOTREF(__pyx_t_12);
22693 __Pyx_GIVEREF(__pyx_t_2);
22694 if (__Pyx_PyList_SET_ITEM(__pyx_t_12, 0, __pyx_t_2)) __PYX_ERR(0, 614, __pyx_L4_error);
22695 __Pyx_GIVEREF(__pyx_t_7);
22696 if (__Pyx_PyList_SET_ITEM(__pyx_t_12, 1, __pyx_t_7)) __PYX_ERR(0, 614, __pyx_L4_error);
22697 __Pyx_GIVEREF(__pyx_t_6);
22698 if (__Pyx_PyList_SET_ITEM(__pyx_t_12, 2, __pyx_t_6)) __PYX_ERR(0, 614, __pyx_L4_error);
22699 __pyx_t_2 = 0;
22700 __pyx_t_7 = 0;
22701 __pyx_t_6 = 0;
22702 __pyx_r = __pyx_t_12;
22703 __pyx_t_12 = 0;
22704 goto __pyx_L8_try_return;
22705 }
22706
22707 /* "pysam/libcvcf.pyx":615
22708 * if len(gts) != 2: raise ValueError()
22709 * if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
22710 * return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])] # <<<<<<<<<<<<<<
22711 * except ValueError:
22712 * self.error(self._line,self.BAD_GENOTYPE,GTstring)
22713 */
22714 __Pyx_XDECREF(__pyx_r);
22715 __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_gts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 615, __pyx_L4_error)
22716 __Pyx_GOTREF(__pyx_t_12);
22717 __pyx_t_6 = __Pyx_PyNumber_Int(__pyx_t_12); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 615, __pyx_L4_error)
22718 __Pyx_GOTREF(__pyx_t_6);
22719 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
22720 __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_gts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 615, __pyx_L4_error)
22721 __Pyx_GOTREF(__pyx_t_12);
22722 __pyx_t_11 = PyObject_Length(__pyx_t_12); if (unlikely(__pyx_t_11 == ((Py_ssize_t)-1))) __PYX_ERR(0, 615, __pyx_L4_error)
22723 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
22724 __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_gts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 615, __pyx_L4_error)
22725 __Pyx_GOTREF(__pyx_t_12);
22726 __pyx_t_9 = PyObject_Length(__pyx_t_12); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 615, __pyx_L4_error)
22727 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
22728 __pyx_t_12 = __Pyx_PyObject_GetSlice(__pyx_v_GTstring, __pyx_t_11, (-__pyx_t_9), NULL, NULL, NULL, 1, 1, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 615, __pyx_L4_error)
22729 __Pyx_GOTREF(__pyx_t_12);
22730 __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 615, __pyx_L4_error)
22731 __Pyx_GOTREF(__pyx_t_7);
22732 __pyx_t_2 = __Pyx_PyNumber_Int(__pyx_t_7); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 615, __pyx_L4_error)
22733 __Pyx_GOTREF(__pyx_t_2);
22734 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
22735 __pyx_t_7 = PyList_New(3); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 615, __pyx_L4_error)
22736 __Pyx_GOTREF(__pyx_t_7);
22737 __Pyx_GIVEREF(__pyx_t_6);
22738 if (__Pyx_PyList_SET_ITEM(__pyx_t_7, 0, __pyx_t_6)) __PYX_ERR(0, 615, __pyx_L4_error);
22739 __Pyx_GIVEREF(__pyx_t_12);
22740 if (__Pyx_PyList_SET_ITEM(__pyx_t_7, 1, __pyx_t_12)) __PYX_ERR(0, 615, __pyx_L4_error);
22741 __Pyx_GIVEREF(__pyx_t_2);
22742 if (__Pyx_PyList_SET_ITEM(__pyx_t_7, 2, __pyx_t_2)) __PYX_ERR(0, 615, __pyx_L4_error);
22743 __pyx_t_6 = 0;
22744 __pyx_t_12 = 0;
22745 __pyx_t_2 = 0;
22746 __pyx_r = __pyx_t_7;
22747 __pyx_t_7 = 0;
22748 goto __pyx_L8_try_return;
22749
22750 /* "pysam/libcvcf.pyx":610
22751 * def convertGT(self, GTstring):
22752 * if GTstring == ".": return ["."]
22753 * try: # <<<<<<<<<<<<<<
22754 * gts = gtsRegEx.split(GTstring)
22755 * if len(gts) == 1: return [int(gts[0])]
22756 */
22757 }
22758 __pyx_L4_error:;
22759 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
22760 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
22761 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
22762 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
22763
22764 /* "pysam/libcvcf.pyx":616
22765 * if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
22766 * return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
22767 * except ValueError: # <<<<<<<<<<<<<<
22768 * self.error(self._line,self.BAD_GENOTYPE,GTstring)
22769 * return [".","|","."]
22770 */
22771 __pyx_t_13 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_ValueError);
22772 if (__pyx_t_13) {
22773 __Pyx_AddTraceback("pysam.libcvcf.VCF.convertGT", __pyx_clineno, __pyx_lineno, __pyx_filename);
22774 if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_2, &__pyx_t_12) < 0) __PYX_ERR(0, 616, __pyx_L6_except_error)
22775 __Pyx_XGOTREF(__pyx_t_7);
22776 __Pyx_XGOTREF(__pyx_t_2);
22777 __Pyx_XGOTREF(__pyx_t_12);
22778
22779 /* "pysam/libcvcf.pyx":617
22780 * return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
22781 * except ValueError:
22782 * self.error(self._line,self.BAD_GENOTYPE,GTstring) # <<<<<<<<<<<<<<
22783 * return [".","|","."]
22784 *
22785 */
22786 __pyx_t_14 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 617, __pyx_L6_except_error)
22787 __Pyx_GOTREF(__pyx_t_14);
22788 __pyx_t_15 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_line_2); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 617, __pyx_L6_except_error)
22789 __Pyx_GOTREF(__pyx_t_15);
22790 __pyx_t_16 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_BAD_GENOTYPE); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 617, __pyx_L6_except_error)
22791 __Pyx_GOTREF(__pyx_t_16);
22792 __pyx_t_17 = NULL;
22793 __pyx_t_8 = 0;
22794 #if CYTHON_UNPACK_METHODS
22795 if (likely(PyMethod_Check(__pyx_t_14))) {
22796 __pyx_t_17 = PyMethod_GET_SELF(__pyx_t_14);
22797 if (likely(__pyx_t_17)) {
22798 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_14);
22799 __Pyx_INCREF(__pyx_t_17);
22800 __Pyx_INCREF(function);
22801 __Pyx_DECREF_SET(__pyx_t_14, function);
22802 __pyx_t_8 = 1;
22803 }
22804 }
22805 #endif
22806 {
22807 PyObject *__pyx_callargs[4] = {__pyx_t_17, __pyx_t_15, __pyx_t_16, __pyx_v_GTstring};
22808 __pyx_t_6 = __Pyx_PyObject_FastCall(__pyx_t_14, __pyx_callargs+1-__pyx_t_8, 3+__pyx_t_8);
22809 __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
22810 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
22811 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
22812 if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 617, __pyx_L6_except_error)
22813 __Pyx_GOTREF(__pyx_t_6);
22814 __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
22815 }
22816 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
22817
22818 /* "pysam/libcvcf.pyx":618
22819 * except ValueError:
22820 * self.error(self._line,self.BAD_GENOTYPE,GTstring)
22821 * return [".","|","."] # <<<<<<<<<<<<<<
22822 *
22823 * def convertGTback(self, GTdata):
22824 */
22825 __Pyx_XDECREF(__pyx_r);
22826 __pyx_t_6 = PyList_New(3); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 618, __pyx_L6_except_error)
22827 __Pyx_GOTREF(__pyx_t_6);
22828 __Pyx_INCREF(__pyx_kp_u__5);
22829 __Pyx_GIVEREF(__pyx_kp_u__5);
22830 if (__Pyx_PyList_SET_ITEM(__pyx_t_6, 0, __pyx_kp_u__5)) __PYX_ERR(0, 618, __pyx_L6_except_error);
22831 __Pyx_INCREF(__pyx_kp_u__27);
22832 __Pyx_GIVEREF(__pyx_kp_u__27);
22833 if (__Pyx_PyList_SET_ITEM(__pyx_t_6, 1, __pyx_kp_u__27)) __PYX_ERR(0, 618, __pyx_L6_except_error);
22834 __Pyx_INCREF(__pyx_kp_u__5);
22835 __Pyx_GIVEREF(__pyx_kp_u__5);
22836 if (__Pyx_PyList_SET_ITEM(__pyx_t_6, 2, __pyx_kp_u__5)) __PYX_ERR(0, 618, __pyx_L6_except_error);
22837 __pyx_r = __pyx_t_6;
22838 __pyx_t_6 = 0;
22839 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
22840 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
22841 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
22842 goto __pyx_L7_except_return;
22843 }
22844 goto __pyx_L6_except_error;
22845
22846 /* "pysam/libcvcf.pyx":610
22847 * def convertGT(self, GTstring):
22848 * if GTstring == ".": return ["."]
22849 * try: # <<<<<<<<<<<<<<
22850 * gts = gtsRegEx.split(GTstring)
22851 * if len(gts) == 1: return [int(gts[0])]
22852 */
22853 __pyx_L6_except_error:;
22854 __Pyx_XGIVEREF(__pyx_t_3);
22855 __Pyx_XGIVEREF(__pyx_t_4);
22856 __Pyx_XGIVEREF(__pyx_t_5);
22857 __Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
22858 goto __pyx_L1_error;
22859 __pyx_L8_try_return:;
22860 __Pyx_XGIVEREF(__pyx_t_3);
22861 __Pyx_XGIVEREF(__pyx_t_4);
22862 __Pyx_XGIVEREF(__pyx_t_5);
22863 __Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
22864 goto __pyx_L0;
22865 __pyx_L7_except_return:;
22866 __Pyx_XGIVEREF(__pyx_t_3);
22867 __Pyx_XGIVEREF(__pyx_t_4);
22868 __Pyx_XGIVEREF(__pyx_t_5);
22869 __Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
22870 goto __pyx_L0;
22871 }
22872
22873 /* "pysam/libcvcf.pyx":608
22874 * stream.write("#" + "\t".join(self._required + self._samples) + "\n")
22875 *
22876 * def convertGT(self, GTstring): # <<<<<<<<<<<<<<
22877 * if GTstring == ".": return ["."]
22878 * try:
22879 */
22880
22881 /* function exit code */
22882 __pyx_L1_error:;
22883 __Pyx_XDECREF(__pyx_t_2);
22884 __Pyx_XDECREF(__pyx_t_6);
22885 __Pyx_XDECREF(__pyx_t_7);
22886 __Pyx_XDECREF(__pyx_t_12);
22887 __Pyx_XDECREF(__pyx_t_14);
22888 __Pyx_XDECREF(__pyx_t_15);
22889 __Pyx_XDECREF(__pyx_t_16);
22890 __Pyx_XDECREF(__pyx_t_17);
22891 __Pyx_AddTraceback("pysam.libcvcf.VCF.convertGT", __pyx_clineno, __pyx_lineno, __pyx_filename);
22892 __pyx_r = NULL;
22893 __pyx_L0:;
22894 __Pyx_XDECREF(__pyx_v_gts);
22895 __Pyx_XGIVEREF(__pyx_r);
22896 __Pyx_RefNannyFinishContext();
22897 return __pyx_r;
22898 }
22899
22900 /* "pysam/libcvcf.pyx":620
22901 * return [".","|","."]
22902 *
22903 * def convertGTback(self, GTdata): # <<<<<<<<<<<<<<
22904 * return ''.join(map(str,GTdata))
22905 *
22906 */
22907
22908 /* Python wrapper */
22909 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_27convertGTback(PyObject *__pyx_self,
22910 #if CYTHON_METH_FASTCALL
22911 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
22912 #else
22913 PyObject *__pyx_args, PyObject *__pyx_kwds
22914 #endif
22915 ); /*proto*/
22916 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_26convertGTback, "VCF.convertGTback(self, GTdata)");
22917 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_27convertGTback = {"convertGTback", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_27convertGTback, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_26convertGTback};
22918 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_27convertGTback(PyObject *__pyx_self,
22919 #if CYTHON_METH_FASTCALL
22920 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
22921 #else
22922 PyObject *__pyx_args, PyObject *__pyx_kwds
22923 #endif
22924 ) {
22925 CYTHON_UNUSED PyObject *__pyx_v_self = 0;
22926 PyObject *__pyx_v_GTdata = 0;
22927 #if !CYTHON_METH_FASTCALL
22928 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
22929 #endif
22930 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
22931 PyObject* values[2] = {0,0};
22932 int __pyx_lineno = 0;
22933 const char *__pyx_filename = NULL;
22934 int __pyx_clineno = 0;
22935 PyObject *__pyx_r = 0;
22936 __Pyx_RefNannyDeclarations
22937 __Pyx_RefNannySetupContext("convertGTback (wrapper)", 0);
22938 #if !CYTHON_METH_FASTCALL
22939 #if CYTHON_ASSUME_SAFE_MACROS
22940 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
22941 #else
22942 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
22943 #endif
22944 #endif
22945 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
22946 {
22947 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_GTdata,0};
22948 if (__pyx_kwds) {
22949 Py_ssize_t kw_args;
22950 switch (__pyx_nargs) {
22951 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
22952 CYTHON_FALLTHROUGH;
22953 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
22954 CYTHON_FALLTHROUGH;
22955 case 0: break;
22956 default: goto __pyx_L5_argtuple_error;
22957 }
22958 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
22959 switch (__pyx_nargs) {
22960 case 0:
22961 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
22962 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
22963 kw_args--;
22964 }
22965 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 620, __pyx_L3_error)
22966 else goto __pyx_L5_argtuple_error;
22967 CYTHON_FALLTHROUGH;
22968 case 1:
22969 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_GTdata)) != 0)) {
22970 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
22971 kw_args--;
22972 }
22973 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 620, __pyx_L3_error)
22974 else {
22975 __Pyx_RaiseArgtupleInvalid("convertGTback", 1, 2, 2, 1); __PYX_ERR(0, 620, __pyx_L3_error)
22976 }
22977 }
22978 if (unlikely(kw_args > 0)) {
22979 const Py_ssize_t kwd_pos_args = __pyx_nargs;
22980 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "convertGTback") < 0)) __PYX_ERR(0, 620, __pyx_L3_error)
22981 }
22982 } else if (unlikely(__pyx_nargs != 2)) {
22983 goto __pyx_L5_argtuple_error;
22984 } else {
22985 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
22986 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
22987 }
22988 __pyx_v_self = values[0];
22989 __pyx_v_GTdata = values[1];
22990 }
22991 goto __pyx_L6_skip;
22992 __pyx_L5_argtuple_error:;
22993 __Pyx_RaiseArgtupleInvalid("convertGTback", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 620, __pyx_L3_error)
22994 __pyx_L6_skip:;
22995 goto __pyx_L4_argument_unpacking_done;
22996 __pyx_L3_error:;
22997 {
22998 Py_ssize_t __pyx_temp;
22999 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
23000 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
23001 }
23002 }
23003 __Pyx_AddTraceback("pysam.libcvcf.VCF.convertGTback", __pyx_clineno, __pyx_lineno, __pyx_filename);
23004 __Pyx_RefNannyFinishContext();
23005 return NULL;
23006 __pyx_L4_argument_unpacking_done:;
23007 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_26convertGTback(__pyx_self, __pyx_v_self, __pyx_v_GTdata);
23008
23009 /* function exit code */
23010 {
23011 Py_ssize_t __pyx_temp;
23012 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
23013 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
23014 }
23015 }
23016 __Pyx_RefNannyFinishContext();
23017 return __pyx_r;
23018 }
23019
23020 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_GTdata) {
23021 PyObject *__pyx_r = NULL;
23022 __Pyx_RefNannyDeclarations
23023 PyObject *__pyx_t_1 = NULL;
23024 PyObject *__pyx_t_2 = NULL;
23025 int __pyx_lineno = 0;
23026 const char *__pyx_filename = NULL;
23027 int __pyx_clineno = 0;
23028 __Pyx_RefNannySetupContext("convertGTback", 1);
23029
23030 /* "pysam/libcvcf.pyx":621
23031 *
23032 * def convertGTback(self, GTdata):
23033 * return ''.join(map(str,GTdata)) # <<<<<<<<<<<<<<
23034 *
23035 * def parse_formatdata( self, key, value, formatdict, line ):
23036 */
23037 __Pyx_XDECREF(__pyx_r);
23038 __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 621, __pyx_L1_error)
23039 __Pyx_GOTREF(__pyx_t_1);
23040 __Pyx_INCREF((PyObject *)(&PyUnicode_Type));
23041 __Pyx_GIVEREF((PyObject *)(&PyUnicode_Type));
23042 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)(&PyUnicode_Type)))) __PYX_ERR(0, 621, __pyx_L1_error);
23043 __Pyx_INCREF(__pyx_v_GTdata);
23044 __Pyx_GIVEREF(__pyx_v_GTdata);
23045 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_GTdata)) __PYX_ERR(0, 621, __pyx_L1_error);
23046 __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_map, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 621, __pyx_L1_error)
23047 __Pyx_GOTREF(__pyx_t_2);
23048 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
23049 __pyx_t_1 = PyUnicode_Join(__pyx_kp_u_, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 621, __pyx_L1_error)
23050 __Pyx_GOTREF(__pyx_t_1);
23051 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
23052 __pyx_r = __pyx_t_1;
23053 __pyx_t_1 = 0;
23054 goto __pyx_L0;
23055
23056 /* "pysam/libcvcf.pyx":620
23057 * return [".","|","."]
23058 *
23059 * def convertGTback(self, GTdata): # <<<<<<<<<<<<<<
23060 * return ''.join(map(str,GTdata))
23061 *
23062 */
23063
23064 /* function exit code */
23065 __pyx_L1_error:;
23066 __Pyx_XDECREF(__pyx_t_1);
23067 __Pyx_XDECREF(__pyx_t_2);
23068 __Pyx_AddTraceback("pysam.libcvcf.VCF.convertGTback", __pyx_clineno, __pyx_lineno, __pyx_filename);
23069 __pyx_r = NULL;
23070 __pyx_L0:;
23071 __Pyx_XGIVEREF(__pyx_r);
23072 __Pyx_RefNannyFinishContext();
23073 return __pyx_r;
23074 }
23075
23076 /* "pysam/libcvcf.pyx":623
23077 * return ''.join(map(str,GTdata))
23078 *
23079 * def parse_formatdata( self, key, value, formatdict, line ): # <<<<<<<<<<<<<<
23080 * # To do: check that the right number of values is present
23081 * f = formatdict.get(key,None)
23082 */
23083
23084 /* Python wrapper */
23085 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_29parse_formatdata(PyObject *__pyx_self,
23086 #if CYTHON_METH_FASTCALL
23087 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
23088 #else
23089 PyObject *__pyx_args, PyObject *__pyx_kwds
23090 #endif
23091 ); /*proto*/
23092 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_28parse_formatdata, "VCF.parse_formatdata(self, key, value, formatdict, line)");
23093 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_29parse_formatdata = {"parse_formatdata", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_29parse_formatdata, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_28parse_formatdata};
23094 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_29parse_formatdata(PyObject *__pyx_self,
23095 #if CYTHON_METH_FASTCALL
23096 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
23097 #else
23098 PyObject *__pyx_args, PyObject *__pyx_kwds
23099 #endif
23100 ) {
23101 PyObject *__pyx_v_self = 0;
23102 PyObject *__pyx_v_key = 0;
23103 PyObject *__pyx_v_value = 0;
23104 PyObject *__pyx_v_formatdict = 0;
23105 PyObject *__pyx_v_line = 0;
23106 #if !CYTHON_METH_FASTCALL
23107 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
23108 #endif
23109 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
23110 PyObject* values[5] = {0,0,0,0,0};
23111 int __pyx_lineno = 0;
23112 const char *__pyx_filename = NULL;
23113 int __pyx_clineno = 0;
23114 PyObject *__pyx_r = 0;
23115 __Pyx_RefNannyDeclarations
23116 __Pyx_RefNannySetupContext("parse_formatdata (wrapper)", 0);
23117 #if !CYTHON_METH_FASTCALL
23118 #if CYTHON_ASSUME_SAFE_MACROS
23119 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
23120 #else
23121 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
23122 #endif
23123 #endif
23124 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
23125 {
23126 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_key,&__pyx_n_s_value,&__pyx_n_s_formatdict,&__pyx_n_s_line,0};
23127 if (__pyx_kwds) {
23128 Py_ssize_t kw_args;
23129 switch (__pyx_nargs) {
23130 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
23131 CYTHON_FALLTHROUGH;
23132 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
23133 CYTHON_FALLTHROUGH;
23134 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
23135 CYTHON_FALLTHROUGH;
23136 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
23137 CYTHON_FALLTHROUGH;
23138 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
23139 CYTHON_FALLTHROUGH;
23140 case 0: break;
23141 default: goto __pyx_L5_argtuple_error;
23142 }
23143 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
23144 switch (__pyx_nargs) {
23145 case 0:
23146 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
23147 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
23148 kw_args--;
23149 }
23150 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 623, __pyx_L3_error)
23151 else goto __pyx_L5_argtuple_error;
23152 CYTHON_FALLTHROUGH;
23153 case 1:
23154 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_key)) != 0)) {
23155 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
23156 kw_args--;
23157 }
23158 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 623, __pyx_L3_error)
23159 else {
23160 __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 1); __PYX_ERR(0, 623, __pyx_L3_error)
23161 }
23162 CYTHON_FALLTHROUGH;
23163 case 2:
23164 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_value)) != 0)) {
23165 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
23166 kw_args--;
23167 }
23168 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 623, __pyx_L3_error)
23169 else {
23170 __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 2); __PYX_ERR(0, 623, __pyx_L3_error)
23171 }
23172 CYTHON_FALLTHROUGH;
23173 case 3:
23174 if (likely((values[3] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_formatdict)) != 0)) {
23175 (void)__Pyx_Arg_NewRef_FASTCALL(values[3]);
23176 kw_args--;
23177 }
23178 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 623, __pyx_L3_error)
23179 else {
23180 __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 3); __PYX_ERR(0, 623, __pyx_L3_error)
23181 }
23182 CYTHON_FALLTHROUGH;
23183 case 4:
23184 if (likely((values[4] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_line)) != 0)) {
23185 (void)__Pyx_Arg_NewRef_FASTCALL(values[4]);
23186 kw_args--;
23187 }
23188 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 623, __pyx_L3_error)
23189 else {
23190 __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 4); __PYX_ERR(0, 623, __pyx_L3_error)
23191 }
23192 }
23193 if (unlikely(kw_args > 0)) {
23194 const Py_ssize_t kwd_pos_args = __pyx_nargs;
23195 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "parse_formatdata") < 0)) __PYX_ERR(0, 623, __pyx_L3_error)
23196 }
23197 } else if (unlikely(__pyx_nargs != 5)) {
23198 goto __pyx_L5_argtuple_error;
23199 } else {
23200 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
23201 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
23202 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
23203 values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
23204 values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
23205 }
23206 __pyx_v_self = values[0];
23207 __pyx_v_key = values[1];
23208 __pyx_v_value = values[2];
23209 __pyx_v_formatdict = values[3];
23210 __pyx_v_line = values[4];
23211 }
23212 goto __pyx_L6_skip;
23213 __pyx_L5_argtuple_error:;
23214 __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, __pyx_nargs); __PYX_ERR(0, 623, __pyx_L3_error)
23215 __pyx_L6_skip:;
23216 goto __pyx_L4_argument_unpacking_done;
23217 __pyx_L3_error:;
23218 {
23219 Py_ssize_t __pyx_temp;
23220 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
23221 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
23222 }
23223 }
23224 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename);
23225 __Pyx_RefNannyFinishContext();
23226 return NULL;
23227 __pyx_L4_argument_unpacking_done:;
23228 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_28parse_formatdata(__pyx_self, __pyx_v_self, __pyx_v_key, __pyx_v_value, __pyx_v_formatdict, __pyx_v_line);
23229
23230 /* function exit code */
23231 {
23232 Py_ssize_t __pyx_temp;
23233 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
23234 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
23235 }
23236 }
23237 __Pyx_RefNannyFinishContext();
23238 return __pyx_r;
23239 }
23240
23241 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_line) {
23242 PyObject *__pyx_v_f = NULL;
23243 PyObject *__pyx_v_values = NULL;
23244 PyObject *__pyx_v_idx = NULL;
23245 PyObject *__pyx_v_v = NULL;
23246 PyObject *__pyx_r = NULL;
23247 __Pyx_RefNannyDeclarations
23248 PyObject *__pyx_t_1 = NULL;
23249 PyObject *__pyx_t_2 = NULL;
23250 PyObject *__pyx_t_3 = NULL;
23251 unsigned int __pyx_t_4;
23252 int __pyx_t_5;
23253 PyObject *__pyx_t_6 = NULL;
23254 int __pyx_t_7;
23255 int __pyx_t_8;
23256 Py_ssize_t __pyx_t_9;
23257 PyObject *__pyx_t_10 = NULL;
23258 PyObject *(*__pyx_t_11)(PyObject *);
23259 PyObject *__pyx_t_12 = NULL;
23260 PyObject *__pyx_t_13 = NULL;
23261 PyObject *__pyx_t_14 = NULL;
23262 PyObject *__pyx_t_15 = NULL;
23263 PyObject *__pyx_t_16 = NULL;
23264 PyObject *__pyx_t_17 = NULL;
23265 PyObject *__pyx_t_18 = NULL;
23266 Py_ssize_t __pyx_t_19;
23267 Py_UCS4 __pyx_t_20;
23268 PyObject *__pyx_t_21 = NULL;
23269 int __pyx_lineno = 0;
23270 const char *__pyx_filename = NULL;
23271 int __pyx_clineno = 0;
23272 __Pyx_RefNannySetupContext("parse_formatdata", 1);
23273
23274 /* "pysam/libcvcf.pyx":625
23275 * def parse_formatdata( self, key, value, formatdict, line ):
23276 * # To do: check that the right number of values is present
23277 * f = formatdict.get(key,None) # <<<<<<<<<<<<<<
23278 * if f == None:
23279 * self._add_definition(formatdict, key, value, line )
23280 */
23281 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_formatdict, __pyx_n_s_get); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 625, __pyx_L1_error)
23282 __Pyx_GOTREF(__pyx_t_2);
23283 __pyx_t_3 = NULL;
23284 __pyx_t_4 = 0;
23285 #if CYTHON_UNPACK_METHODS
23286 if (likely(PyMethod_Check(__pyx_t_2))) {
23287 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
23288 if (likely(__pyx_t_3)) {
23289 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
23290 __Pyx_INCREF(__pyx_t_3);
23291 __Pyx_INCREF(function);
23292 __Pyx_DECREF_SET(__pyx_t_2, function);
23293 __pyx_t_4 = 1;
23294 }
23295 }
23296 #endif
23297 {
23298 PyObject *__pyx_callargs[3] = {__pyx_t_3, __pyx_v_key, Py_None};
23299 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
23300 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
23301 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 625, __pyx_L1_error)
23302 __Pyx_GOTREF(__pyx_t_1);
23303 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
23304 }
23305 __pyx_v_f = __pyx_t_1;
23306 __pyx_t_1 = 0;
23307
23308 /* "pysam/libcvcf.pyx":626
23309 * # To do: check that the right number of values is present
23310 * f = formatdict.get(key,None)
23311 * if f == None: # <<<<<<<<<<<<<<
23312 * self._add_definition(formatdict, key, value, line )
23313 * f = formatdict[key]
23314 */
23315 __pyx_t_1 = PyObject_RichCompare(__pyx_v_f, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 626, __pyx_L1_error)
23316 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 626, __pyx_L1_error)
23317 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
23318 if (__pyx_t_5) {
23319
23320 /* "pysam/libcvcf.pyx":627
23321 * f = formatdict.get(key,None)
23322 * if f == None:
23323 * self._add_definition(formatdict, key, value, line ) # <<<<<<<<<<<<<<
23324 * f = formatdict[key]
23325 * if f.type == "Flag":
23326 */
23327 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_add_definition); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 627, __pyx_L1_error)
23328 __Pyx_GOTREF(__pyx_t_2);
23329 __pyx_t_3 = NULL;
23330 __pyx_t_4 = 0;
23331 #if CYTHON_UNPACK_METHODS
23332 if (likely(PyMethod_Check(__pyx_t_2))) {
23333 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
23334 if (likely(__pyx_t_3)) {
23335 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
23336 __Pyx_INCREF(__pyx_t_3);
23337 __Pyx_INCREF(function);
23338 __Pyx_DECREF_SET(__pyx_t_2, function);
23339 __pyx_t_4 = 1;
23340 }
23341 }
23342 #endif
23343 {
23344 PyObject *__pyx_callargs[5] = {__pyx_t_3, __pyx_v_formatdict, __pyx_v_key, __pyx_v_value, __pyx_v_line};
23345 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 4+__pyx_t_4);
23346 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
23347 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 627, __pyx_L1_error)
23348 __Pyx_GOTREF(__pyx_t_1);
23349 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
23350 }
23351 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
23352
23353 /* "pysam/libcvcf.pyx":628
23354 * if f == None:
23355 * self._add_definition(formatdict, key, value, line )
23356 * f = formatdict[key] # <<<<<<<<<<<<<<
23357 * if f.type == "Flag":
23358 * if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
23359 */
23360 __pyx_t_1 = __Pyx_PyObject_GetItem(__pyx_v_formatdict, __pyx_v_key); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 628, __pyx_L1_error)
23361 __Pyx_GOTREF(__pyx_t_1);
23362 __Pyx_DECREF_SET(__pyx_v_f, __pyx_t_1);
23363 __pyx_t_1 = 0;
23364
23365 /* "pysam/libcvcf.pyx":626
23366 * # To do: check that the right number of values is present
23367 * f = formatdict.get(key,None)
23368 * if f == None: # <<<<<<<<<<<<<<
23369 * self._add_definition(formatdict, key, value, line )
23370 * f = formatdict[key]
23371 */
23372 }
23373
23374 /* "pysam/libcvcf.pyx":629
23375 * self._add_definition(formatdict, key, value, line )
23376 * f = formatdict[key]
23377 * if f.type == "Flag": # <<<<<<<<<<<<<<
23378 * if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
23379 * return []
23380 */
23381 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 629, __pyx_L1_error)
23382 __Pyx_GOTREF(__pyx_t_1);
23383 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_t_1, __pyx_n_u_Flag, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 629, __pyx_L1_error)
23384 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
23385 if (__pyx_t_5) {
23386
23387 /* "pysam/libcvcf.pyx":630
23388 * f = formatdict[key]
23389 * if f.type == "Flag":
23390 * if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE) # <<<<<<<<<<<<<<
23391 * return []
23392 * values = value.split(',')
23393 */
23394 __pyx_t_5 = (__pyx_v_value != Py_None);
23395 if (__pyx_t_5) {
23396 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 630, __pyx_L1_error)
23397 __Pyx_GOTREF(__pyx_t_2);
23398 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_ERROR_FLAG_HAS_VALUE); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 630, __pyx_L1_error)
23399 __Pyx_GOTREF(__pyx_t_3);
23400 __pyx_t_6 = NULL;
23401 __pyx_t_4 = 0;
23402 #if CYTHON_UNPACK_METHODS
23403 if (likely(PyMethod_Check(__pyx_t_2))) {
23404 __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_2);
23405 if (likely(__pyx_t_6)) {
23406 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
23407 __Pyx_INCREF(__pyx_t_6);
23408 __Pyx_INCREF(function);
23409 __Pyx_DECREF_SET(__pyx_t_2, function);
23410 __pyx_t_4 = 1;
23411 }
23412 }
23413 #endif
23414 {
23415 PyObject *__pyx_callargs[3] = {__pyx_t_6, __pyx_v_line, __pyx_t_3};
23416 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
23417 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
23418 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
23419 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 630, __pyx_L1_error)
23420 __Pyx_GOTREF(__pyx_t_1);
23421 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
23422 }
23423 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
23424 }
23425
23426 /* "pysam/libcvcf.pyx":631
23427 * if f.type == "Flag":
23428 * if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
23429 * return [] # <<<<<<<<<<<<<<
23430 * values = value.split(',')
23431 * # deal with trailing data in some early VCF files
23432 */
23433 __Pyx_XDECREF(__pyx_r);
23434 __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 631, __pyx_L1_error)
23435 __Pyx_GOTREF(__pyx_t_1);
23436 __pyx_r = __pyx_t_1;
23437 __pyx_t_1 = 0;
23438 goto __pyx_L0;
23439
23440 /* "pysam/libcvcf.pyx":629
23441 * self._add_definition(formatdict, key, value, line )
23442 * f = formatdict[key]
23443 * if f.type == "Flag": # <<<<<<<<<<<<<<
23444 * if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
23445 * return []
23446 */
23447 }
23448
23449 /* "pysam/libcvcf.pyx":632
23450 * if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
23451 * return []
23452 * values = value.split(',') # <<<<<<<<<<<<<<
23453 * # deal with trailing data in some early VCF files
23454 * if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
23455 */
23456 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_value, __pyx_n_s_split); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 632, __pyx_L1_error)
23457 __Pyx_GOTREF(__pyx_t_2);
23458 __pyx_t_3 = NULL;
23459 __pyx_t_4 = 0;
23460 #if CYTHON_UNPACK_METHODS
23461 if (likely(PyMethod_Check(__pyx_t_2))) {
23462 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
23463 if (likely(__pyx_t_3)) {
23464 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
23465 __Pyx_INCREF(__pyx_t_3);
23466 __Pyx_INCREF(function);
23467 __Pyx_DECREF_SET(__pyx_t_2, function);
23468 __pyx_t_4 = 1;
23469 }
23470 }
23471 #endif
23472 {
23473 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_kp_u__2};
23474 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
23475 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
23476 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 632, __pyx_L1_error)
23477 __Pyx_GOTREF(__pyx_t_1);
23478 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
23479 }
23480 __pyx_v_values = __pyx_t_1;
23481 __pyx_t_1 = 0;
23482
23483 /* "pysam/libcvcf.pyx":634
23484 * values = value.split(',')
23485 * # deal with trailing data in some early VCF files
23486 * if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: # <<<<<<<<<<<<<<
23487 * self.error(line,self.ERROR_TRAILING_DATA,values[-1])
23488 * values[-1] = values[-1].split(';')[0]
23489 */
23490 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 634, __pyx_L1_error)
23491 __Pyx_GOTREF(__pyx_t_1);
23492 __pyx_t_8 = (__Pyx_PyUnicode_Equals(__pyx_t_1, __pyx_n_u_Float, Py_EQ)); if (unlikely((__pyx_t_8 < 0))) __PYX_ERR(0, 634, __pyx_L1_error)
23493 if (!__pyx_t_8) {
23494 } else {
23495 __pyx_t_7 = __pyx_t_8;
23496 goto __pyx_L9_bool_binop_done;
23497 }
23498 __pyx_t_8 = (__Pyx_PyUnicode_Equals(__pyx_t_1, __pyx_n_u_Integer, Py_EQ)); if (unlikely((__pyx_t_8 < 0))) __PYX_ERR(0, 634, __pyx_L1_error)
23499 __pyx_t_7 = __pyx_t_8;
23500 __pyx_L9_bool_binop_done:;
23501 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
23502 __pyx_t_8 = __pyx_t_7;
23503 if (__pyx_t_8) {
23504 } else {
23505 __pyx_t_5 = __pyx_t_8;
23506 goto __pyx_L7_bool_binop_done;
23507 }
23508 __pyx_t_9 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 634, __pyx_L1_error)
23509 __pyx_t_8 = (__pyx_t_9 > 0);
23510 if (__pyx_t_8) {
23511 } else {
23512 __pyx_t_5 = __pyx_t_8;
23513 goto __pyx_L7_bool_binop_done;
23514 }
23515 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_values, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 634, __pyx_L1_error)
23516 __Pyx_GOTREF(__pyx_t_2);
23517 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_find); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 634, __pyx_L1_error)
23518 __Pyx_GOTREF(__pyx_t_3);
23519 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
23520 __pyx_t_2 = NULL;
23521 __pyx_t_4 = 0;
23522 #if CYTHON_UNPACK_METHODS
23523 if (likely(PyMethod_Check(__pyx_t_3))) {
23524 __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_3);
23525 if (likely(__pyx_t_2)) {
23526 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
23527 __Pyx_INCREF(__pyx_t_2);
23528 __Pyx_INCREF(function);
23529 __Pyx_DECREF_SET(__pyx_t_3, function);
23530 __pyx_t_4 = 1;
23531 }
23532 }
23533 #endif
23534 {
23535 PyObject *__pyx_callargs[2] = {__pyx_t_2, __pyx_kp_u__6};
23536 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
23537 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
23538 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 634, __pyx_L1_error)
23539 __Pyx_GOTREF(__pyx_t_1);
23540 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
23541 }
23542 __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_int_neg_1, Py_GT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 634, __pyx_L1_error)
23543 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
23544 __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_8 < 0))) __PYX_ERR(0, 634, __pyx_L1_error)
23545 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
23546 __pyx_t_5 = __pyx_t_8;
23547 __pyx_L7_bool_binop_done:;
23548 if (__pyx_t_5) {
23549
23550 /* "pysam/libcvcf.pyx":635
23551 * # deal with trailing data in some early VCF files
23552 * if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
23553 * self.error(line,self.ERROR_TRAILING_DATA,values[-1]) # <<<<<<<<<<<<<<
23554 * values[-1] = values[-1].split(';')[0]
23555 * if f.type == "Integer":
23556 */
23557 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 635, __pyx_L1_error)
23558 __Pyx_GOTREF(__pyx_t_1);
23559 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_ERROR_TRAILING_DATA); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 635, __pyx_L1_error)
23560 __Pyx_GOTREF(__pyx_t_2);
23561 __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_values, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 635, __pyx_L1_error)
23562 __Pyx_GOTREF(__pyx_t_6);
23563 __pyx_t_10 = NULL;
23564 __pyx_t_4 = 0;
23565 #if CYTHON_UNPACK_METHODS
23566 if (likely(PyMethod_Check(__pyx_t_1))) {
23567 __pyx_t_10 = PyMethod_GET_SELF(__pyx_t_1);
23568 if (likely(__pyx_t_10)) {
23569 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
23570 __Pyx_INCREF(__pyx_t_10);
23571 __Pyx_INCREF(function);
23572 __Pyx_DECREF_SET(__pyx_t_1, function);
23573 __pyx_t_4 = 1;
23574 }
23575 }
23576 #endif
23577 {
23578 PyObject *__pyx_callargs[4] = {__pyx_t_10, __pyx_v_line, __pyx_t_2, __pyx_t_6};
23579 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
23580 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
23581 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
23582 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
23583 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 635, __pyx_L1_error)
23584 __Pyx_GOTREF(__pyx_t_3);
23585 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
23586 }
23587 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
23588
23589 /* "pysam/libcvcf.pyx":636
23590 * if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
23591 * self.error(line,self.ERROR_TRAILING_DATA,values[-1])
23592 * values[-1] = values[-1].split(';')[0] # <<<<<<<<<<<<<<
23593 * if f.type == "Integer":
23594 * for idx,v in enumerate(values):
23595 */
23596 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_values, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 636, __pyx_L1_error)
23597 __Pyx_GOTREF(__pyx_t_1);
23598 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_split); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 636, __pyx_L1_error)
23599 __Pyx_GOTREF(__pyx_t_6);
23600 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
23601 __pyx_t_1 = NULL;
23602 __pyx_t_4 = 0;
23603 #if CYTHON_UNPACK_METHODS
23604 if (likely(PyMethod_Check(__pyx_t_6))) {
23605 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_6);
23606 if (likely(__pyx_t_1)) {
23607 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
23608 __Pyx_INCREF(__pyx_t_1);
23609 __Pyx_INCREF(function);
23610 __Pyx_DECREF_SET(__pyx_t_6, function);
23611 __pyx_t_4 = 1;
23612 }
23613 }
23614 #endif
23615 {
23616 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_kp_u__6};
23617 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
23618 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
23619 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 636, __pyx_L1_error)
23620 __Pyx_GOTREF(__pyx_t_3);
23621 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
23622 }
23623 __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 636, __pyx_L1_error)
23624 __Pyx_GOTREF(__pyx_t_6);
23625 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
23626 if (unlikely((__Pyx_SetItemInt(__pyx_v_values, -1L, __pyx_t_6, long, 1, __Pyx_PyInt_From_long, 0, 1, 1) < 0))) __PYX_ERR(0, 636, __pyx_L1_error)
23627 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
23628
23629 /* "pysam/libcvcf.pyx":634
23630 * values = value.split(',')
23631 * # deal with trailing data in some early VCF files
23632 * if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: # <<<<<<<<<<<<<<
23633 * self.error(line,self.ERROR_TRAILING_DATA,values[-1])
23634 * values[-1] = values[-1].split(';')[0]
23635 */
23636 }
23637
23638 /* "pysam/libcvcf.pyx":637
23639 * self.error(line,self.ERROR_TRAILING_DATA,values[-1])
23640 * values[-1] = values[-1].split(';')[0]
23641 * if f.type == "Integer": # <<<<<<<<<<<<<<
23642 * for idx,v in enumerate(values):
23643 * try:
23644 */
23645 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_type); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 637, __pyx_L1_error)
23646 __Pyx_GOTREF(__pyx_t_6);
23647 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_t_6, __pyx_n_u_Integer, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 637, __pyx_L1_error)
23648 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
23649 if (__pyx_t_5) {
23650
23651 /* "pysam/libcvcf.pyx":638
23652 * values[-1] = values[-1].split(';')[0]
23653 * if f.type == "Integer":
23654 * for idx,v in enumerate(values): # <<<<<<<<<<<<<<
23655 * try:
23656 * if v == ".": values[idx] = f.missingvalue
23657 */
23658 __Pyx_INCREF(__pyx_int_0);
23659 __pyx_t_6 = __pyx_int_0;
23660 if (likely(PyList_CheckExact(__pyx_v_values)) || PyTuple_CheckExact(__pyx_v_values)) {
23661 __pyx_t_3 = __pyx_v_values; __Pyx_INCREF(__pyx_t_3);
23662 __pyx_t_9 = 0;
23663 __pyx_t_11 = NULL;
23664 } else {
23665 __pyx_t_9 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 638, __pyx_L1_error)
23666 __Pyx_GOTREF(__pyx_t_3);
23667 __pyx_t_11 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_3); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 638, __pyx_L1_error)
23668 }
23669 for (;;) {
23670 if (likely(!__pyx_t_11)) {
23671 if (likely(PyList_CheckExact(__pyx_t_3))) {
23672 {
23673 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_3);
23674 #if !CYTHON_ASSUME_SAFE_MACROS
23675 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 638, __pyx_L1_error)
23676 #endif
23677 if (__pyx_t_9 >= __pyx_temp) break;
23678 }
23679 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
23680 __pyx_t_1 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_9); __Pyx_INCREF(__pyx_t_1); __pyx_t_9++; if (unlikely((0 < 0))) __PYX_ERR(0, 638, __pyx_L1_error)
23681 #else
23682 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_3, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 638, __pyx_L1_error)
23683 __Pyx_GOTREF(__pyx_t_1);
23684 #endif
23685 } else {
23686 {
23687 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_3);
23688 #if !CYTHON_ASSUME_SAFE_MACROS
23689 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 638, __pyx_L1_error)
23690 #endif
23691 if (__pyx_t_9 >= __pyx_temp) break;
23692 }
23693 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
23694 __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_9); __Pyx_INCREF(__pyx_t_1); __pyx_t_9++; if (unlikely((0 < 0))) __PYX_ERR(0, 638, __pyx_L1_error)
23695 #else
23696 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_3, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 638, __pyx_L1_error)
23697 __Pyx_GOTREF(__pyx_t_1);
23698 #endif
23699 }
23700 } else {
23701 __pyx_t_1 = __pyx_t_11(__pyx_t_3);
23702 if (unlikely(!__pyx_t_1)) {
23703 PyObject* exc_type = PyErr_Occurred();
23704 if (exc_type) {
23705 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
23706 else __PYX_ERR(0, 638, __pyx_L1_error)
23707 }
23708 break;
23709 }
23710 __Pyx_GOTREF(__pyx_t_1);
23711 }
23712 __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_1);
23713 __pyx_t_1 = 0;
23714 __Pyx_INCREF(__pyx_t_6);
23715 __Pyx_XDECREF_SET(__pyx_v_idx, __pyx_t_6);
23716 __pyx_t_1 = __Pyx_PyInt_AddObjC(__pyx_t_6, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 638, __pyx_L1_error)
23717 __Pyx_GOTREF(__pyx_t_1);
23718 __Pyx_DECREF(__pyx_t_6);
23719 __pyx_t_6 = __pyx_t_1;
23720 __pyx_t_1 = 0;
23721
23722 /* "pysam/libcvcf.pyx":639
23723 * if f.type == "Integer":
23724 * for idx,v in enumerate(values):
23725 * try: # <<<<<<<<<<<<<<
23726 * if v == ".": values[idx] = f.missingvalue
23727 * else: values[idx] = int(v)
23728 */
23729 {
23730 __Pyx_PyThreadState_declare
23731 __Pyx_PyThreadState_assign
23732 __Pyx_ExceptionSave(&__pyx_t_12, &__pyx_t_13, &__pyx_t_14);
23733 __Pyx_XGOTREF(__pyx_t_12);
23734 __Pyx_XGOTREF(__pyx_t_13);
23735 __Pyx_XGOTREF(__pyx_t_14);
23736 /*try:*/ {
23737
23738 /* "pysam/libcvcf.pyx":640
23739 * for idx,v in enumerate(values):
23740 * try:
23741 * if v == ".": values[idx] = f.missingvalue # <<<<<<<<<<<<<<
23742 * else: values[idx] = int(v)
23743 * except:
23744 */
23745 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_v_v, __pyx_kp_u__5, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 640, __pyx_L15_error)
23746 if (__pyx_t_5) {
23747 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_missingvalue); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 640, __pyx_L15_error)
23748 __Pyx_GOTREF(__pyx_t_1);
23749 if (unlikely((PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_1) < 0))) __PYX_ERR(0, 640, __pyx_L15_error)
23750 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
23751 goto __pyx_L23;
23752 }
23753
23754 /* "pysam/libcvcf.pyx":641
23755 * try:
23756 * if v == ".": values[idx] = f.missingvalue
23757 * else: values[idx] = int(v) # <<<<<<<<<<<<<<
23758 * except:
23759 * self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values)))
23760 */
23761 /*else*/ {
23762 __pyx_t_1 = __Pyx_PyNumber_Int(__pyx_v_v); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 641, __pyx_L15_error)
23763 __Pyx_GOTREF(__pyx_t_1);
23764 if (unlikely((PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_1) < 0))) __PYX_ERR(0, 641, __pyx_L15_error)
23765 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
23766 }
23767 __pyx_L23:;
23768
23769 /* "pysam/libcvcf.pyx":639
23770 * if f.type == "Integer":
23771 * for idx,v in enumerate(values):
23772 * try: # <<<<<<<<<<<<<<
23773 * if v == ".": values[idx] = f.missingvalue
23774 * else: values[idx] = int(v)
23775 */
23776 }
23777 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
23778 __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
23779 __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
23780 goto __pyx_L22_try_end;
23781 __pyx_L15_error:;
23782 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
23783 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
23784 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
23785
23786 /* "pysam/libcvcf.pyx":642
23787 * if v == ".": values[idx] = f.missingvalue
23788 * else: values[idx] = int(v)
23789 * except: # <<<<<<<<<<<<<<
23790 * self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values)))
23791 * return [0] * len(values)
23792 */
23793 /*except:*/ {
23794 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename);
23795 if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_2, &__pyx_t_10) < 0) __PYX_ERR(0, 642, __pyx_L17_except_error)
23796 __Pyx_XGOTREF(__pyx_t_1);
23797 __Pyx_XGOTREF(__pyx_t_2);
23798 __Pyx_XGOTREF(__pyx_t_10);
23799
23800 /* "pysam/libcvcf.pyx":643
23801 * else: values[idx] = int(v)
23802 * except:
23803 * self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values))) # <<<<<<<<<<<<<<
23804 * return [0] * len(values)
23805 * return values
23806 */
23807 __pyx_t_16 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 643, __pyx_L17_except_error)
23808 __Pyx_GOTREF(__pyx_t_16);
23809 __pyx_t_17 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_ERROR_FORMAT_NOT_INTEGER); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 643, __pyx_L17_except_error)
23810 __Pyx_GOTREF(__pyx_t_17);
23811 __pyx_t_18 = PyTuple_New(3); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 643, __pyx_L17_except_error)
23812 __Pyx_GOTREF(__pyx_t_18);
23813 __pyx_t_19 = 0;
23814 __pyx_t_20 = 127;
23815 __pyx_t_21 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_key), __pyx_empty_unicode); if (unlikely(!__pyx_t_21)) __PYX_ERR(0, 643, __pyx_L17_except_error)
23816 __Pyx_GOTREF(__pyx_t_21);
23817 __pyx_t_20 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_21) > __pyx_t_20) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_21) : __pyx_t_20;
23818 __pyx_t_19 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_21);
23819 __Pyx_GIVEREF(__pyx_t_21);
23820 PyTuple_SET_ITEM(__pyx_t_18, 0, __pyx_t_21);
23821 __pyx_t_21 = 0;
23822 __Pyx_INCREF(__pyx_kp_u__7);
23823 __pyx_t_19 += 1;
23824 __Pyx_GIVEREF(__pyx_kp_u__7);
23825 PyTuple_SET_ITEM(__pyx_t_18, 1, __pyx_kp_u__7);
23826 __pyx_t_21 = __Pyx_PyObject_Unicode(__pyx_v_values); if (unlikely(!__pyx_t_21)) __PYX_ERR(0, 643, __pyx_L17_except_error)
23827 __Pyx_GOTREF(__pyx_t_21);
23828 __pyx_t_20 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_21) > __pyx_t_20) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_21) : __pyx_t_20;
23829 __pyx_t_19 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_21);
23830 __Pyx_GIVEREF(__pyx_t_21);
23831 PyTuple_SET_ITEM(__pyx_t_18, 2, __pyx_t_21);
23832 __pyx_t_21 = 0;
23833 __pyx_t_21 = __Pyx_PyUnicode_Join(__pyx_t_18, 3, __pyx_t_19, __pyx_t_20); if (unlikely(!__pyx_t_21)) __PYX_ERR(0, 643, __pyx_L17_except_error)
23834 __Pyx_GOTREF(__pyx_t_21);
23835 __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
23836 __pyx_t_18 = NULL;
23837 __pyx_t_4 = 0;
23838 #if CYTHON_UNPACK_METHODS
23839 if (likely(PyMethod_Check(__pyx_t_16))) {
23840 __pyx_t_18 = PyMethod_GET_SELF(__pyx_t_16);
23841 if (likely(__pyx_t_18)) {
23842 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_16);
23843 __Pyx_INCREF(__pyx_t_18);
23844 __Pyx_INCREF(function);
23845 __Pyx_DECREF_SET(__pyx_t_16, function);
23846 __pyx_t_4 = 1;
23847 }
23848 }
23849 #endif
23850 {
23851 PyObject *__pyx_callargs[4] = {__pyx_t_18, __pyx_v_line, __pyx_t_17, __pyx_t_21};
23852 __pyx_t_15 = __Pyx_PyObject_FastCall(__pyx_t_16, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
23853 __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
23854 __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
23855 __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
23856 if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 643, __pyx_L17_except_error)
23857 __Pyx_GOTREF(__pyx_t_15);
23858 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
23859 }
23860 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
23861
23862 /* "pysam/libcvcf.pyx":644
23863 * except:
23864 * self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values)))
23865 * return [0] * len(values) # <<<<<<<<<<<<<<
23866 * return values
23867 * elif f.type == "String":
23868 */
23869 __Pyx_XDECREF(__pyx_r);
23870 __pyx_t_19 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_19 == ((Py_ssize_t)-1))) __PYX_ERR(0, 644, __pyx_L17_except_error)
23871 __pyx_t_15 = PyList_New(1 * ((__pyx_t_19<0) ? 0:__pyx_t_19)); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 644, __pyx_L17_except_error)
23872 __Pyx_GOTREF(__pyx_t_15);
23873 { Py_ssize_t __pyx_temp;
23874 for (__pyx_temp=0; __pyx_temp < __pyx_t_19; __pyx_temp++) {
23875 __Pyx_INCREF(__pyx_int_0);
23876 __Pyx_GIVEREF(__pyx_int_0);
23877 if (__Pyx_PyList_SET_ITEM(__pyx_t_15, __pyx_temp, __pyx_int_0)) __PYX_ERR(0, 644, __pyx_L17_except_error);
23878 }
23879 }
23880 __pyx_r = __pyx_t_15;
23881 __pyx_t_15 = 0;
23882 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
23883 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
23884 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
23885 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
23886 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
23887 goto __pyx_L18_except_return;
23888 }
23889
23890 /* "pysam/libcvcf.pyx":639
23891 * if f.type == "Integer":
23892 * for idx,v in enumerate(values):
23893 * try: # <<<<<<<<<<<<<<
23894 * if v == ".": values[idx] = f.missingvalue
23895 * else: values[idx] = int(v)
23896 */
23897 __pyx_L17_except_error:;
23898 __Pyx_XGIVEREF(__pyx_t_12);
23899 __Pyx_XGIVEREF(__pyx_t_13);
23900 __Pyx_XGIVEREF(__pyx_t_14);
23901 __Pyx_ExceptionReset(__pyx_t_12, __pyx_t_13, __pyx_t_14);
23902 goto __pyx_L1_error;
23903 __pyx_L18_except_return:;
23904 __Pyx_XGIVEREF(__pyx_t_12);
23905 __Pyx_XGIVEREF(__pyx_t_13);
23906 __Pyx_XGIVEREF(__pyx_t_14);
23907 __Pyx_ExceptionReset(__pyx_t_12, __pyx_t_13, __pyx_t_14);
23908 goto __pyx_L0;
23909 __pyx_L22_try_end:;
23910 }
23911
23912 /* "pysam/libcvcf.pyx":638
23913 * values[-1] = values[-1].split(';')[0]
23914 * if f.type == "Integer":
23915 * for idx,v in enumerate(values): # <<<<<<<<<<<<<<
23916 * try:
23917 * if v == ".": values[idx] = f.missingvalue
23918 */
23919 }
23920 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
23921 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
23922
23923 /* "pysam/libcvcf.pyx":645
23924 * self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values)))
23925 * return [0] * len(values)
23926 * return values # <<<<<<<<<<<<<<
23927 * elif f.type == "String":
23928 * self._line = line
23929 */
23930 __Pyx_XDECREF(__pyx_r);
23931 __Pyx_INCREF(__pyx_v_values);
23932 __pyx_r = __pyx_v_values;
23933 goto __pyx_L0;
23934
23935 /* "pysam/libcvcf.pyx":637
23936 * self.error(line,self.ERROR_TRAILING_DATA,values[-1])
23937 * values[-1] = values[-1].split(';')[0]
23938 * if f.type == "Integer": # <<<<<<<<<<<<<<
23939 * for idx,v in enumerate(values):
23940 * try:
23941 */
23942 }
23943
23944 /* "pysam/libcvcf.pyx":646
23945 * return [0] * len(values)
23946 * return values
23947 * elif f.type == "String": # <<<<<<<<<<<<<<
23948 * self._line = line
23949 * if f.id == "GT": values = list(map( self.convertGT, values ))
23950 */
23951 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_type); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 646, __pyx_L1_error)
23952 __Pyx_GOTREF(__pyx_t_6);
23953 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_t_6, __pyx_n_u_String, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 646, __pyx_L1_error)
23954 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
23955 if (__pyx_t_5) {
23956
23957 /* "pysam/libcvcf.pyx":647
23958 * return values
23959 * elif f.type == "String":
23960 * self._line = line # <<<<<<<<<<<<<<
23961 * if f.id == "GT": values = list(map( self.convertGT, values ))
23962 * return values
23963 */
23964 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_line_2, __pyx_v_line) < 0) __PYX_ERR(0, 647, __pyx_L1_error)
23965
23966 /* "pysam/libcvcf.pyx":648
23967 * elif f.type == "String":
23968 * self._line = line
23969 * if f.id == "GT": values = list(map( self.convertGT, values )) # <<<<<<<<<<<<<<
23970 * return values
23971 * elif f.type == "Character":
23972 */
23973 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_id_2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 648, __pyx_L1_error)
23974 __Pyx_GOTREF(__pyx_t_6);
23975 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_t_6, __pyx_n_u_GT, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 648, __pyx_L1_error)
23976 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
23977 if (__pyx_t_5) {
23978 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_convertGT); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 648, __pyx_L1_error)
23979 __Pyx_GOTREF(__pyx_t_6);
23980 __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 648, __pyx_L1_error)
23981 __Pyx_GOTREF(__pyx_t_3);
23982 __Pyx_GIVEREF(__pyx_t_6);
23983 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_6)) __PYX_ERR(0, 648, __pyx_L1_error);
23984 __Pyx_INCREF(__pyx_v_values);
23985 __Pyx_GIVEREF(__pyx_v_values);
23986 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_values)) __PYX_ERR(0, 648, __pyx_L1_error);
23987 __pyx_t_6 = 0;
23988 __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_map, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 648, __pyx_L1_error)
23989 __Pyx_GOTREF(__pyx_t_6);
23990 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
23991 __pyx_t_3 = __Pyx_PySequence_ListKeepNew(__pyx_t_6); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 648, __pyx_L1_error)
23992 __Pyx_GOTREF(__pyx_t_3);
23993 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
23994 __Pyx_DECREF_SET(__pyx_v_values, __pyx_t_3);
23995 __pyx_t_3 = 0;
23996 }
23997
23998 /* "pysam/libcvcf.pyx":649
23999 * self._line = line
24000 * if f.id == "GT": values = list(map( self.convertGT, values ))
24001 * return values # <<<<<<<<<<<<<<
24002 * elif f.type == "Character":
24003 * for v in values:
24004 */
24005 __Pyx_XDECREF(__pyx_r);
24006 __Pyx_INCREF(__pyx_v_values);
24007 __pyx_r = __pyx_v_values;
24008 goto __pyx_L0;
24009
24010 /* "pysam/libcvcf.pyx":646
24011 * return [0] * len(values)
24012 * return values
24013 * elif f.type == "String": # <<<<<<<<<<<<<<
24014 * self._line = line
24015 * if f.id == "GT": values = list(map( self.convertGT, values ))
24016 */
24017 }
24018
24019 /* "pysam/libcvcf.pyx":650
24020 * if f.id == "GT": values = list(map( self.convertGT, values ))
24021 * return values
24022 * elif f.type == "Character": # <<<<<<<<<<<<<<
24023 * for v in values:
24024 * if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
24025 */
24026 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_type); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 650, __pyx_L1_error)
24027 __Pyx_GOTREF(__pyx_t_3);
24028 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_t_3, __pyx_n_u_Character, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 650, __pyx_L1_error)
24029 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
24030 if (__pyx_t_5) {
24031
24032 /* "pysam/libcvcf.pyx":651
24033 * return values
24034 * elif f.type == "Character":
24035 * for v in values: # <<<<<<<<<<<<<<
24036 * if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
24037 * return values
24038 */
24039 if (likely(PyList_CheckExact(__pyx_v_values)) || PyTuple_CheckExact(__pyx_v_values)) {
24040 __pyx_t_3 = __pyx_v_values; __Pyx_INCREF(__pyx_t_3);
24041 __pyx_t_9 = 0;
24042 __pyx_t_11 = NULL;
24043 } else {
24044 __pyx_t_9 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 651, __pyx_L1_error)
24045 __Pyx_GOTREF(__pyx_t_3);
24046 __pyx_t_11 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_3); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 651, __pyx_L1_error)
24047 }
24048 for (;;) {
24049 if (likely(!__pyx_t_11)) {
24050 if (likely(PyList_CheckExact(__pyx_t_3))) {
24051 {
24052 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_3);
24053 #if !CYTHON_ASSUME_SAFE_MACROS
24054 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 651, __pyx_L1_error)
24055 #endif
24056 if (__pyx_t_9 >= __pyx_temp) break;
24057 }
24058 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
24059 __pyx_t_6 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_9); __Pyx_INCREF(__pyx_t_6); __pyx_t_9++; if (unlikely((0 < 0))) __PYX_ERR(0, 651, __pyx_L1_error)
24060 #else
24061 __pyx_t_6 = __Pyx_PySequence_ITEM(__pyx_t_3, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 651, __pyx_L1_error)
24062 __Pyx_GOTREF(__pyx_t_6);
24063 #endif
24064 } else {
24065 {
24066 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_3);
24067 #if !CYTHON_ASSUME_SAFE_MACROS
24068 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 651, __pyx_L1_error)
24069 #endif
24070 if (__pyx_t_9 >= __pyx_temp) break;
24071 }
24072 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
24073 __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_9); __Pyx_INCREF(__pyx_t_6); __pyx_t_9++; if (unlikely((0 < 0))) __PYX_ERR(0, 651, __pyx_L1_error)
24074 #else
24075 __pyx_t_6 = __Pyx_PySequence_ITEM(__pyx_t_3, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 651, __pyx_L1_error)
24076 __Pyx_GOTREF(__pyx_t_6);
24077 #endif
24078 }
24079 } else {
24080 __pyx_t_6 = __pyx_t_11(__pyx_t_3);
24081 if (unlikely(!__pyx_t_6)) {
24082 PyObject* exc_type = PyErr_Occurred();
24083 if (exc_type) {
24084 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
24085 else __PYX_ERR(0, 651, __pyx_L1_error)
24086 }
24087 break;
24088 }
24089 __Pyx_GOTREF(__pyx_t_6);
24090 }
24091 __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_6);
24092 __pyx_t_6 = 0;
24093
24094 /* "pysam/libcvcf.pyx":652
24095 * elif f.type == "Character":
24096 * for v in values:
24097 * if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR) # <<<<<<<<<<<<<<
24098 * return values
24099 * elif f.type == "Float":
24100 */
24101 __pyx_t_19 = PyObject_Length(__pyx_v_v); if (unlikely(__pyx_t_19 == ((Py_ssize_t)-1))) __PYX_ERR(0, 652, __pyx_L1_error)
24102 __pyx_t_5 = (__pyx_t_19 != 1);
24103 if (__pyx_t_5) {
24104 __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 652, __pyx_L1_error)
24105 __Pyx_GOTREF(__pyx_t_10);
24106 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_ERROR_FORMAT_NOT_CHAR); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 652, __pyx_L1_error)
24107 __Pyx_GOTREF(__pyx_t_2);
24108 __pyx_t_1 = NULL;
24109 __pyx_t_4 = 0;
24110 #if CYTHON_UNPACK_METHODS
24111 if (likely(PyMethod_Check(__pyx_t_10))) {
24112 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_10);
24113 if (likely(__pyx_t_1)) {
24114 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_10);
24115 __Pyx_INCREF(__pyx_t_1);
24116 __Pyx_INCREF(function);
24117 __Pyx_DECREF_SET(__pyx_t_10, function);
24118 __pyx_t_4 = 1;
24119 }
24120 }
24121 #endif
24122 {
24123 PyObject *__pyx_callargs[3] = {__pyx_t_1, __pyx_v_line, __pyx_t_2};
24124 __pyx_t_6 = __Pyx_PyObject_FastCall(__pyx_t_10, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
24125 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
24126 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
24127 if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 652, __pyx_L1_error)
24128 __Pyx_GOTREF(__pyx_t_6);
24129 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
24130 }
24131 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
24132 }
24133
24134 /* "pysam/libcvcf.pyx":651
24135 * return values
24136 * elif f.type == "Character":
24137 * for v in values: # <<<<<<<<<<<<<<
24138 * if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
24139 * return values
24140 */
24141 }
24142 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
24143
24144 /* "pysam/libcvcf.pyx":653
24145 * for v in values:
24146 * if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
24147 * return values # <<<<<<<<<<<<<<
24148 * elif f.type == "Float":
24149 * for idx,v in enumerate(values):
24150 */
24151 __Pyx_XDECREF(__pyx_r);
24152 __Pyx_INCREF(__pyx_v_values);
24153 __pyx_r = __pyx_v_values;
24154 goto __pyx_L0;
24155
24156 /* "pysam/libcvcf.pyx":650
24157 * if f.id == "GT": values = list(map( self.convertGT, values ))
24158 * return values
24159 * elif f.type == "Character": # <<<<<<<<<<<<<<
24160 * for v in values:
24161 * if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
24162 */
24163 }
24164
24165 /* "pysam/libcvcf.pyx":654
24166 * if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
24167 * return values
24168 * elif f.type == "Float": # <<<<<<<<<<<<<<
24169 * for idx,v in enumerate(values):
24170 * if v == ".": values[idx] = f.missingvalue
24171 */
24172 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_type); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 654, __pyx_L1_error)
24173 __Pyx_GOTREF(__pyx_t_3);
24174 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_t_3, __pyx_n_u_Float, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 654, __pyx_L1_error)
24175 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
24176 if (__pyx_t_5) {
24177
24178 /* "pysam/libcvcf.pyx":655
24179 * return values
24180 * elif f.type == "Float":
24181 * for idx,v in enumerate(values): # <<<<<<<<<<<<<<
24182 * if v == ".": values[idx] = f.missingvalue
24183 * try: return list(map(float,values))
24184 */
24185 __Pyx_INCREF(__pyx_int_0);
24186 __pyx_t_3 = __pyx_int_0;
24187 if (likely(PyList_CheckExact(__pyx_v_values)) || PyTuple_CheckExact(__pyx_v_values)) {
24188 __pyx_t_6 = __pyx_v_values; __Pyx_INCREF(__pyx_t_6);
24189 __pyx_t_9 = 0;
24190 __pyx_t_11 = NULL;
24191 } else {
24192 __pyx_t_9 = -1; __pyx_t_6 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 655, __pyx_L1_error)
24193 __Pyx_GOTREF(__pyx_t_6);
24194 __pyx_t_11 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_6); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 655, __pyx_L1_error)
24195 }
24196 for (;;) {
24197 if (likely(!__pyx_t_11)) {
24198 if (likely(PyList_CheckExact(__pyx_t_6))) {
24199 {
24200 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_6);
24201 #if !CYTHON_ASSUME_SAFE_MACROS
24202 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 655, __pyx_L1_error)
24203 #endif
24204 if (__pyx_t_9 >= __pyx_temp) break;
24205 }
24206 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
24207 __pyx_t_10 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_10); __pyx_t_9++; if (unlikely((0 < 0))) __PYX_ERR(0, 655, __pyx_L1_error)
24208 #else
24209 __pyx_t_10 = __Pyx_PySequence_ITEM(__pyx_t_6, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 655, __pyx_L1_error)
24210 __Pyx_GOTREF(__pyx_t_10);
24211 #endif
24212 } else {
24213 {
24214 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_6);
24215 #if !CYTHON_ASSUME_SAFE_MACROS
24216 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 655, __pyx_L1_error)
24217 #endif
24218 if (__pyx_t_9 >= __pyx_temp) break;
24219 }
24220 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
24221 __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_10); __pyx_t_9++; if (unlikely((0 < 0))) __PYX_ERR(0, 655, __pyx_L1_error)
24222 #else
24223 __pyx_t_10 = __Pyx_PySequence_ITEM(__pyx_t_6, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 655, __pyx_L1_error)
24224 __Pyx_GOTREF(__pyx_t_10);
24225 #endif
24226 }
24227 } else {
24228 __pyx_t_10 = __pyx_t_11(__pyx_t_6);
24229 if (unlikely(!__pyx_t_10)) {
24230 PyObject* exc_type = PyErr_Occurred();
24231 if (exc_type) {
24232 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
24233 else __PYX_ERR(0, 655, __pyx_L1_error)
24234 }
24235 break;
24236 }
24237 __Pyx_GOTREF(__pyx_t_10);
24238 }
24239 __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_10);
24240 __pyx_t_10 = 0;
24241 __Pyx_INCREF(__pyx_t_3);
24242 __Pyx_XDECREF_SET(__pyx_v_idx, __pyx_t_3);
24243 __pyx_t_10 = __Pyx_PyInt_AddObjC(__pyx_t_3, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 655, __pyx_L1_error)
24244 __Pyx_GOTREF(__pyx_t_10);
24245 __Pyx_DECREF(__pyx_t_3);
24246 __pyx_t_3 = __pyx_t_10;
24247 __pyx_t_10 = 0;
24248
24249 /* "pysam/libcvcf.pyx":656
24250 * elif f.type == "Float":
24251 * for idx,v in enumerate(values):
24252 * if v == ".": values[idx] = f.missingvalue # <<<<<<<<<<<<<<
24253 * try: return list(map(float,values))
24254 * except:
24255 */
24256 __pyx_t_5 = (__Pyx_PyUnicode_Equals(__pyx_v_v, __pyx_kp_u__5, Py_EQ)); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 656, __pyx_L1_error)
24257 if (__pyx_t_5) {
24258 __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_missingvalue); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 656, __pyx_L1_error)
24259 __Pyx_GOTREF(__pyx_t_10);
24260 if (unlikely((PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_10) < 0))) __PYX_ERR(0, 656, __pyx_L1_error)
24261 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
24262 }
24263
24264 /* "pysam/libcvcf.pyx":655
24265 * return values
24266 * elif f.type == "Float":
24267 * for idx,v in enumerate(values): # <<<<<<<<<<<<<<
24268 * if v == ".": values[idx] = f.missingvalue
24269 * try: return list(map(float,values))
24270 */
24271 }
24272 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
24273 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
24274
24275 /* "pysam/libcvcf.pyx":657
24276 * for idx,v in enumerate(values):
24277 * if v == ".": values[idx] = f.missingvalue
24278 * try: return list(map(float,values)) # <<<<<<<<<<<<<<
24279 * except:
24280 * self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values)))
24281 */
24282 {
24283 __Pyx_PyThreadState_declare
24284 __Pyx_PyThreadState_assign
24285 __Pyx_ExceptionSave(&__pyx_t_14, &__pyx_t_13, &__pyx_t_12);
24286 __Pyx_XGOTREF(__pyx_t_14);
24287 __Pyx_XGOTREF(__pyx_t_13);
24288 __Pyx_XGOTREF(__pyx_t_12);
24289 /*try:*/ {
24290 __Pyx_XDECREF(__pyx_r);
24291 __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 657, __pyx_L36_error)
24292 __Pyx_GOTREF(__pyx_t_3);
24293 __Pyx_INCREF((PyObject *)(&PyFloat_Type));
24294 __Pyx_GIVEREF((PyObject *)(&PyFloat_Type));
24295 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)(&PyFloat_Type)))) __PYX_ERR(0, 657, __pyx_L36_error);
24296 __Pyx_INCREF(__pyx_v_values);
24297 __Pyx_GIVEREF(__pyx_v_values);
24298 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_values)) __PYX_ERR(0, 657, __pyx_L36_error);
24299 __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_map, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 657, __pyx_L36_error)
24300 __Pyx_GOTREF(__pyx_t_6);
24301 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
24302 __pyx_t_3 = __Pyx_PySequence_ListKeepNew(__pyx_t_6); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 657, __pyx_L36_error)
24303 __Pyx_GOTREF(__pyx_t_3);
24304 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
24305 __pyx_r = __pyx_t_3;
24306 __pyx_t_3 = 0;
24307 goto __pyx_L40_try_return;
24308 }
24309 __pyx_L36_error:;
24310 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
24311 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
24312 __Pyx_XDECREF(__pyx_t_15); __pyx_t_15 = 0;
24313 __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
24314 __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
24315 __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
24316 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
24317 __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
24318 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
24319 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
24320
24321 /* "pysam/libcvcf.pyx":658
24322 * if v == ".": values[idx] = f.missingvalue
24323 * try: return list(map(float,values))
24324 * except: # <<<<<<<<<<<<<<
24325 * self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values)))
24326 * return [0.0] * len(values)
24327 */
24328 /*except:*/ {
24329 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename);
24330 if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_6, &__pyx_t_10) < 0) __PYX_ERR(0, 658, __pyx_L38_except_error)
24331 __Pyx_XGOTREF(__pyx_t_3);
24332 __Pyx_XGOTREF(__pyx_t_6);
24333 __Pyx_XGOTREF(__pyx_t_10);
24334
24335 /* "pysam/libcvcf.pyx":659
24336 * try: return list(map(float,values))
24337 * except:
24338 * self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values))) # <<<<<<<<<<<<<<
24339 * return [0.0] * len(values)
24340 * else:
24341 */
24342 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 659, __pyx_L38_except_error)
24343 __Pyx_GOTREF(__pyx_t_1);
24344 __pyx_t_15 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_ERROR_FORMAT_NOT_NUMERICAL); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 659, __pyx_L38_except_error)
24345 __Pyx_GOTREF(__pyx_t_15);
24346 __pyx_t_16 = PyTuple_New(3); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 659, __pyx_L38_except_error)
24347 __Pyx_GOTREF(__pyx_t_16);
24348 __pyx_t_9 = 0;
24349 __pyx_t_20 = 127;
24350 __pyx_t_21 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_key), __pyx_empty_unicode); if (unlikely(!__pyx_t_21)) __PYX_ERR(0, 659, __pyx_L38_except_error)
24351 __Pyx_GOTREF(__pyx_t_21);
24352 __pyx_t_20 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_21) > __pyx_t_20) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_21) : __pyx_t_20;
24353 __pyx_t_9 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_21);
24354 __Pyx_GIVEREF(__pyx_t_21);
24355 PyTuple_SET_ITEM(__pyx_t_16, 0, __pyx_t_21);
24356 __pyx_t_21 = 0;
24357 __Pyx_INCREF(__pyx_kp_u__7);
24358 __pyx_t_9 += 1;
24359 __Pyx_GIVEREF(__pyx_kp_u__7);
24360 PyTuple_SET_ITEM(__pyx_t_16, 1, __pyx_kp_u__7);
24361 __pyx_t_21 = __Pyx_PyObject_Unicode(__pyx_v_values); if (unlikely(!__pyx_t_21)) __PYX_ERR(0, 659, __pyx_L38_except_error)
24362 __Pyx_GOTREF(__pyx_t_21);
24363 __pyx_t_20 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_21) > __pyx_t_20) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_21) : __pyx_t_20;
24364 __pyx_t_9 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_21);
24365 __Pyx_GIVEREF(__pyx_t_21);
24366 PyTuple_SET_ITEM(__pyx_t_16, 2, __pyx_t_21);
24367 __pyx_t_21 = 0;
24368 __pyx_t_21 = __Pyx_PyUnicode_Join(__pyx_t_16, 3, __pyx_t_9, __pyx_t_20); if (unlikely(!__pyx_t_21)) __PYX_ERR(0, 659, __pyx_L38_except_error)
24369 __Pyx_GOTREF(__pyx_t_21);
24370 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
24371 __pyx_t_16 = NULL;
24372 __pyx_t_4 = 0;
24373 #if CYTHON_UNPACK_METHODS
24374 if (likely(PyMethod_Check(__pyx_t_1))) {
24375 __pyx_t_16 = PyMethod_GET_SELF(__pyx_t_1);
24376 if (likely(__pyx_t_16)) {
24377 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
24378 __Pyx_INCREF(__pyx_t_16);
24379 __Pyx_INCREF(function);
24380 __Pyx_DECREF_SET(__pyx_t_1, function);
24381 __pyx_t_4 = 1;
24382 }
24383 }
24384 #endif
24385 {
24386 PyObject *__pyx_callargs[4] = {__pyx_t_16, __pyx_v_line, __pyx_t_15, __pyx_t_21};
24387 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
24388 __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
24389 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
24390 __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
24391 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 659, __pyx_L38_except_error)
24392 __Pyx_GOTREF(__pyx_t_2);
24393 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
24394 }
24395 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
24396
24397 /* "pysam/libcvcf.pyx":660
24398 * except:
24399 * self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values)))
24400 * return [0.0] * len(values) # <<<<<<<<<<<<<<
24401 * else:
24402 * # can't happen
24403 */
24404 __Pyx_XDECREF(__pyx_r);
24405 __pyx_t_9 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 660, __pyx_L38_except_error)
24406 __pyx_t_2 = PyList_New(1 * ((__pyx_t_9<0) ? 0:__pyx_t_9)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 660, __pyx_L38_except_error)
24407 __Pyx_GOTREF(__pyx_t_2);
24408 { Py_ssize_t __pyx_temp;
24409 for (__pyx_temp=0; __pyx_temp < __pyx_t_9; __pyx_temp++) {
24410 __Pyx_INCREF(__pyx_float_0_0);
24411 __Pyx_GIVEREF(__pyx_float_0_0);
24412 if (__Pyx_PyList_SET_ITEM(__pyx_t_2, __pyx_temp, __pyx_float_0_0)) __PYX_ERR(0, 660, __pyx_L38_except_error);
24413 }
24414 }
24415 __pyx_r = __pyx_t_2;
24416 __pyx_t_2 = 0;
24417 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
24418 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
24419 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
24420 goto __pyx_L39_except_return;
24421 }
24422
24423 /* "pysam/libcvcf.pyx":657
24424 * for idx,v in enumerate(values):
24425 * if v == ".": values[idx] = f.missingvalue
24426 * try: return list(map(float,values)) # <<<<<<<<<<<<<<
24427 * except:
24428 * self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values)))
24429 */
24430 __pyx_L38_except_error:;
24431 __Pyx_XGIVEREF(__pyx_t_14);
24432 __Pyx_XGIVEREF(__pyx_t_13);
24433 __Pyx_XGIVEREF(__pyx_t_12);
24434 __Pyx_ExceptionReset(__pyx_t_14, __pyx_t_13, __pyx_t_12);
24435 goto __pyx_L1_error;
24436 __pyx_L40_try_return:;
24437 __Pyx_XGIVEREF(__pyx_t_14);
24438 __Pyx_XGIVEREF(__pyx_t_13);
24439 __Pyx_XGIVEREF(__pyx_t_12);
24440 __Pyx_ExceptionReset(__pyx_t_14, __pyx_t_13, __pyx_t_12);
24441 goto __pyx_L0;
24442 __pyx_L39_except_return:;
24443 __Pyx_XGIVEREF(__pyx_t_14);
24444 __Pyx_XGIVEREF(__pyx_t_13);
24445 __Pyx_XGIVEREF(__pyx_t_12);
24446 __Pyx_ExceptionReset(__pyx_t_14, __pyx_t_13, __pyx_t_12);
24447 goto __pyx_L0;
24448 }
24449
24450 /* "pysam/libcvcf.pyx":654
24451 * if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
24452 * return values
24453 * elif f.type == "Float": # <<<<<<<<<<<<<<
24454 * for idx,v in enumerate(values):
24455 * if v == ".": values[idx] = f.missingvalue
24456 */
24457 }
24458
24459 /* "pysam/libcvcf.pyx":663
24460 * else:
24461 * # can't happen
24462 * self.error(line,self.ERROR_INFO_STRING) # <<<<<<<<<<<<<<
24463 *
24464 * def inregion(self, chrom, pos):
24465 */
24466 /*else*/ {
24467 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 663, __pyx_L1_error)
24468 __Pyx_GOTREF(__pyx_t_6);
24469 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_ERROR_INFO_STRING); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 663, __pyx_L1_error)
24470 __Pyx_GOTREF(__pyx_t_3);
24471 __pyx_t_2 = NULL;
24472 __pyx_t_4 = 0;
24473 #if CYTHON_UNPACK_METHODS
24474 if (likely(PyMethod_Check(__pyx_t_6))) {
24475 __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_6);
24476 if (likely(__pyx_t_2)) {
24477 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
24478 __Pyx_INCREF(__pyx_t_2);
24479 __Pyx_INCREF(function);
24480 __Pyx_DECREF_SET(__pyx_t_6, function);
24481 __pyx_t_4 = 1;
24482 }
24483 }
24484 #endif
24485 {
24486 PyObject *__pyx_callargs[3] = {__pyx_t_2, __pyx_v_line, __pyx_t_3};
24487 __pyx_t_10 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
24488 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
24489 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
24490 if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 663, __pyx_L1_error)
24491 __Pyx_GOTREF(__pyx_t_10);
24492 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
24493 }
24494 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
24495 }
24496
24497 /* "pysam/libcvcf.pyx":623
24498 * return ''.join(map(str,GTdata))
24499 *
24500 * def parse_formatdata( self, key, value, formatdict, line ): # <<<<<<<<<<<<<<
24501 * # To do: check that the right number of values is present
24502 * f = formatdict.get(key,None)
24503 */
24504
24505 /* function exit code */
24506 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
24507 goto __pyx_L0;
24508 __pyx_L1_error:;
24509 __Pyx_XDECREF(__pyx_t_1);
24510 __Pyx_XDECREF(__pyx_t_2);
24511 __Pyx_XDECREF(__pyx_t_3);
24512 __Pyx_XDECREF(__pyx_t_6);
24513 __Pyx_XDECREF(__pyx_t_10);
24514 __Pyx_XDECREF(__pyx_t_15);
24515 __Pyx_XDECREF(__pyx_t_16);
24516 __Pyx_XDECREF(__pyx_t_17);
24517 __Pyx_XDECREF(__pyx_t_18);
24518 __Pyx_XDECREF(__pyx_t_21);
24519 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename);
24520 __pyx_r = NULL;
24521 __pyx_L0:;
24522 __Pyx_XDECREF(__pyx_v_f);
24523 __Pyx_XDECREF(__pyx_v_values);
24524 __Pyx_XDECREF(__pyx_v_idx);
24525 __Pyx_XDECREF(__pyx_v_v);
24526 __Pyx_XGIVEREF(__pyx_r);
24527 __Pyx_RefNannyFinishContext();
24528 return __pyx_r;
24529 }
24530
24531 /* "pysam/libcvcf.pyx":665
24532 * self.error(line,self.ERROR_INFO_STRING)
24533 *
24534 * def inregion(self, chrom, pos): # <<<<<<<<<<<<<<
24535 * if not self._regions: return True
24536 * for r in self._regions:
24537 */
24538
24539 /* Python wrapper */
24540 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_31inregion(PyObject *__pyx_self,
24541 #if CYTHON_METH_FASTCALL
24542 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
24543 #else
24544 PyObject *__pyx_args, PyObject *__pyx_kwds
24545 #endif
24546 ); /*proto*/
24547 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_30inregion, "VCF.inregion(self, chrom, pos)");
24548 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_31inregion = {"inregion", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_31inregion, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_30inregion};
24549 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_31inregion(PyObject *__pyx_self,
24550 #if CYTHON_METH_FASTCALL
24551 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
24552 #else
24553 PyObject *__pyx_args, PyObject *__pyx_kwds
24554 #endif
24555 ) {
24556 PyObject *__pyx_v_self = 0;
24557 PyObject *__pyx_v_chrom = 0;
24558 PyObject *__pyx_v_pos = 0;
24559 #if !CYTHON_METH_FASTCALL
24560 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
24561 #endif
24562 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
24563 PyObject* values[3] = {0,0,0};
24564 int __pyx_lineno = 0;
24565 const char *__pyx_filename = NULL;
24566 int __pyx_clineno = 0;
24567 PyObject *__pyx_r = 0;
24568 __Pyx_RefNannyDeclarations
24569 __Pyx_RefNannySetupContext("inregion (wrapper)", 0);
24570 #if !CYTHON_METH_FASTCALL
24571 #if CYTHON_ASSUME_SAFE_MACROS
24572 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
24573 #else
24574 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
24575 #endif
24576 #endif
24577 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
24578 {
24579 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_chrom,&__pyx_n_s_pos,0};
24580 if (__pyx_kwds) {
24581 Py_ssize_t kw_args;
24582 switch (__pyx_nargs) {
24583 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
24584 CYTHON_FALLTHROUGH;
24585 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
24586 CYTHON_FALLTHROUGH;
24587 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
24588 CYTHON_FALLTHROUGH;
24589 case 0: break;
24590 default: goto __pyx_L5_argtuple_error;
24591 }
24592 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
24593 switch (__pyx_nargs) {
24594 case 0:
24595 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
24596 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
24597 kw_args--;
24598 }
24599 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 665, __pyx_L3_error)
24600 else goto __pyx_L5_argtuple_error;
24601 CYTHON_FALLTHROUGH;
24602 case 1:
24603 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_chrom)) != 0)) {
24604 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
24605 kw_args--;
24606 }
24607 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 665, __pyx_L3_error)
24608 else {
24609 __Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, 1); __PYX_ERR(0, 665, __pyx_L3_error)
24610 }
24611 CYTHON_FALLTHROUGH;
24612 case 2:
24613 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pos)) != 0)) {
24614 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
24615 kw_args--;
24616 }
24617 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 665, __pyx_L3_error)
24618 else {
24619 __Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, 2); __PYX_ERR(0, 665, __pyx_L3_error)
24620 }
24621 }
24622 if (unlikely(kw_args > 0)) {
24623 const Py_ssize_t kwd_pos_args = __pyx_nargs;
24624 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "inregion") < 0)) __PYX_ERR(0, 665, __pyx_L3_error)
24625 }
24626 } else if (unlikely(__pyx_nargs != 3)) {
24627 goto __pyx_L5_argtuple_error;
24628 } else {
24629 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
24630 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
24631 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
24632 }
24633 __pyx_v_self = values[0];
24634 __pyx_v_chrom = values[1];
24635 __pyx_v_pos = values[2];
24636 }
24637 goto __pyx_L6_skip;
24638 __pyx_L5_argtuple_error:;
24639 __Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 665, __pyx_L3_error)
24640 __pyx_L6_skip:;
24641 goto __pyx_L4_argument_unpacking_done;
24642 __pyx_L3_error:;
24643 {
24644 Py_ssize_t __pyx_temp;
24645 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
24646 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
24647 }
24648 }
24649 __Pyx_AddTraceback("pysam.libcvcf.VCF.inregion", __pyx_clineno, __pyx_lineno, __pyx_filename);
24650 __Pyx_RefNannyFinishContext();
24651 return NULL;
24652 __pyx_L4_argument_unpacking_done:;
24653 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_30inregion(__pyx_self, __pyx_v_self, __pyx_v_chrom, __pyx_v_pos);
24654
24655 /* function exit code */
24656 {
24657 Py_ssize_t __pyx_temp;
24658 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
24659 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
24660 }
24661 }
24662 __Pyx_RefNannyFinishContext();
24663 return __pyx_r;
24664 }
24665
24666 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_pos) {
24667 PyObject *__pyx_v_r = NULL;
24668 PyObject *__pyx_r = NULL;
24669 __Pyx_RefNannyDeclarations
24670 PyObject *__pyx_t_1 = NULL;
24671 int __pyx_t_2;
24672 int __pyx_t_3;
24673 PyObject *__pyx_t_4 = NULL;
24674 Py_ssize_t __pyx_t_5;
24675 PyObject *(*__pyx_t_6)(PyObject *);
24676 PyObject *__pyx_t_7 = NULL;
24677 PyObject *__pyx_t_8 = NULL;
24678 int __pyx_lineno = 0;
24679 const char *__pyx_filename = NULL;
24680 int __pyx_clineno = 0;
24681 __Pyx_RefNannySetupContext("inregion", 1);
24682
24683 /* "pysam/libcvcf.pyx":666
24684 *
24685 * def inregion(self, chrom, pos):
24686 * if not self._regions: return True # <<<<<<<<<<<<<<
24687 * for r in self._regions:
24688 * if r[0] == chrom and r[1] <= pos < r[2]: return True
24689 */
24690 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_regions_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 666, __pyx_L1_error)
24691 __Pyx_GOTREF(__pyx_t_1);
24692 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 666, __pyx_L1_error)
24693 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
24694 __pyx_t_3 = (!__pyx_t_2);
24695 if (__pyx_t_3) {
24696 __Pyx_XDECREF(__pyx_r);
24697 __Pyx_INCREF(Py_True);
24698 __pyx_r = Py_True;
24699 goto __pyx_L0;
24700 }
24701
24702 /* "pysam/libcvcf.pyx":667
24703 * def inregion(self, chrom, pos):
24704 * if not self._regions: return True
24705 * for r in self._regions: # <<<<<<<<<<<<<<
24706 * if r[0] == chrom and r[1] <= pos < r[2]: return True
24707 * return False
24708 */
24709 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_regions_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 667, __pyx_L1_error)
24710 __Pyx_GOTREF(__pyx_t_1);
24711 if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) {
24712 __pyx_t_4 = __pyx_t_1; __Pyx_INCREF(__pyx_t_4);
24713 __pyx_t_5 = 0;
24714 __pyx_t_6 = NULL;
24715 } else {
24716 __pyx_t_5 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 667, __pyx_L1_error)
24717 __Pyx_GOTREF(__pyx_t_4);
24718 __pyx_t_6 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_4); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 667, __pyx_L1_error)
24719 }
24720 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
24721 for (;;) {
24722 if (likely(!__pyx_t_6)) {
24723 if (likely(PyList_CheckExact(__pyx_t_4))) {
24724 {
24725 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_4);
24726 #if !CYTHON_ASSUME_SAFE_MACROS
24727 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 667, __pyx_L1_error)
24728 #endif
24729 if (__pyx_t_5 >= __pyx_temp) break;
24730 }
24731 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
24732 __pyx_t_1 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely((0 < 0))) __PYX_ERR(0, 667, __pyx_L1_error)
24733 #else
24734 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 667, __pyx_L1_error)
24735 __Pyx_GOTREF(__pyx_t_1);
24736 #endif
24737 } else {
24738 {
24739 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_4);
24740 #if !CYTHON_ASSUME_SAFE_MACROS
24741 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 667, __pyx_L1_error)
24742 #endif
24743 if (__pyx_t_5 >= __pyx_temp) break;
24744 }
24745 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
24746 __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely((0 < 0))) __PYX_ERR(0, 667, __pyx_L1_error)
24747 #else
24748 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 667, __pyx_L1_error)
24749 __Pyx_GOTREF(__pyx_t_1);
24750 #endif
24751 }
24752 } else {
24753 __pyx_t_1 = __pyx_t_6(__pyx_t_4);
24754 if (unlikely(!__pyx_t_1)) {
24755 PyObject* exc_type = PyErr_Occurred();
24756 if (exc_type) {
24757 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
24758 else __PYX_ERR(0, 667, __pyx_L1_error)
24759 }
24760 break;
24761 }
24762 __Pyx_GOTREF(__pyx_t_1);
24763 }
24764 __Pyx_XDECREF_SET(__pyx_v_r, __pyx_t_1);
24765 __pyx_t_1 = 0;
24766
24767 /* "pysam/libcvcf.pyx":668
24768 * if not self._regions: return True
24769 * for r in self._regions:
24770 * if r[0] == chrom and r[1] <= pos < r[2]: return True # <<<<<<<<<<<<<<
24771 * return False
24772 *
24773 */
24774 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_r, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 668, __pyx_L1_error)
24775 __Pyx_GOTREF(__pyx_t_1);
24776 __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_v_chrom, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 668, __pyx_L1_error)
24777 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
24778 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 668, __pyx_L1_error)
24779 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
24780 if (__pyx_t_2) {
24781 } else {
24782 __pyx_t_3 = __pyx_t_2;
24783 goto __pyx_L7_bool_binop_done;
24784 }
24785 __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_r, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 668, __pyx_L1_error)
24786 __Pyx_GOTREF(__pyx_t_7);
24787 __pyx_t_1 = PyObject_RichCompare(__pyx_t_7, __pyx_v_pos, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 668, __pyx_L1_error)
24788 if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
24789 __Pyx_DECREF(__pyx_t_1);
24790 __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_r, 2, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 668, __pyx_L1_error)
24791 __Pyx_GOTREF(__pyx_t_8);
24792 __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos, __pyx_t_8, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 668, __pyx_L1_error)
24793 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
24794 }
24795 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
24796 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 668, __pyx_L1_error)
24797 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
24798 __pyx_t_3 = __pyx_t_2;
24799 __pyx_L7_bool_binop_done:;
24800 if (__pyx_t_3) {
24801 __Pyx_XDECREF(__pyx_r);
24802 __Pyx_INCREF(Py_True);
24803 __pyx_r = Py_True;
24804 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
24805 goto __pyx_L0;
24806 }
24807
24808 /* "pysam/libcvcf.pyx":667
24809 * def inregion(self, chrom, pos):
24810 * if not self._regions: return True
24811 * for r in self._regions: # <<<<<<<<<<<<<<
24812 * if r[0] == chrom and r[1] <= pos < r[2]: return True
24813 * return False
24814 */
24815 }
24816 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
24817
24818 /* "pysam/libcvcf.pyx":669
24819 * for r in self._regions:
24820 * if r[0] == chrom and r[1] <= pos < r[2]: return True
24821 * return False # <<<<<<<<<<<<<<
24822 *
24823 * def parse_data( self, line, lineparse=False ):
24824 */
24825 __Pyx_XDECREF(__pyx_r);
24826 __Pyx_INCREF(Py_False);
24827 __pyx_r = Py_False;
24828 goto __pyx_L0;
24829
24830 /* "pysam/libcvcf.pyx":665
24831 * self.error(line,self.ERROR_INFO_STRING)
24832 *
24833 * def inregion(self, chrom, pos): # <<<<<<<<<<<<<<
24834 * if not self._regions: return True
24835 * for r in self._regions:
24836 */
24837
24838 /* function exit code */
24839 __pyx_L1_error:;
24840 __Pyx_XDECREF(__pyx_t_1);
24841 __Pyx_XDECREF(__pyx_t_4);
24842 __Pyx_XDECREF(__pyx_t_7);
24843 __Pyx_XDECREF(__pyx_t_8);
24844 __Pyx_AddTraceback("pysam.libcvcf.VCF.inregion", __pyx_clineno, __pyx_lineno, __pyx_filename);
24845 __pyx_r = NULL;
24846 __pyx_L0:;
24847 __Pyx_XDECREF(__pyx_v_r);
24848 __Pyx_XGIVEREF(__pyx_r);
24849 __Pyx_RefNannyFinishContext();
24850 return __pyx_r;
24851 }
24852
24853 /* "pysam/libcvcf.pyx":671
24854 * return False
24855 *
24856 * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<<
24857 * cols = line.split('\t')
24858 * if len(cols) != len(self._samples)+9:
24859 */
24860
24861 /* Python wrapper */
24862 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_33parse_data(PyObject *__pyx_self,
24863 #if CYTHON_METH_FASTCALL
24864 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
24865 #else
24866 PyObject *__pyx_args, PyObject *__pyx_kwds
24867 #endif
24868 ); /*proto*/
24869 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_32parse_data, "VCF.parse_data(self, line, lineparse=False)");
24870 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_33parse_data = {"parse_data", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_33parse_data, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_32parse_data};
24871 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_33parse_data(PyObject *__pyx_self,
24872 #if CYTHON_METH_FASTCALL
24873 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
24874 #else
24875 PyObject *__pyx_args, PyObject *__pyx_kwds
24876 #endif
24877 ) {
24878 PyObject *__pyx_v_self = 0;
24879 PyObject *__pyx_v_line = 0;
24880 PyObject *__pyx_v_lineparse = 0;
24881 #if !CYTHON_METH_FASTCALL
24882 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
24883 #endif
24884 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
24885 PyObject* values[3] = {0,0,0};
24886 int __pyx_lineno = 0;
24887 const char *__pyx_filename = NULL;
24888 int __pyx_clineno = 0;
24889 PyObject *__pyx_r = 0;
24890 __Pyx_RefNannyDeclarations
24891 __Pyx_RefNannySetupContext("parse_data (wrapper)", 0);
24892 #if !CYTHON_METH_FASTCALL
24893 #if CYTHON_ASSUME_SAFE_MACROS
24894 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
24895 #else
24896 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
24897 #endif
24898 #endif
24899 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
24900 {
24901 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_line,&__pyx_n_s_lineparse,0};
24902 values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False)));
24903 if (__pyx_kwds) {
24904 Py_ssize_t kw_args;
24905 switch (__pyx_nargs) {
24906 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
24907 CYTHON_FALLTHROUGH;
24908 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
24909 CYTHON_FALLTHROUGH;
24910 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
24911 CYTHON_FALLTHROUGH;
24912 case 0: break;
24913 default: goto __pyx_L5_argtuple_error;
24914 }
24915 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
24916 switch (__pyx_nargs) {
24917 case 0:
24918 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
24919 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
24920 kw_args--;
24921 }
24922 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 671, __pyx_L3_error)
24923 else goto __pyx_L5_argtuple_error;
24924 CYTHON_FALLTHROUGH;
24925 case 1:
24926 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_line)) != 0)) {
24927 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
24928 kw_args--;
24929 }
24930 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 671, __pyx_L3_error)
24931 else {
24932 __Pyx_RaiseArgtupleInvalid("parse_data", 0, 2, 3, 1); __PYX_ERR(0, 671, __pyx_L3_error)
24933 }
24934 CYTHON_FALLTHROUGH;
24935 case 2:
24936 if (kw_args > 0) {
24937 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_lineparse);
24938 if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
24939 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 671, __pyx_L3_error)
24940 }
24941 }
24942 if (unlikely(kw_args > 0)) {
24943 const Py_ssize_t kwd_pos_args = __pyx_nargs;
24944 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "parse_data") < 0)) __PYX_ERR(0, 671, __pyx_L3_error)
24945 }
24946 } else {
24947 switch (__pyx_nargs) {
24948 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
24949 CYTHON_FALLTHROUGH;
24950 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
24951 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
24952 break;
24953 default: goto __pyx_L5_argtuple_error;
24954 }
24955 }
24956 __pyx_v_self = values[0];
24957 __pyx_v_line = values[1];
24958 __pyx_v_lineparse = values[2];
24959 }
24960 goto __pyx_L6_skip;
24961 __pyx_L5_argtuple_error:;
24962 __Pyx_RaiseArgtupleInvalid("parse_data", 0, 2, 3, __pyx_nargs); __PYX_ERR(0, 671, __pyx_L3_error)
24963 __pyx_L6_skip:;
24964 goto __pyx_L4_argument_unpacking_done;
24965 __pyx_L3_error:;
24966 {
24967 Py_ssize_t __pyx_temp;
24968 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
24969 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
24970 }
24971 }
24972 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
24973 __Pyx_RefNannyFinishContext();
24974 return NULL;
24975 __pyx_L4_argument_unpacking_done:;
24976 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_32parse_data(__pyx_self, __pyx_v_self, __pyx_v_line, __pyx_v_lineparse);
24977
24978 /* function exit code */
24979 {
24980 Py_ssize_t __pyx_temp;
24981 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
24982 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
24983 }
24984 }
24985 __Pyx_RefNannyFinishContext();
24986 return __pyx_r;
24987 }
24988
24989 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_lineparse) {
24990 PyObject *__pyx_v_cols = NULL;
24991 PyObject *__pyx_v_chrom = NULL;
24992 PyObject *__pyx_v_pos = NULL;
24993 PyObject *__pyx_v_id = NULL;
24994 PyObject *__pyx_v_ref = NULL;
24995 PyObject *__pyx_v_c = NULL;
24996 PyObject *__pyx_v_left = NULL;
24997 PyObject *__pyx_v_faref_leftflank = NULL;
24998 PyObject *__pyx_v_faref = NULL;
24999 PyObject *__pyx_v_alt = NULL;
25000 double __pyx_v_qual;
25001 PyObject *__pyx_v_filter = NULL;
25002 PyObject *__pyx_v_info = NULL;
25003 PyObject *__pyx_v_blurp = NULL;
25004 PyObject *__pyx_v_elts = NULL;
25005 PyObject *__pyx_v_v = NULL;
25006 PyObject *__pyx_v_format = NULL;
25007 PyObject *__pyx_v_f = NULL;
25008 PyObject *__pyx_v_newalts = NULL;
25009 int __pyx_v_have_deletions;
25010 PyObject *__pyx_v_a = NULL;
25011 PyObject *__pyx_v_l = NULL;
25012 PyObject *__pyx_v_addns = NULL;
25013 PyObject *__pyx_v_i = NULL;
25014 PyObject *__pyx_v_na = NULL;
25015 PyObject *__pyx_v_s = NULL;
25016 PyObject *__pyx_v_addn = NULL;
25017 PyObject *__pyx_v_allele = NULL;
25018 int __pyx_v_movable;
25019 PyObject *__pyx_v_longest = NULL;
25020 PyObject *__pyx_v_shortest = NULL;
25021 PyObject *__pyx_v_samples = NULL;
25022 PyObject *__pyx_v_sample = NULL;
25023 PyObject *__pyx_v_dict = NULL;
25024 PyObject *__pyx_v_values = NULL;
25025 Py_ssize_t __pyx_v_idx;
25026 PyObject *__pyx_v_expected = NULL;
25027 PyObject *__pyx_v_value = NULL;
25028 PyObject *__pyx_v_d = NULL;
25029 PyObject *__pyx_v_key = NULL;
25030 PyObject *__pyx_8genexpr3__pyx_v_allele = NULL;
25031 PyObject *__pyx_8genexpr4__pyx_v_allele = NULL;
25032 PyObject *__pyx_8genexpr5__pyx_v_allele = NULL;
25033 PyObject *__pyx_8genexpr6__pyx_v_allele = NULL;
25034 PyObject *__pyx_8genexpr7__pyx_v_allele = NULL;
25035 PyObject *__pyx_r = NULL;
25036 __Pyx_RefNannyDeclarations
25037 PyObject *__pyx_t_1 = NULL;
25038 PyObject *__pyx_t_2 = NULL;
25039 PyObject *__pyx_t_3 = NULL;
25040 unsigned int __pyx_t_4;
25041 Py_ssize_t __pyx_t_5;
25042 Py_ssize_t __pyx_t_6;
25043 int __pyx_t_7;
25044 int __pyx_t_8;
25045 PyObject *__pyx_t_9 = NULL;
25046 Py_UCS4 __pyx_t_10;
25047 PyObject *__pyx_t_11 = NULL;
25048 PyObject *__pyx_t_12 = NULL;
25049 PyObject *__pyx_t_13 = NULL;
25050 PyObject *__pyx_t_14 = NULL;
25051 PyObject *__pyx_t_15 = NULL;
25052 PyObject *__pyx_t_16 = NULL;
25053 int __pyx_t_17;
25054 PyObject *(*__pyx_t_18)(PyObject *);
25055 long __pyx_t_19;
25056 double __pyx_t_20;
25057 int __pyx_t_21;
25058 Py_ssize_t __pyx_t_22;
25059 PyObject *__pyx_t_23 = NULL;
25060 PyObject *__pyx_t_24 = NULL;
25061 PyObject *__pyx_t_25 = NULL;
25062 int __pyx_t_26;
25063 PyObject *__pyx_t_27 = NULL;
25064 PyObject *__pyx_t_28 = NULL;
25065 PyObject *__pyx_t_29 = NULL;
25066 Py_ssize_t __pyx_t_30;
25067 Py_ssize_t __pyx_t_31;
25068 PyObject *(*__pyx_t_32)(PyObject *);
25069 int __pyx_lineno = 0;
25070 const char *__pyx_filename = NULL;
25071 int __pyx_clineno = 0;
25072 __Pyx_RefNannySetupContext("parse_data", 1);
25073
25074 /* "pysam/libcvcf.pyx":672
25075 *
25076 * def parse_data( self, line, lineparse=False ):
25077 * cols = line.split('\t') # <<<<<<<<<<<<<<
25078 * if len(cols) != len(self._samples)+9:
25079 * # gracefully deal with absent FORMAT column
25080 */
25081 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_split); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 672, __pyx_L1_error)
25082 __Pyx_GOTREF(__pyx_t_2);
25083 __pyx_t_3 = NULL;
25084 __pyx_t_4 = 0;
25085 #if CYTHON_UNPACK_METHODS
25086 if (likely(PyMethod_Check(__pyx_t_2))) {
25087 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
25088 if (likely(__pyx_t_3)) {
25089 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
25090 __Pyx_INCREF(__pyx_t_3);
25091 __Pyx_INCREF(function);
25092 __Pyx_DECREF_SET(__pyx_t_2, function);
25093 __pyx_t_4 = 1;
25094 }
25095 }
25096 #endif
25097 {
25098 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_kp_u__25};
25099 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
25100 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
25101 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 672, __pyx_L1_error)
25102 __Pyx_GOTREF(__pyx_t_1);
25103 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25104 }
25105 __pyx_v_cols = __pyx_t_1;
25106 __pyx_t_1 = 0;
25107
25108 /* "pysam/libcvcf.pyx":673
25109 * def parse_data( self, line, lineparse=False ):
25110 * cols = line.split('\t')
25111 * if len(cols) != len(self._samples)+9: # <<<<<<<<<<<<<<
25112 * # gracefully deal with absent FORMAT column
25113 * # and those missing samples
25114 */
25115 __pyx_t_5 = PyObject_Length(__pyx_v_cols); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 673, __pyx_L1_error)
25116 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_samples); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 673, __pyx_L1_error)
25117 __Pyx_GOTREF(__pyx_t_1);
25118 __pyx_t_6 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 673, __pyx_L1_error)
25119 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
25120 __pyx_t_7 = (__pyx_t_5 != (__pyx_t_6 + 9));
25121 if (__pyx_t_7) {
25122
25123 /* "pysam/libcvcf.pyx":676
25124 * # gracefully deal with absent FORMAT column
25125 * # and those missing samples
25126 * if len(cols) == 8: # <<<<<<<<<<<<<<
25127 * cols.append("")
25128 * else:
25129 */
25130 __pyx_t_6 = PyObject_Length(__pyx_v_cols); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 676, __pyx_L1_error)
25131 __pyx_t_7 = (__pyx_t_6 == 8);
25132 if (__pyx_t_7) {
25133
25134 /* "pysam/libcvcf.pyx":677
25135 * # and those missing samples
25136 * if len(cols) == 8:
25137 * cols.append("") # <<<<<<<<<<<<<<
25138 * else:
25139 * self.error(line,
25140 */
25141 __pyx_t_8 = __Pyx_PyObject_Append(__pyx_v_cols, __pyx_kp_u_); if (unlikely(__pyx_t_8 == ((int)-1))) __PYX_ERR(0, 677, __pyx_L1_error)
25142
25143 /* "pysam/libcvcf.pyx":676
25144 * # gracefully deal with absent FORMAT column
25145 * # and those missing samples
25146 * if len(cols) == 8: # <<<<<<<<<<<<<<
25147 * cols.append("")
25148 * else:
25149 */
25150 goto __pyx_L4;
25151 }
25152
25153 /* "pysam/libcvcf.pyx":679
25154 * cols.append("")
25155 * else:
25156 * self.error(line, # <<<<<<<<<<<<<<
25157 * self.BAD_NUMBER_OF_COLUMNS,
25158 * "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols)))
25159 */
25160 /*else*/ {
25161 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 679, __pyx_L1_error)
25162 __Pyx_GOTREF(__pyx_t_2);
25163
25164 /* "pysam/libcvcf.pyx":680
25165 * else:
25166 * self.error(line,
25167 * self.BAD_NUMBER_OF_COLUMNS, # <<<<<<<<<<<<<<
25168 * "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols)))
25169 *
25170 */
25171 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_BAD_NUMBER_OF_COLUMNS); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 680, __pyx_L1_error)
25172 __Pyx_GOTREF(__pyx_t_3);
25173
25174 /* "pysam/libcvcf.pyx":681
25175 * self.error(line,
25176 * self.BAD_NUMBER_OF_COLUMNS,
25177 * "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols))) # <<<<<<<<<<<<<<
25178 *
25179 * chrom = cols[0]
25180 */
25181 __pyx_t_9 = PyTuple_New(8); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 681, __pyx_L1_error)
25182 __Pyx_GOTREF(__pyx_t_9);
25183 __pyx_t_6 = 0;
25184 __pyx_t_10 = 127;
25185 __Pyx_INCREF(__pyx_kp_u_expected_3);
25186 __pyx_t_6 += 9;
25187 __Pyx_GIVEREF(__pyx_kp_u_expected_3);
25188 PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_kp_u_expected_3);
25189 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_samples); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 681, __pyx_L1_error)
25190 __Pyx_GOTREF(__pyx_t_11);
25191 __pyx_t_5 = PyObject_Length(__pyx_t_11); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 681, __pyx_L1_error)
25192 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
25193 __pyx_t_11 = __Pyx_PyUnicode_From_Py_ssize_t((__pyx_t_5 + 9), 0, ' ', 'd'); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 681, __pyx_L1_error)
25194 __Pyx_GOTREF(__pyx_t_11);
25195 __pyx_t_6 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_11);
25196 __Pyx_GIVEREF(__pyx_t_11);
25197 PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_11);
25198 __pyx_t_11 = 0;
25199 __Pyx_INCREF(__pyx_kp_u_for);
25200 __pyx_t_6 += 5;
25201 __Pyx_GIVEREF(__pyx_kp_u_for);
25202 PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_kp_u_for);
25203 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_samples); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 681, __pyx_L1_error)
25204 __Pyx_GOTREF(__pyx_t_11);
25205 __pyx_t_5 = PyObject_Length(__pyx_t_11); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 681, __pyx_L1_error)
25206 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
25207 __pyx_t_11 = __Pyx_PyUnicode_From_Py_ssize_t(__pyx_t_5, 0, ' ', 'd'); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 681, __pyx_L1_error)
25208 __Pyx_GOTREF(__pyx_t_11);
25209 __pyx_t_6 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_11);
25210 __Pyx_GIVEREF(__pyx_t_11);
25211 PyTuple_SET_ITEM(__pyx_t_9, 3, __pyx_t_11);
25212 __pyx_t_11 = 0;
25213 __Pyx_INCREF(__pyx_kp_u_samples_2);
25214 __pyx_t_6 += 10;
25215 __Pyx_GIVEREF(__pyx_kp_u_samples_2);
25216 PyTuple_SET_ITEM(__pyx_t_9, 4, __pyx_kp_u_samples_2);
25217 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_samples); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 681, __pyx_L1_error)
25218 __Pyx_GOTREF(__pyx_t_11);
25219 __pyx_t_12 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_11), __pyx_empty_unicode); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 681, __pyx_L1_error)
25220 __Pyx_GOTREF(__pyx_t_12);
25221 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
25222 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_12) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_12) : __pyx_t_10;
25223 __pyx_t_6 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_12);
25224 __Pyx_GIVEREF(__pyx_t_12);
25225 PyTuple_SET_ITEM(__pyx_t_9, 5, __pyx_t_12);
25226 __pyx_t_12 = 0;
25227 __Pyx_INCREF(__pyx_kp_u_got);
25228 __pyx_t_6 += 7;
25229 __Pyx_GIVEREF(__pyx_kp_u_got);
25230 PyTuple_SET_ITEM(__pyx_t_9, 6, __pyx_kp_u_got);
25231 __pyx_t_5 = PyObject_Length(__pyx_v_cols); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 681, __pyx_L1_error)
25232 __pyx_t_12 = __Pyx_PyUnicode_From_Py_ssize_t(__pyx_t_5, 0, ' ', 'd'); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 681, __pyx_L1_error)
25233 __Pyx_GOTREF(__pyx_t_12);
25234 __pyx_t_6 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_12);
25235 __Pyx_GIVEREF(__pyx_t_12);
25236 PyTuple_SET_ITEM(__pyx_t_9, 7, __pyx_t_12);
25237 __pyx_t_12 = 0;
25238 __pyx_t_12 = __Pyx_PyUnicode_Join(__pyx_t_9, 8, __pyx_t_6, __pyx_t_10); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 681, __pyx_L1_error)
25239 __Pyx_GOTREF(__pyx_t_12);
25240 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
25241 __pyx_t_9 = NULL;
25242 __pyx_t_4 = 0;
25243 #if CYTHON_UNPACK_METHODS
25244 if (likely(PyMethod_Check(__pyx_t_2))) {
25245 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_2);
25246 if (likely(__pyx_t_9)) {
25247 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
25248 __Pyx_INCREF(__pyx_t_9);
25249 __Pyx_INCREF(function);
25250 __Pyx_DECREF_SET(__pyx_t_2, function);
25251 __pyx_t_4 = 1;
25252 }
25253 }
25254 #endif
25255 {
25256 PyObject *__pyx_callargs[4] = {__pyx_t_9, __pyx_v_line, __pyx_t_3, __pyx_t_12};
25257 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
25258 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
25259 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
25260 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
25261 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 679, __pyx_L1_error)
25262 __Pyx_GOTREF(__pyx_t_1);
25263 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25264 }
25265 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
25266 }
25267 __pyx_L4:;
25268
25269 /* "pysam/libcvcf.pyx":673
25270 * def parse_data( self, line, lineparse=False ):
25271 * cols = line.split('\t')
25272 * if len(cols) != len(self._samples)+9: # <<<<<<<<<<<<<<
25273 * # gracefully deal with absent FORMAT column
25274 * # and those missing samples
25275 */
25276 }
25277
25278 /* "pysam/libcvcf.pyx":683
25279 * "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols)))
25280 *
25281 * chrom = cols[0] # <<<<<<<<<<<<<<
25282 *
25283 * # get 0-based position
25284 */
25285 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_cols, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 683, __pyx_L1_error)
25286 __Pyx_GOTREF(__pyx_t_1);
25287 __pyx_v_chrom = __pyx_t_1;
25288 __pyx_t_1 = 0;
25289
25290 /* "pysam/libcvcf.pyx":686
25291 *
25292 * # get 0-based position
25293 * try: pos = int(cols[1])-1 # <<<<<<<<<<<<<<
25294 * except: self.error(line,self.POS_NOT_NUMERICAL)
25295 * if pos < 0: self.error(line,self.POS_NOT_POSITIVE)
25296 */
25297 {
25298 __Pyx_PyThreadState_declare
25299 __Pyx_PyThreadState_assign
25300 __Pyx_ExceptionSave(&__pyx_t_13, &__pyx_t_14, &__pyx_t_15);
25301 __Pyx_XGOTREF(__pyx_t_13);
25302 __Pyx_XGOTREF(__pyx_t_14);
25303 __Pyx_XGOTREF(__pyx_t_15);
25304 /*try:*/ {
25305 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_cols, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 686, __pyx_L5_error)
25306 __Pyx_GOTREF(__pyx_t_1);
25307 __pyx_t_2 = __Pyx_PyNumber_Int(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 686, __pyx_L5_error)
25308 __Pyx_GOTREF(__pyx_t_2);
25309 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
25310 __pyx_t_1 = __Pyx_PyInt_SubtractObjC(__pyx_t_2, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 686, __pyx_L5_error)
25311 __Pyx_GOTREF(__pyx_t_1);
25312 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25313 __pyx_v_pos = __pyx_t_1;
25314 __pyx_t_1 = 0;
25315 }
25316 __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
25317 __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
25318 __Pyx_XDECREF(__pyx_t_15); __pyx_t_15 = 0;
25319 goto __pyx_L10_try_end;
25320 __pyx_L5_error:;
25321 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
25322 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
25323 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
25324 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
25325 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
25326 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
25327
25328 /* "pysam/libcvcf.pyx":687
25329 * # get 0-based position
25330 * try: pos = int(cols[1])-1
25331 * except: self.error(line,self.POS_NOT_NUMERICAL) # <<<<<<<<<<<<<<
25332 * if pos < 0: self.error(line,self.POS_NOT_POSITIVE)
25333 *
25334 */
25335 /*except:*/ {
25336 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
25337 if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_2, &__pyx_t_12) < 0) __PYX_ERR(0, 687, __pyx_L7_except_error)
25338 __Pyx_XGOTREF(__pyx_t_1);
25339 __Pyx_XGOTREF(__pyx_t_2);
25340 __Pyx_XGOTREF(__pyx_t_12);
25341 __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 687, __pyx_L7_except_error)
25342 __Pyx_GOTREF(__pyx_t_9);
25343 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_POS_NOT_NUMERICAL); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 687, __pyx_L7_except_error)
25344 __Pyx_GOTREF(__pyx_t_11);
25345 __pyx_t_16 = NULL;
25346 __pyx_t_4 = 0;
25347 #if CYTHON_UNPACK_METHODS
25348 if (likely(PyMethod_Check(__pyx_t_9))) {
25349 __pyx_t_16 = PyMethod_GET_SELF(__pyx_t_9);
25350 if (likely(__pyx_t_16)) {
25351 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_9);
25352 __Pyx_INCREF(__pyx_t_16);
25353 __Pyx_INCREF(function);
25354 __Pyx_DECREF_SET(__pyx_t_9, function);
25355 __pyx_t_4 = 1;
25356 }
25357 }
25358 #endif
25359 {
25360 PyObject *__pyx_callargs[3] = {__pyx_t_16, __pyx_v_line, __pyx_t_11};
25361 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
25362 __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
25363 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
25364 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 687, __pyx_L7_except_error)
25365 __Pyx_GOTREF(__pyx_t_3);
25366 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
25367 }
25368 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
25369 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
25370 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
25371 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
25372 goto __pyx_L6_exception_handled;
25373 }
25374
25375 /* "pysam/libcvcf.pyx":686
25376 *
25377 * # get 0-based position
25378 * try: pos = int(cols[1])-1 # <<<<<<<<<<<<<<
25379 * except: self.error(line,self.POS_NOT_NUMERICAL)
25380 * if pos < 0: self.error(line,self.POS_NOT_POSITIVE)
25381 */
25382 __pyx_L7_except_error:;
25383 __Pyx_XGIVEREF(__pyx_t_13);
25384 __Pyx_XGIVEREF(__pyx_t_14);
25385 __Pyx_XGIVEREF(__pyx_t_15);
25386 __Pyx_ExceptionReset(__pyx_t_13, __pyx_t_14, __pyx_t_15);
25387 goto __pyx_L1_error;
25388 __pyx_L6_exception_handled:;
25389 __Pyx_XGIVEREF(__pyx_t_13);
25390 __Pyx_XGIVEREF(__pyx_t_14);
25391 __Pyx_XGIVEREF(__pyx_t_15);
25392 __Pyx_ExceptionReset(__pyx_t_13, __pyx_t_14, __pyx_t_15);
25393 __pyx_L10_try_end:;
25394 }
25395
25396 /* "pysam/libcvcf.pyx":688
25397 * try: pos = int(cols[1])-1
25398 * except: self.error(line,self.POS_NOT_NUMERICAL)
25399 * if pos < 0: self.error(line,self.POS_NOT_POSITIVE) # <<<<<<<<<<<<<<
25400 *
25401 * # implement filtering
25402 */
25403 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 688, __pyx_L1_error) }
25404 __pyx_t_12 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_12); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 688, __pyx_L1_error)
25405 __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_12); if (unlikely((__pyx_t_7 < 0))) __PYX_ERR(0, 688, __pyx_L1_error)
25406 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
25407 if (__pyx_t_7) {
25408 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 688, __pyx_L1_error)
25409 __Pyx_GOTREF(__pyx_t_2);
25410 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_POS_NOT_POSITIVE); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 688, __pyx_L1_error)
25411 __Pyx_GOTREF(__pyx_t_1);
25412 __pyx_t_3 = NULL;
25413 __pyx_t_4 = 0;
25414 #if CYTHON_UNPACK_METHODS
25415 if (likely(PyMethod_Check(__pyx_t_2))) {
25416 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
25417 if (likely(__pyx_t_3)) {
25418 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
25419 __Pyx_INCREF(__pyx_t_3);
25420 __Pyx_INCREF(function);
25421 __Pyx_DECREF_SET(__pyx_t_2, function);
25422 __pyx_t_4 = 1;
25423 }
25424 }
25425 #endif
25426 {
25427 PyObject *__pyx_callargs[3] = {__pyx_t_3, __pyx_v_line, __pyx_t_1};
25428 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
25429 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
25430 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
25431 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 688, __pyx_L1_error)
25432 __Pyx_GOTREF(__pyx_t_12);
25433 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25434 }
25435 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
25436 }
25437
25438 /* "pysam/libcvcf.pyx":691
25439 *
25440 * # implement filtering
25441 * if not self.inregion(chrom,pos): return None # <<<<<<<<<<<<<<
25442 *
25443 * # end of first-pass parse for sortedVCF
25444 */
25445 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_inregion); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 691, __pyx_L1_error)
25446 __Pyx_GOTREF(__pyx_t_2);
25447 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 691, __pyx_L1_error) }
25448 __pyx_t_1 = NULL;
25449 __pyx_t_4 = 0;
25450 #if CYTHON_UNPACK_METHODS
25451 if (likely(PyMethod_Check(__pyx_t_2))) {
25452 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_2);
25453 if (likely(__pyx_t_1)) {
25454 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
25455 __Pyx_INCREF(__pyx_t_1);
25456 __Pyx_INCREF(function);
25457 __Pyx_DECREF_SET(__pyx_t_2, function);
25458 __pyx_t_4 = 1;
25459 }
25460 }
25461 #endif
25462 {
25463 PyObject *__pyx_callargs[3] = {__pyx_t_1, __pyx_v_chrom, __pyx_v_pos};
25464 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
25465 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
25466 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 691, __pyx_L1_error)
25467 __Pyx_GOTREF(__pyx_t_12);
25468 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25469 }
25470 __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_12); if (unlikely((__pyx_t_7 < 0))) __PYX_ERR(0, 691, __pyx_L1_error)
25471 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
25472 __pyx_t_17 = (!__pyx_t_7);
25473 if (__pyx_t_17) {
25474 __Pyx_XDECREF(__pyx_r);
25475 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
25476 goto __pyx_L0;
25477 }
25478
25479 /* "pysam/libcvcf.pyx":694
25480 *
25481 * # end of first-pass parse for sortedVCF
25482 * if lineparse: return chrom, pos, line # <<<<<<<<<<<<<<
25483 *
25484 * id = cols[2]
25485 */
25486 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_v_lineparse); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 694, __pyx_L1_error)
25487 if (__pyx_t_17) {
25488 __Pyx_XDECREF(__pyx_r);
25489 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 694, __pyx_L1_error) }
25490 __pyx_t_12 = PyTuple_New(3); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 694, __pyx_L1_error)
25491 __Pyx_GOTREF(__pyx_t_12);
25492 __Pyx_INCREF(__pyx_v_chrom);
25493 __Pyx_GIVEREF(__pyx_v_chrom);
25494 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_v_chrom)) __PYX_ERR(0, 694, __pyx_L1_error);
25495 __Pyx_INCREF(__pyx_v_pos);
25496 __Pyx_GIVEREF(__pyx_v_pos);
25497 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_12, 1, __pyx_v_pos)) __PYX_ERR(0, 694, __pyx_L1_error);
25498 __Pyx_INCREF(__pyx_v_line);
25499 __Pyx_GIVEREF(__pyx_v_line);
25500 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_12, 2, __pyx_v_line)) __PYX_ERR(0, 694, __pyx_L1_error);
25501 __pyx_r = __pyx_t_12;
25502 __pyx_t_12 = 0;
25503 goto __pyx_L0;
25504 }
25505
25506 /* "pysam/libcvcf.pyx":696
25507 * if lineparse: return chrom, pos, line
25508 *
25509 * id = cols[2] # <<<<<<<<<<<<<<
25510 *
25511 * ref = cols[3].upper()
25512 */
25513 __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_cols, 2, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 696, __pyx_L1_error)
25514 __Pyx_GOTREF(__pyx_t_12);
25515 __pyx_v_id = __pyx_t_12;
25516 __pyx_t_12 = 0;
25517
25518 /* "pysam/libcvcf.pyx":698
25519 * id = cols[2]
25520 *
25521 * ref = cols[3].upper() # <<<<<<<<<<<<<<
25522 * if ref == ".":
25523 * self.error(line,self.MISSING_REF)
25524 */
25525 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_cols, 3, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 698, __pyx_L1_error)
25526 __Pyx_GOTREF(__pyx_t_2);
25527 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_upper); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 698, __pyx_L1_error)
25528 __Pyx_GOTREF(__pyx_t_1);
25529 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25530 __pyx_t_2 = NULL;
25531 __pyx_t_4 = 0;
25532 #if CYTHON_UNPACK_METHODS
25533 if (likely(PyMethod_Check(__pyx_t_1))) {
25534 __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_1);
25535 if (likely(__pyx_t_2)) {
25536 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
25537 __Pyx_INCREF(__pyx_t_2);
25538 __Pyx_INCREF(function);
25539 __Pyx_DECREF_SET(__pyx_t_1, function);
25540 __pyx_t_4 = 1;
25541 }
25542 }
25543 #endif
25544 {
25545 PyObject *__pyx_callargs[2] = {__pyx_t_2, NULL};
25546 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
25547 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
25548 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 698, __pyx_L1_error)
25549 __Pyx_GOTREF(__pyx_t_12);
25550 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
25551 }
25552 __pyx_v_ref = __pyx_t_12;
25553 __pyx_t_12 = 0;
25554
25555 /* "pysam/libcvcf.pyx":699
25556 *
25557 * ref = cols[3].upper()
25558 * if ref == ".": # <<<<<<<<<<<<<<
25559 * self.error(line,self.MISSING_REF)
25560 * if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
25561 */
25562 __pyx_t_17 = (__Pyx_PyUnicode_Equals(__pyx_v_ref, __pyx_kp_u__5, Py_EQ)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 699, __pyx_L1_error)
25563 if (__pyx_t_17) {
25564
25565 /* "pysam/libcvcf.pyx":700
25566 * ref = cols[3].upper()
25567 * if ref == ".":
25568 * self.error(line,self.MISSING_REF) # <<<<<<<<<<<<<<
25569 * if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
25570 * else: ref = ""
25571 */
25572 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 700, __pyx_L1_error)
25573 __Pyx_GOTREF(__pyx_t_1);
25574 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_MISSING_REF); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 700, __pyx_L1_error)
25575 __Pyx_GOTREF(__pyx_t_2);
25576 __pyx_t_3 = NULL;
25577 __pyx_t_4 = 0;
25578 #if CYTHON_UNPACK_METHODS
25579 if (likely(PyMethod_Check(__pyx_t_1))) {
25580 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_1);
25581 if (likely(__pyx_t_3)) {
25582 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
25583 __Pyx_INCREF(__pyx_t_3);
25584 __Pyx_INCREF(function);
25585 __Pyx_DECREF_SET(__pyx_t_1, function);
25586 __pyx_t_4 = 1;
25587 }
25588 }
25589 #endif
25590 {
25591 PyObject *__pyx_callargs[3] = {__pyx_t_3, __pyx_v_line, __pyx_t_2};
25592 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
25593 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
25594 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25595 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 700, __pyx_L1_error)
25596 __Pyx_GOTREF(__pyx_t_12);
25597 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
25598 }
25599 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
25600
25601 /* "pysam/libcvcf.pyx":701
25602 * if ref == ".":
25603 * self.error(line,self.MISSING_REF)
25604 * if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference) # <<<<<<<<<<<<<<
25605 * else: ref = ""
25606 * else:
25607 */
25608 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_version); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 701, __pyx_L1_error)
25609 __Pyx_GOTREF(__pyx_t_12);
25610 __pyx_t_17 = (__Pyx_PyInt_BoolEqObjC(__pyx_t_12, __pyx_int_33, 33, 0)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 701, __pyx_L1_error)
25611 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
25612 if (__pyx_t_17) {
25613 __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_get_sequence); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 701, __pyx_L1_error)
25614 __Pyx_GOTREF(__pyx_t_1);
25615 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 701, __pyx_L1_error) }
25616 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 701, __pyx_L1_error) }
25617 __pyx_t_2 = __Pyx_PyInt_AddObjC(__pyx_v_pos, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 701, __pyx_L1_error)
25618 __Pyx_GOTREF(__pyx_t_2);
25619 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_reference_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 701, __pyx_L1_error)
25620 __Pyx_GOTREF(__pyx_t_3);
25621 __pyx_t_9 = NULL;
25622 __pyx_t_4 = 0;
25623 #if CYTHON_UNPACK_METHODS
25624 if (unlikely(PyMethod_Check(__pyx_t_1))) {
25625 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_1);
25626 if (likely(__pyx_t_9)) {
25627 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
25628 __Pyx_INCREF(__pyx_t_9);
25629 __Pyx_INCREF(function);
25630 __Pyx_DECREF_SET(__pyx_t_1, function);
25631 __pyx_t_4 = 1;
25632 }
25633 }
25634 #endif
25635 {
25636 PyObject *__pyx_callargs[5] = {__pyx_t_9, __pyx_v_chrom, __pyx_v_pos, __pyx_t_2, __pyx_t_3};
25637 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 4+__pyx_t_4);
25638 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
25639 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25640 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
25641 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 701, __pyx_L1_error)
25642 __Pyx_GOTREF(__pyx_t_12);
25643 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
25644 }
25645 __Pyx_DECREF_SET(__pyx_v_ref, __pyx_t_12);
25646 __pyx_t_12 = 0;
25647 goto __pyx_L17;
25648 }
25649
25650 /* "pysam/libcvcf.pyx":702
25651 * self.error(line,self.MISSING_REF)
25652 * if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
25653 * else: ref = "" # <<<<<<<<<<<<<<
25654 * else:
25655 * for c in ref:
25656 */
25657 /*else*/ {
25658 __Pyx_INCREF(__pyx_kp_u_);
25659 __Pyx_DECREF_SET(__pyx_v_ref, __pyx_kp_u_);
25660 }
25661 __pyx_L17:;
25662
25663 /* "pysam/libcvcf.pyx":699
25664 *
25665 * ref = cols[3].upper()
25666 * if ref == ".": # <<<<<<<<<<<<<<
25667 * self.error(line,self.MISSING_REF)
25668 * if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
25669 */
25670 goto __pyx_L16;
25671 }
25672
25673 /* "pysam/libcvcf.pyx":704
25674 * else: ref = ""
25675 * else:
25676 * for c in ref: # <<<<<<<<<<<<<<
25677 * if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF)
25678 * if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference)
25679 */
25680 /*else*/ {
25681 if (likely(PyList_CheckExact(__pyx_v_ref)) || PyTuple_CheckExact(__pyx_v_ref)) {
25682 __pyx_t_12 = __pyx_v_ref; __Pyx_INCREF(__pyx_t_12);
25683 __pyx_t_6 = 0;
25684 __pyx_t_18 = NULL;
25685 } else {
25686 __pyx_t_6 = -1; __pyx_t_12 = PyObject_GetIter(__pyx_v_ref); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 704, __pyx_L1_error)
25687 __Pyx_GOTREF(__pyx_t_12);
25688 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_12); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 704, __pyx_L1_error)
25689 }
25690 for (;;) {
25691 if (likely(!__pyx_t_18)) {
25692 if (likely(PyList_CheckExact(__pyx_t_12))) {
25693 {
25694 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_12);
25695 #if !CYTHON_ASSUME_SAFE_MACROS
25696 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 704, __pyx_L1_error)
25697 #endif
25698 if (__pyx_t_6 >= __pyx_temp) break;
25699 }
25700 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
25701 __pyx_t_1 = PyList_GET_ITEM(__pyx_t_12, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 704, __pyx_L1_error)
25702 #else
25703 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_12, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 704, __pyx_L1_error)
25704 __Pyx_GOTREF(__pyx_t_1);
25705 #endif
25706 } else {
25707 {
25708 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_12);
25709 #if !CYTHON_ASSUME_SAFE_MACROS
25710 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 704, __pyx_L1_error)
25711 #endif
25712 if (__pyx_t_6 >= __pyx_temp) break;
25713 }
25714 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
25715 __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_12, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 704, __pyx_L1_error)
25716 #else
25717 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_12, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 704, __pyx_L1_error)
25718 __Pyx_GOTREF(__pyx_t_1);
25719 #endif
25720 }
25721 } else {
25722 __pyx_t_1 = __pyx_t_18(__pyx_t_12);
25723 if (unlikely(!__pyx_t_1)) {
25724 PyObject* exc_type = PyErr_Occurred();
25725 if (exc_type) {
25726 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
25727 else __PYX_ERR(0, 704, __pyx_L1_error)
25728 }
25729 break;
25730 }
25731 __Pyx_GOTREF(__pyx_t_1);
25732 }
25733 __Pyx_XDECREF_SET(__pyx_v_c, __pyx_t_1);
25734 __pyx_t_1 = 0;
25735
25736 /* "pysam/libcvcf.pyx":705
25737 * else:
25738 * for c in ref:
25739 * if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF) # <<<<<<<<<<<<<<
25740 * if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference)
25741 *
25742 */
25743 __pyx_t_17 = (__Pyx_PyUnicode_ContainsTF(__pyx_v_c, __pyx_n_u_ACGTN, Py_NE)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 705, __pyx_L1_error)
25744 if (__pyx_t_17) {
25745 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 705, __pyx_L1_error)
25746 __Pyx_GOTREF(__pyx_t_3);
25747 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_UNKNOWN_CHAR_IN_REF); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 705, __pyx_L1_error)
25748 __Pyx_GOTREF(__pyx_t_2);
25749 __pyx_t_9 = NULL;
25750 __pyx_t_4 = 0;
25751 #if CYTHON_UNPACK_METHODS
25752 if (likely(PyMethod_Check(__pyx_t_3))) {
25753 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_3);
25754 if (likely(__pyx_t_9)) {
25755 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
25756 __Pyx_INCREF(__pyx_t_9);
25757 __Pyx_INCREF(function);
25758 __Pyx_DECREF_SET(__pyx_t_3, function);
25759 __pyx_t_4 = 1;
25760 }
25761 }
25762 #endif
25763 {
25764 PyObject *__pyx_callargs[3] = {__pyx_t_9, __pyx_v_line, __pyx_t_2};
25765 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
25766 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
25767 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25768 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 705, __pyx_L1_error)
25769 __Pyx_GOTREF(__pyx_t_1);
25770 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
25771 }
25772 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
25773 }
25774
25775 /* "pysam/libcvcf.pyx":704
25776 * else: ref = ""
25777 * else:
25778 * for c in ref: # <<<<<<<<<<<<<<
25779 * if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF)
25780 * if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference)
25781 */
25782 }
25783 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
25784
25785 /* "pysam/libcvcf.pyx":706
25786 * for c in ref:
25787 * if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF)
25788 * if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference) # <<<<<<<<<<<<<<
25789 *
25790 * # make sure reference is sane
25791 */
25792 __pyx_t_17 = (__Pyx_PySequence_ContainsTF(__pyx_n_u_N, __pyx_v_ref, Py_EQ)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 706, __pyx_L1_error)
25793 if (__pyx_t_17) {
25794 __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_get_sequence); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 706, __pyx_L1_error)
25795 __Pyx_GOTREF(__pyx_t_1);
25796 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 706, __pyx_L1_error) }
25797 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 706, __pyx_L1_error) }
25798 __pyx_t_6 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 706, __pyx_L1_error)
25799 __pyx_t_3 = PyInt_FromSsize_t(__pyx_t_6); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 706, __pyx_L1_error)
25800 __Pyx_GOTREF(__pyx_t_3);
25801 __pyx_t_2 = PyNumber_Add(__pyx_v_pos, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 706, __pyx_L1_error)
25802 __Pyx_GOTREF(__pyx_t_2);
25803 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
25804 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_reference_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 706, __pyx_L1_error)
25805 __Pyx_GOTREF(__pyx_t_3);
25806 __pyx_t_9 = NULL;
25807 __pyx_t_4 = 0;
25808 #if CYTHON_UNPACK_METHODS
25809 if (unlikely(PyMethod_Check(__pyx_t_1))) {
25810 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_1);
25811 if (likely(__pyx_t_9)) {
25812 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
25813 __Pyx_INCREF(__pyx_t_9);
25814 __Pyx_INCREF(function);
25815 __Pyx_DECREF_SET(__pyx_t_1, function);
25816 __pyx_t_4 = 1;
25817 }
25818 }
25819 #endif
25820 {
25821 PyObject *__pyx_callargs[5] = {__pyx_t_9, __pyx_v_chrom, __pyx_v_pos, __pyx_t_2, __pyx_t_3};
25822 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 4+__pyx_t_4);
25823 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
25824 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25825 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
25826 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 706, __pyx_L1_error)
25827 __Pyx_GOTREF(__pyx_t_12);
25828 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
25829 }
25830 __Pyx_DECREF_SET(__pyx_v_ref, __pyx_t_12);
25831 __pyx_t_12 = 0;
25832 }
25833 }
25834 __pyx_L16:;
25835
25836 /* "pysam/libcvcf.pyx":709
25837 *
25838 * # make sure reference is sane
25839 * if self._reference: # <<<<<<<<<<<<<<
25840 * left = max(0,pos-100)
25841 * faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
25842 */
25843 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_reference_2); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 709, __pyx_L1_error)
25844 __Pyx_GOTREF(__pyx_t_12);
25845 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_12); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 709, __pyx_L1_error)
25846 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
25847 if (__pyx_t_17) {
25848
25849 /* "pysam/libcvcf.pyx":710
25850 * # make sure reference is sane
25851 * if self._reference:
25852 * left = max(0,pos-100) # <<<<<<<<<<<<<<
25853 * faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
25854 * faref = faref_leftflank[pos-left:]
25855 */
25856 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 710, __pyx_L1_error) }
25857 __pyx_t_12 = __Pyx_PyInt_SubtractObjC(__pyx_v_pos, __pyx_int_100, 0x64, 0, 0); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 710, __pyx_L1_error)
25858 __Pyx_GOTREF(__pyx_t_12);
25859 __pyx_t_19 = 0;
25860 __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_t_19); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 710, __pyx_L1_error)
25861 __Pyx_GOTREF(__pyx_t_3);
25862 __pyx_t_2 = PyObject_RichCompare(__pyx_t_12, __pyx_t_3, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 710, __pyx_L1_error)
25863 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
25864 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 710, __pyx_L1_error)
25865 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25866 if (__pyx_t_17) {
25867 __Pyx_INCREF(__pyx_t_12);
25868 __pyx_t_1 = __pyx_t_12;
25869 } else {
25870 __pyx_t_2 = __Pyx_PyInt_From_long(__pyx_t_19); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 710, __pyx_L1_error)
25871 __Pyx_GOTREF(__pyx_t_2);
25872 __pyx_t_1 = __pyx_t_2;
25873 __pyx_t_2 = 0;
25874 }
25875 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
25876 __pyx_t_12 = __pyx_t_1;
25877 __Pyx_INCREF(__pyx_t_12);
25878 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
25879 __pyx_v_left = __pyx_t_12;
25880 __pyx_t_12 = 0;
25881
25882 /* "pysam/libcvcf.pyx":711
25883 * if self._reference:
25884 * left = max(0,pos-100)
25885 * faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference) # <<<<<<<<<<<<<<
25886 * faref = faref_leftflank[pos-left:]
25887 * if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
25888 */
25889 __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_get_sequence); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 711, __pyx_L1_error)
25890 __Pyx_GOTREF(__pyx_t_1);
25891 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 711, __pyx_L1_error) }
25892 __pyx_t_6 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 711, __pyx_L1_error)
25893 __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_6); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 711, __pyx_L1_error)
25894 __Pyx_GOTREF(__pyx_t_2);
25895 __pyx_t_3 = PyNumber_Add(__pyx_v_pos, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 711, __pyx_L1_error)
25896 __Pyx_GOTREF(__pyx_t_3);
25897 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25898 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_reference_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 711, __pyx_L1_error)
25899 __Pyx_GOTREF(__pyx_t_2);
25900 __pyx_t_9 = NULL;
25901 __pyx_t_4 = 0;
25902 #if CYTHON_UNPACK_METHODS
25903 if (unlikely(PyMethod_Check(__pyx_t_1))) {
25904 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_1);
25905 if (likely(__pyx_t_9)) {
25906 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
25907 __Pyx_INCREF(__pyx_t_9);
25908 __Pyx_INCREF(function);
25909 __Pyx_DECREF_SET(__pyx_t_1, function);
25910 __pyx_t_4 = 1;
25911 }
25912 }
25913 #endif
25914 {
25915 PyObject *__pyx_callargs[5] = {__pyx_t_9, __pyx_v_chrom, __pyx_v_left, __pyx_t_3, __pyx_t_2};
25916 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 4+__pyx_t_4);
25917 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
25918 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
25919 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
25920 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 711, __pyx_L1_error)
25921 __Pyx_GOTREF(__pyx_t_12);
25922 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
25923 }
25924 __pyx_v_faref_leftflank = __pyx_t_12;
25925 __pyx_t_12 = 0;
25926
25927 /* "pysam/libcvcf.pyx":712
25928 * left = max(0,pos-100)
25929 * faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
25930 * faref = faref_leftflank[pos-left:] # <<<<<<<<<<<<<<
25931 * if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
25932 * ref = faref
25933 */
25934 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 712, __pyx_L1_error) }
25935 __pyx_t_12 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 712, __pyx_L1_error)
25936 __Pyx_GOTREF(__pyx_t_12);
25937 __pyx_t_1 = __Pyx_PyObject_GetSlice(__pyx_v_faref_leftflank, 0, 0, &__pyx_t_12, NULL, NULL, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 712, __pyx_L1_error)
25938 __Pyx_GOTREF(__pyx_t_1);
25939 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
25940 __pyx_v_faref = __pyx_t_1;
25941 __pyx_t_1 = 0;
25942
25943 /* "pysam/libcvcf.pyx":713
25944 * faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
25945 * faref = faref_leftflank[pos-left:]
25946 * if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref)) # <<<<<<<<<<<<<<
25947 * ref = faref
25948 *
25949 */
25950 __pyx_t_1 = PyObject_RichCompare(__pyx_v_faref, __pyx_v_ref, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 713, __pyx_L1_error)
25951 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 713, __pyx_L1_error)
25952 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
25953 if (__pyx_t_17) {
25954 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 713, __pyx_L1_error)
25955 __Pyx_GOTREF(__pyx_t_12);
25956 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_WRONG_REF); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 713, __pyx_L1_error)
25957 __Pyx_GOTREF(__pyx_t_2);
25958 __pyx_t_3 = PyTuple_New(5); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 713, __pyx_L1_error)
25959 __Pyx_GOTREF(__pyx_t_3);
25960 __pyx_t_6 = 0;
25961 __pyx_t_10 = 127;
25962 __Pyx_INCREF(__pyx_kp_u_reference_is);
25963 __pyx_t_6 += 14;
25964 __Pyx_GIVEREF(__pyx_kp_u_reference_is);
25965 PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_kp_u_reference_is);
25966 __pyx_t_9 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_faref), __pyx_empty_unicode); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 713, __pyx_L1_error)
25967 __Pyx_GOTREF(__pyx_t_9);
25968 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_9) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_9) : __pyx_t_10;
25969 __pyx_t_6 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_9);
25970 __Pyx_GIVEREF(__pyx_t_9);
25971 PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_9);
25972 __pyx_t_9 = 0;
25973 __Pyx_INCREF(__pyx_kp_u_VCF_says);
25974 __pyx_t_6 += 11;
25975 __Pyx_GIVEREF(__pyx_kp_u_VCF_says);
25976 PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_kp_u_VCF_says);
25977 __pyx_t_9 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_ref), __pyx_empty_unicode); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 713, __pyx_L1_error)
25978 __Pyx_GOTREF(__pyx_t_9);
25979 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_9) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_9) : __pyx_t_10;
25980 __pyx_t_6 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_9);
25981 __Pyx_GIVEREF(__pyx_t_9);
25982 PyTuple_SET_ITEM(__pyx_t_3, 3, __pyx_t_9);
25983 __pyx_t_9 = 0;
25984 __Pyx_INCREF(__pyx_kp_u__8);
25985 __pyx_t_6 += 1;
25986 __Pyx_GIVEREF(__pyx_kp_u__8);
25987 PyTuple_SET_ITEM(__pyx_t_3, 4, __pyx_kp_u__8);
25988 __pyx_t_9 = __Pyx_PyUnicode_Join(__pyx_t_3, 5, __pyx_t_6, __pyx_t_10); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 713, __pyx_L1_error)
25989 __Pyx_GOTREF(__pyx_t_9);
25990 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
25991 __pyx_t_3 = NULL;
25992 __pyx_t_4 = 0;
25993 #if CYTHON_UNPACK_METHODS
25994 if (likely(PyMethod_Check(__pyx_t_12))) {
25995 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_12);
25996 if (likely(__pyx_t_3)) {
25997 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_12);
25998 __Pyx_INCREF(__pyx_t_3);
25999 __Pyx_INCREF(function);
26000 __Pyx_DECREF_SET(__pyx_t_12, function);
26001 __pyx_t_4 = 1;
26002 }
26003 }
26004 #endif
26005 {
26006 PyObject *__pyx_callargs[4] = {__pyx_t_3, __pyx_v_line, __pyx_t_2, __pyx_t_9};
26007 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_12, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
26008 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
26009 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
26010 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
26011 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 713, __pyx_L1_error)
26012 __Pyx_GOTREF(__pyx_t_1);
26013 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26014 }
26015 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26016 }
26017
26018 /* "pysam/libcvcf.pyx":714
26019 * faref = faref_leftflank[pos-left:]
26020 * if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
26021 * ref = faref # <<<<<<<<<<<<<<
26022 *
26023 * # convert v3.3 to v4.0 alleles below
26024 */
26025 __Pyx_INCREF(__pyx_v_faref);
26026 __Pyx_DECREF_SET(__pyx_v_ref, __pyx_v_faref);
26027
26028 /* "pysam/libcvcf.pyx":709
26029 *
26030 * # make sure reference is sane
26031 * if self._reference: # <<<<<<<<<<<<<<
26032 * left = max(0,pos-100)
26033 * faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
26034 */
26035 }
26036
26037 /* "pysam/libcvcf.pyx":717
26038 *
26039 * # convert v3.3 to v4.0 alleles below
26040 * if cols[4] == ".": alt = [] # <<<<<<<<<<<<<<
26041 * else: alt = cols[4].upper().split(',')
26042 *
26043 */
26044 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_cols, 4, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 717, __pyx_L1_error)
26045 __Pyx_GOTREF(__pyx_t_1);
26046 __pyx_t_17 = (__Pyx_PyUnicode_Equals(__pyx_t_1, __pyx_kp_u__5, Py_EQ)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 717, __pyx_L1_error)
26047 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26048 if (__pyx_t_17) {
26049 __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 717, __pyx_L1_error)
26050 __Pyx_GOTREF(__pyx_t_1);
26051 __pyx_v_alt = __pyx_t_1;
26052 __pyx_t_1 = 0;
26053 goto __pyx_L25;
26054 }
26055
26056 /* "pysam/libcvcf.pyx":718
26057 * # convert v3.3 to v4.0 alleles below
26058 * if cols[4] == ".": alt = []
26059 * else: alt = cols[4].upper().split(',') # <<<<<<<<<<<<<<
26060 *
26061 * if cols[5] == ".": qual = -1
26062 */
26063 /*else*/ {
26064 __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 4, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 718, __pyx_L1_error)
26065 __Pyx_GOTREF(__pyx_t_9);
26066 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_9, __pyx_n_s_upper); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 718, __pyx_L1_error)
26067 __Pyx_GOTREF(__pyx_t_2);
26068 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
26069 __pyx_t_9 = NULL;
26070 __pyx_t_4 = 0;
26071 #if CYTHON_UNPACK_METHODS
26072 if (likely(PyMethod_Check(__pyx_t_2))) {
26073 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_2);
26074 if (likely(__pyx_t_9)) {
26075 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
26076 __Pyx_INCREF(__pyx_t_9);
26077 __Pyx_INCREF(function);
26078 __Pyx_DECREF_SET(__pyx_t_2, function);
26079 __pyx_t_4 = 1;
26080 }
26081 }
26082 #endif
26083 {
26084 PyObject *__pyx_callargs[2] = {__pyx_t_9, NULL};
26085 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
26086 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
26087 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 718, __pyx_L1_error)
26088 __Pyx_GOTREF(__pyx_t_12);
26089 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
26090 }
26091 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_12, __pyx_n_s_split); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 718, __pyx_L1_error)
26092 __Pyx_GOTREF(__pyx_t_2);
26093 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26094 __pyx_t_12 = NULL;
26095 __pyx_t_4 = 0;
26096 #if CYTHON_UNPACK_METHODS
26097 if (likely(PyMethod_Check(__pyx_t_2))) {
26098 __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_2);
26099 if (likely(__pyx_t_12)) {
26100 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
26101 __Pyx_INCREF(__pyx_t_12);
26102 __Pyx_INCREF(function);
26103 __Pyx_DECREF_SET(__pyx_t_2, function);
26104 __pyx_t_4 = 1;
26105 }
26106 }
26107 #endif
26108 {
26109 PyObject *__pyx_callargs[2] = {__pyx_t_12, __pyx_kp_u__2};
26110 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
26111 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
26112 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 718, __pyx_L1_error)
26113 __Pyx_GOTREF(__pyx_t_1);
26114 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
26115 }
26116 __pyx_v_alt = __pyx_t_1;
26117 __pyx_t_1 = 0;
26118 }
26119 __pyx_L25:;
26120
26121 /* "pysam/libcvcf.pyx":720
26122 * else: alt = cols[4].upper().split(',')
26123 *
26124 * if cols[5] == ".": qual = -1 # <<<<<<<<<<<<<<
26125 * else:
26126 * try: qual = float(cols[5])
26127 */
26128 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_cols, 5, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 720, __pyx_L1_error)
26129 __Pyx_GOTREF(__pyx_t_1);
26130 __pyx_t_17 = (__Pyx_PyUnicode_Equals(__pyx_t_1, __pyx_kp_u__5, Py_EQ)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 720, __pyx_L1_error)
26131 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26132 if (__pyx_t_17) {
26133 __pyx_v_qual = -1.0;
26134 goto __pyx_L26;
26135 }
26136
26137 /* "pysam/libcvcf.pyx":722
26138 * if cols[5] == ".": qual = -1
26139 * else:
26140 * try: qual = float(cols[5]) # <<<<<<<<<<<<<<
26141 * except: self.error(line,self.QUAL_NOT_NUMERICAL)
26142 *
26143 */
26144 /*else*/ {
26145 {
26146 __Pyx_PyThreadState_declare
26147 __Pyx_PyThreadState_assign
26148 __Pyx_ExceptionSave(&__pyx_t_15, &__pyx_t_14, &__pyx_t_13);
26149 __Pyx_XGOTREF(__pyx_t_15);
26150 __Pyx_XGOTREF(__pyx_t_14);
26151 __Pyx_XGOTREF(__pyx_t_13);
26152 /*try:*/ {
26153 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_cols, 5, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 722, __pyx_L27_error)
26154 __Pyx_GOTREF(__pyx_t_1);
26155 __pyx_t_20 = __Pyx_PyObject_AsDouble(__pyx_t_1); if (unlikely(__pyx_t_20 == ((double)((double)-1)) && PyErr_Occurred())) __PYX_ERR(0, 722, __pyx_L27_error)
26156 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26157 __pyx_v_qual = __pyx_t_20;
26158 }
26159 __Pyx_XDECREF(__pyx_t_15); __pyx_t_15 = 0;
26160 __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
26161 __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
26162 goto __pyx_L32_try_end;
26163 __pyx_L27_error:;
26164 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
26165 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
26166 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
26167 __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
26168 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
26169 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
26170 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
26171
26172 /* "pysam/libcvcf.pyx":723
26173 * else:
26174 * try: qual = float(cols[5])
26175 * except: self.error(line,self.QUAL_NOT_NUMERICAL) # <<<<<<<<<<<<<<
26176 *
26177 * # postpone checking that filters exist. Encode missing filter or no filtering as empty list
26178 */
26179 /*except:*/ {
26180 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
26181 if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_2, &__pyx_t_12) < 0) __PYX_ERR(0, 723, __pyx_L29_except_error)
26182 __Pyx_XGOTREF(__pyx_t_1);
26183 __Pyx_XGOTREF(__pyx_t_2);
26184 __Pyx_XGOTREF(__pyx_t_12);
26185 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 723, __pyx_L29_except_error)
26186 __Pyx_GOTREF(__pyx_t_3);
26187 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_QUAL_NOT_NUMERICAL); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 723, __pyx_L29_except_error)
26188 __Pyx_GOTREF(__pyx_t_11);
26189 __pyx_t_16 = NULL;
26190 __pyx_t_4 = 0;
26191 #if CYTHON_UNPACK_METHODS
26192 if (likely(PyMethod_Check(__pyx_t_3))) {
26193 __pyx_t_16 = PyMethod_GET_SELF(__pyx_t_3);
26194 if (likely(__pyx_t_16)) {
26195 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
26196 __Pyx_INCREF(__pyx_t_16);
26197 __Pyx_INCREF(function);
26198 __Pyx_DECREF_SET(__pyx_t_3, function);
26199 __pyx_t_4 = 1;
26200 }
26201 }
26202 #endif
26203 {
26204 PyObject *__pyx_callargs[3] = {__pyx_t_16, __pyx_v_line, __pyx_t_11};
26205 __pyx_t_9 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
26206 __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
26207 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
26208 if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 723, __pyx_L29_except_error)
26209 __Pyx_GOTREF(__pyx_t_9);
26210 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
26211 }
26212 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
26213 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
26214 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
26215 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
26216 goto __pyx_L28_exception_handled;
26217 }
26218
26219 /* "pysam/libcvcf.pyx":722
26220 * if cols[5] == ".": qual = -1
26221 * else:
26222 * try: qual = float(cols[5]) # <<<<<<<<<<<<<<
26223 * except: self.error(line,self.QUAL_NOT_NUMERICAL)
26224 *
26225 */
26226 __pyx_L29_except_error:;
26227 __Pyx_XGIVEREF(__pyx_t_15);
26228 __Pyx_XGIVEREF(__pyx_t_14);
26229 __Pyx_XGIVEREF(__pyx_t_13);
26230 __Pyx_ExceptionReset(__pyx_t_15, __pyx_t_14, __pyx_t_13);
26231 goto __pyx_L1_error;
26232 __pyx_L28_exception_handled:;
26233 __Pyx_XGIVEREF(__pyx_t_15);
26234 __Pyx_XGIVEREF(__pyx_t_14);
26235 __Pyx_XGIVEREF(__pyx_t_13);
26236 __Pyx_ExceptionReset(__pyx_t_15, __pyx_t_14, __pyx_t_13);
26237 __pyx_L32_try_end:;
26238 }
26239 }
26240 __pyx_L26:;
26241
26242 /* "pysam/libcvcf.pyx":726
26243 *
26244 * # postpone checking that filters exist. Encode missing filter or no filtering as empty list
26245 * if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = [] # <<<<<<<<<<<<<<
26246 * else: filter = cols[6].split(';')
26247 *
26248 */
26249 __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_cols, 6, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 726, __pyx_L1_error)
26250 __Pyx_GOTREF(__pyx_t_12);
26251 __pyx_t_7 = (__Pyx_PyUnicode_Equals(__pyx_t_12, __pyx_kp_u__5, Py_EQ)); if (unlikely((__pyx_t_7 < 0))) __PYX_ERR(0, 726, __pyx_L1_error)
26252 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26253 if (!__pyx_t_7) {
26254 } else {
26255 __pyx_t_17 = __pyx_t_7;
26256 goto __pyx_L36_bool_binop_done;
26257 }
26258 __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_cols, 6, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 726, __pyx_L1_error)
26259 __Pyx_GOTREF(__pyx_t_12);
26260 __pyx_t_7 = (__Pyx_PyUnicode_Equals(__pyx_t_12, __pyx_n_u_PASS, Py_EQ)); if (unlikely((__pyx_t_7 < 0))) __PYX_ERR(0, 726, __pyx_L1_error)
26261 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26262 if (!__pyx_t_7) {
26263 } else {
26264 __pyx_t_17 = __pyx_t_7;
26265 goto __pyx_L36_bool_binop_done;
26266 }
26267 __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_cols, 6, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 726, __pyx_L1_error)
26268 __Pyx_GOTREF(__pyx_t_12);
26269 __pyx_t_7 = (__Pyx_PyUnicode_Equals(__pyx_t_12, __pyx_kp_u_0, Py_EQ)); if (unlikely((__pyx_t_7 < 0))) __PYX_ERR(0, 726, __pyx_L1_error)
26270 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26271 __pyx_t_17 = __pyx_t_7;
26272 __pyx_L36_bool_binop_done:;
26273 if (__pyx_t_17) {
26274 __pyx_t_12 = PyList_New(0); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 726, __pyx_L1_error)
26275 __Pyx_GOTREF(__pyx_t_12);
26276 __pyx_v_filter = __pyx_t_12;
26277 __pyx_t_12 = 0;
26278 goto __pyx_L35;
26279 }
26280
26281 /* "pysam/libcvcf.pyx":727
26282 * # postpone checking that filters exist. Encode missing filter or no filtering as empty list
26283 * if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = []
26284 * else: filter = cols[6].split(';') # <<<<<<<<<<<<<<
26285 *
26286 * # dictionary of keys, and list of values
26287 */
26288 /*else*/ {
26289 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_cols, 6, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 727, __pyx_L1_error)
26290 __Pyx_GOTREF(__pyx_t_2);
26291 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_split); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 727, __pyx_L1_error)
26292 __Pyx_GOTREF(__pyx_t_1);
26293 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
26294 __pyx_t_2 = NULL;
26295 __pyx_t_4 = 0;
26296 #if CYTHON_UNPACK_METHODS
26297 if (likely(PyMethod_Check(__pyx_t_1))) {
26298 __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_1);
26299 if (likely(__pyx_t_2)) {
26300 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
26301 __Pyx_INCREF(__pyx_t_2);
26302 __Pyx_INCREF(function);
26303 __Pyx_DECREF_SET(__pyx_t_1, function);
26304 __pyx_t_4 = 1;
26305 }
26306 }
26307 #endif
26308 {
26309 PyObject *__pyx_callargs[2] = {__pyx_t_2, __pyx_kp_u__6};
26310 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
26311 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
26312 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 727, __pyx_L1_error)
26313 __Pyx_GOTREF(__pyx_t_12);
26314 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26315 }
26316 __pyx_v_filter = __pyx_t_12;
26317 __pyx_t_12 = 0;
26318 }
26319 __pyx_L35:;
26320
26321 /* "pysam/libcvcf.pyx":730
26322 *
26323 * # dictionary of keys, and list of values
26324 * info = {} # <<<<<<<<<<<<<<
26325 * if cols[7] != ".":
26326 * for blurp in cols[7].split(';'):
26327 */
26328 __pyx_t_12 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 730, __pyx_L1_error)
26329 __Pyx_GOTREF(__pyx_t_12);
26330 __pyx_v_info = ((PyObject*)__pyx_t_12);
26331 __pyx_t_12 = 0;
26332
26333 /* "pysam/libcvcf.pyx":731
26334 * # dictionary of keys, and list of values
26335 * info = {}
26336 * if cols[7] != ".": # <<<<<<<<<<<<<<
26337 * for blurp in cols[7].split(';'):
26338 * elts = blurp.split('=')
26339 */
26340 __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_cols, 7, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 731, __pyx_L1_error)
26341 __Pyx_GOTREF(__pyx_t_12);
26342 __pyx_t_17 = (__Pyx_PyUnicode_Equals(__pyx_t_12, __pyx_kp_u__5, Py_NE)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 731, __pyx_L1_error)
26343 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26344 if (__pyx_t_17) {
26345
26346 /* "pysam/libcvcf.pyx":732
26347 * info = {}
26348 * if cols[7] != ".":
26349 * for blurp in cols[7].split(';'): # <<<<<<<<<<<<<<
26350 * elts = blurp.split('=')
26351 * if len(elts) == 1: v = None
26352 */
26353 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_cols, 7, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 732, __pyx_L1_error)
26354 __Pyx_GOTREF(__pyx_t_1);
26355 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_split); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 732, __pyx_L1_error)
26356 __Pyx_GOTREF(__pyx_t_2);
26357 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26358 __pyx_t_1 = NULL;
26359 __pyx_t_4 = 0;
26360 #if CYTHON_UNPACK_METHODS
26361 if (likely(PyMethod_Check(__pyx_t_2))) {
26362 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_2);
26363 if (likely(__pyx_t_1)) {
26364 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
26365 __Pyx_INCREF(__pyx_t_1);
26366 __Pyx_INCREF(function);
26367 __Pyx_DECREF_SET(__pyx_t_2, function);
26368 __pyx_t_4 = 1;
26369 }
26370 }
26371 #endif
26372 {
26373 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_kp_u__6};
26374 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
26375 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
26376 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 732, __pyx_L1_error)
26377 __Pyx_GOTREF(__pyx_t_12);
26378 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
26379 }
26380 if (likely(PyList_CheckExact(__pyx_t_12)) || PyTuple_CheckExact(__pyx_t_12)) {
26381 __pyx_t_2 = __pyx_t_12; __Pyx_INCREF(__pyx_t_2);
26382 __pyx_t_6 = 0;
26383 __pyx_t_18 = NULL;
26384 } else {
26385 __pyx_t_6 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_12); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 732, __pyx_L1_error)
26386 __Pyx_GOTREF(__pyx_t_2);
26387 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_2); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 732, __pyx_L1_error)
26388 }
26389 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26390 for (;;) {
26391 if (likely(!__pyx_t_18)) {
26392 if (likely(PyList_CheckExact(__pyx_t_2))) {
26393 {
26394 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2);
26395 #if !CYTHON_ASSUME_SAFE_MACROS
26396 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 732, __pyx_L1_error)
26397 #endif
26398 if (__pyx_t_6 >= __pyx_temp) break;
26399 }
26400 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
26401 __pyx_t_12 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_12); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 732, __pyx_L1_error)
26402 #else
26403 __pyx_t_12 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 732, __pyx_L1_error)
26404 __Pyx_GOTREF(__pyx_t_12);
26405 #endif
26406 } else {
26407 {
26408 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_2);
26409 #if !CYTHON_ASSUME_SAFE_MACROS
26410 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 732, __pyx_L1_error)
26411 #endif
26412 if (__pyx_t_6 >= __pyx_temp) break;
26413 }
26414 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
26415 __pyx_t_12 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_12); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 732, __pyx_L1_error)
26416 #else
26417 __pyx_t_12 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 732, __pyx_L1_error)
26418 __Pyx_GOTREF(__pyx_t_12);
26419 #endif
26420 }
26421 } else {
26422 __pyx_t_12 = __pyx_t_18(__pyx_t_2);
26423 if (unlikely(!__pyx_t_12)) {
26424 PyObject* exc_type = PyErr_Occurred();
26425 if (exc_type) {
26426 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
26427 else __PYX_ERR(0, 732, __pyx_L1_error)
26428 }
26429 break;
26430 }
26431 __Pyx_GOTREF(__pyx_t_12);
26432 }
26433 __Pyx_XDECREF_SET(__pyx_v_blurp, __pyx_t_12);
26434 __pyx_t_12 = 0;
26435
26436 /* "pysam/libcvcf.pyx":733
26437 * if cols[7] != ".":
26438 * for blurp in cols[7].split(';'):
26439 * elts = blurp.split('=') # <<<<<<<<<<<<<<
26440 * if len(elts) == 1: v = None
26441 * elif len(elts) == 2: v = elts[1]
26442 */
26443 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_blurp, __pyx_n_s_split); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 733, __pyx_L1_error)
26444 __Pyx_GOTREF(__pyx_t_1);
26445 __pyx_t_9 = NULL;
26446 __pyx_t_4 = 0;
26447 #if CYTHON_UNPACK_METHODS
26448 if (likely(PyMethod_Check(__pyx_t_1))) {
26449 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_1);
26450 if (likely(__pyx_t_9)) {
26451 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
26452 __Pyx_INCREF(__pyx_t_9);
26453 __Pyx_INCREF(function);
26454 __Pyx_DECREF_SET(__pyx_t_1, function);
26455 __pyx_t_4 = 1;
26456 }
26457 }
26458 #endif
26459 {
26460 PyObject *__pyx_callargs[2] = {__pyx_t_9, __pyx_kp_u__7};
26461 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
26462 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
26463 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 733, __pyx_L1_error)
26464 __Pyx_GOTREF(__pyx_t_12);
26465 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26466 }
26467 __Pyx_XDECREF_SET(__pyx_v_elts, __pyx_t_12);
26468 __pyx_t_12 = 0;
26469
26470 /* "pysam/libcvcf.pyx":734
26471 * for blurp in cols[7].split(';'):
26472 * elts = blurp.split('=')
26473 * if len(elts) == 1: v = None # <<<<<<<<<<<<<<
26474 * elif len(elts) == 2: v = elts[1]
26475 * else: self.error(line,self.ERROR_INFO_STRING)
26476 */
26477 __pyx_t_5 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 734, __pyx_L1_error)
26478 __pyx_t_17 = (__pyx_t_5 == 1);
26479 if (__pyx_t_17) {
26480 __Pyx_INCREF(Py_None);
26481 __Pyx_XDECREF_SET(__pyx_v_v, Py_None);
26482 goto __pyx_L42;
26483 }
26484
26485 /* "pysam/libcvcf.pyx":735
26486 * elts = blurp.split('=')
26487 * if len(elts) == 1: v = None
26488 * elif len(elts) == 2: v = elts[1] # <<<<<<<<<<<<<<
26489 * else: self.error(line,self.ERROR_INFO_STRING)
26490 * info[elts[0]] = self.parse_formatdata(elts[0],
26491 */
26492 __pyx_t_5 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 735, __pyx_L1_error)
26493 __pyx_t_17 = (__pyx_t_5 == 2);
26494 if (__pyx_t_17) {
26495 __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_elts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 735, __pyx_L1_error)
26496 __Pyx_GOTREF(__pyx_t_12);
26497 __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_12);
26498 __pyx_t_12 = 0;
26499 goto __pyx_L42;
26500 }
26501
26502 /* "pysam/libcvcf.pyx":736
26503 * if len(elts) == 1: v = None
26504 * elif len(elts) == 2: v = elts[1]
26505 * else: self.error(line,self.ERROR_INFO_STRING) # <<<<<<<<<<<<<<
26506 * info[elts[0]] = self.parse_formatdata(elts[0],
26507 * v,
26508 */
26509 /*else*/ {
26510 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 736, __pyx_L1_error)
26511 __Pyx_GOTREF(__pyx_t_1);
26512 __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_ERROR_INFO_STRING); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 736, __pyx_L1_error)
26513 __Pyx_GOTREF(__pyx_t_9);
26514 __pyx_t_3 = NULL;
26515 __pyx_t_4 = 0;
26516 #if CYTHON_UNPACK_METHODS
26517 if (likely(PyMethod_Check(__pyx_t_1))) {
26518 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_1);
26519 if (likely(__pyx_t_3)) {
26520 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
26521 __Pyx_INCREF(__pyx_t_3);
26522 __Pyx_INCREF(function);
26523 __Pyx_DECREF_SET(__pyx_t_1, function);
26524 __pyx_t_4 = 1;
26525 }
26526 }
26527 #endif
26528 {
26529 PyObject *__pyx_callargs[3] = {__pyx_t_3, __pyx_v_line, __pyx_t_9};
26530 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
26531 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
26532 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
26533 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 736, __pyx_L1_error)
26534 __Pyx_GOTREF(__pyx_t_12);
26535 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26536 }
26537 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26538 }
26539 __pyx_L42:;
26540
26541 /* "pysam/libcvcf.pyx":737
26542 * elif len(elts) == 2: v = elts[1]
26543 * else: self.error(line,self.ERROR_INFO_STRING)
26544 * info[elts[0]] = self.parse_formatdata(elts[0], # <<<<<<<<<<<<<<
26545 * v,
26546 * self._info,
26547 */
26548 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parse_formatdata); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 737, __pyx_L1_error)
26549 __Pyx_GOTREF(__pyx_t_1);
26550 __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_elts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 737, __pyx_L1_error)
26551 __Pyx_GOTREF(__pyx_t_9);
26552
26553 /* "pysam/libcvcf.pyx":738
26554 * else: self.error(line,self.ERROR_INFO_STRING)
26555 * info[elts[0]] = self.parse_formatdata(elts[0],
26556 * v, # <<<<<<<<<<<<<<
26557 * self._info,
26558 * line)
26559 */
26560 if (unlikely(!__pyx_v_v)) { __Pyx_RaiseUnboundLocalError("v"); __PYX_ERR(0, 738, __pyx_L1_error) }
26561
26562 /* "pysam/libcvcf.pyx":739
26563 * info[elts[0]] = self.parse_formatdata(elts[0],
26564 * v,
26565 * self._info, # <<<<<<<<<<<<<<
26566 * line)
26567 *
26568 */
26569 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_info); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 739, __pyx_L1_error)
26570 __Pyx_GOTREF(__pyx_t_3);
26571
26572 /* "pysam/libcvcf.pyx":740
26573 * v,
26574 * self._info,
26575 * line) # <<<<<<<<<<<<<<
26576 *
26577 * # Gracefully deal with absent FORMAT column
26578 */
26579 __pyx_t_11 = NULL;
26580 __pyx_t_4 = 0;
26581 #if CYTHON_UNPACK_METHODS
26582 if (likely(PyMethod_Check(__pyx_t_1))) {
26583 __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_1);
26584 if (likely(__pyx_t_11)) {
26585 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
26586 __Pyx_INCREF(__pyx_t_11);
26587 __Pyx_INCREF(function);
26588 __Pyx_DECREF_SET(__pyx_t_1, function);
26589 __pyx_t_4 = 1;
26590 }
26591 }
26592 #endif
26593 {
26594 PyObject *__pyx_callargs[5] = {__pyx_t_11, __pyx_t_9, __pyx_v_v, __pyx_t_3, __pyx_v_line};
26595 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 4+__pyx_t_4);
26596 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
26597 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
26598 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
26599 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 737, __pyx_L1_error)
26600 __Pyx_GOTREF(__pyx_t_12);
26601 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26602 }
26603
26604 /* "pysam/libcvcf.pyx":737
26605 * elif len(elts) == 2: v = elts[1]
26606 * else: self.error(line,self.ERROR_INFO_STRING)
26607 * info[elts[0]] = self.parse_formatdata(elts[0], # <<<<<<<<<<<<<<
26608 * v,
26609 * self._info,
26610 */
26611 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_elts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 737, __pyx_L1_error)
26612 __Pyx_GOTREF(__pyx_t_1);
26613 if (unlikely((PyDict_SetItem(__pyx_v_info, __pyx_t_1, __pyx_t_12) < 0))) __PYX_ERR(0, 737, __pyx_L1_error)
26614 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26615 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26616
26617 /* "pysam/libcvcf.pyx":732
26618 * info = {}
26619 * if cols[7] != ".":
26620 * for blurp in cols[7].split(';'): # <<<<<<<<<<<<<<
26621 * elts = blurp.split('=')
26622 * if len(elts) == 1: v = None
26623 */
26624 }
26625 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
26626
26627 /* "pysam/libcvcf.pyx":731
26628 * # dictionary of keys, and list of values
26629 * info = {}
26630 * if cols[7] != ".": # <<<<<<<<<<<<<<
26631 * for blurp in cols[7].split(';'):
26632 * elts = blurp.split('=')
26633 */
26634 }
26635
26636 /* "pysam/libcvcf.pyx":743
26637 *
26638 * # Gracefully deal with absent FORMAT column
26639 * if cols[8] == "": format = [] # <<<<<<<<<<<<<<
26640 * else: format = cols[8].split(':')
26641 *
26642 */
26643 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_cols, 8, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 743, __pyx_L1_error)
26644 __Pyx_GOTREF(__pyx_t_2);
26645 __pyx_t_17 = (__Pyx_PyUnicode_Equals(__pyx_t_2, __pyx_kp_u_, Py_EQ)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 743, __pyx_L1_error)
26646 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
26647 if (__pyx_t_17) {
26648 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 743, __pyx_L1_error)
26649 __Pyx_GOTREF(__pyx_t_2);
26650 __pyx_v_format = __pyx_t_2;
26651 __pyx_t_2 = 0;
26652 goto __pyx_L44;
26653 }
26654
26655 /* "pysam/libcvcf.pyx":744
26656 * # Gracefully deal with absent FORMAT column
26657 * if cols[8] == "": format = []
26658 * else: format = cols[8].split(':') # <<<<<<<<<<<<<<
26659 *
26660 * # check: all filters are defined
26661 */
26662 /*else*/ {
26663 __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_cols, 8, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 744, __pyx_L1_error)
26664 __Pyx_GOTREF(__pyx_t_12);
26665 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_12, __pyx_n_s_split); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 744, __pyx_L1_error)
26666 __Pyx_GOTREF(__pyx_t_1);
26667 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26668 __pyx_t_12 = NULL;
26669 __pyx_t_4 = 0;
26670 #if CYTHON_UNPACK_METHODS
26671 if (likely(PyMethod_Check(__pyx_t_1))) {
26672 __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_1);
26673 if (likely(__pyx_t_12)) {
26674 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
26675 __Pyx_INCREF(__pyx_t_12);
26676 __Pyx_INCREF(function);
26677 __Pyx_DECREF_SET(__pyx_t_1, function);
26678 __pyx_t_4 = 1;
26679 }
26680 }
26681 #endif
26682 {
26683 PyObject *__pyx_callargs[2] = {__pyx_t_12, __pyx_kp_u__3};
26684 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
26685 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
26686 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 744, __pyx_L1_error)
26687 __Pyx_GOTREF(__pyx_t_2);
26688 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26689 }
26690 __pyx_v_format = __pyx_t_2;
26691 __pyx_t_2 = 0;
26692 }
26693 __pyx_L44:;
26694
26695 /* "pysam/libcvcf.pyx":747
26696 *
26697 * # check: all filters are defined
26698 * for f in filter: # <<<<<<<<<<<<<<
26699 * if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f)
26700 *
26701 */
26702 if (likely(PyList_CheckExact(__pyx_v_filter)) || PyTuple_CheckExact(__pyx_v_filter)) {
26703 __pyx_t_2 = __pyx_v_filter; __Pyx_INCREF(__pyx_t_2);
26704 __pyx_t_6 = 0;
26705 __pyx_t_18 = NULL;
26706 } else {
26707 __pyx_t_6 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_filter); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 747, __pyx_L1_error)
26708 __Pyx_GOTREF(__pyx_t_2);
26709 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_2); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 747, __pyx_L1_error)
26710 }
26711 for (;;) {
26712 if (likely(!__pyx_t_18)) {
26713 if (likely(PyList_CheckExact(__pyx_t_2))) {
26714 {
26715 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2);
26716 #if !CYTHON_ASSUME_SAFE_MACROS
26717 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 747, __pyx_L1_error)
26718 #endif
26719 if (__pyx_t_6 >= __pyx_temp) break;
26720 }
26721 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
26722 __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 747, __pyx_L1_error)
26723 #else
26724 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 747, __pyx_L1_error)
26725 __Pyx_GOTREF(__pyx_t_1);
26726 #endif
26727 } else {
26728 {
26729 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_2);
26730 #if !CYTHON_ASSUME_SAFE_MACROS
26731 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 747, __pyx_L1_error)
26732 #endif
26733 if (__pyx_t_6 >= __pyx_temp) break;
26734 }
26735 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
26736 __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 747, __pyx_L1_error)
26737 #else
26738 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 747, __pyx_L1_error)
26739 __Pyx_GOTREF(__pyx_t_1);
26740 #endif
26741 }
26742 } else {
26743 __pyx_t_1 = __pyx_t_18(__pyx_t_2);
26744 if (unlikely(!__pyx_t_1)) {
26745 PyObject* exc_type = PyErr_Occurred();
26746 if (exc_type) {
26747 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
26748 else __PYX_ERR(0, 747, __pyx_L1_error)
26749 }
26750 break;
26751 }
26752 __Pyx_GOTREF(__pyx_t_1);
26753 }
26754 __Pyx_XDECREF_SET(__pyx_v_f, __pyx_t_1);
26755 __pyx_t_1 = 0;
26756
26757 /* "pysam/libcvcf.pyx":748
26758 * # check: all filters are defined
26759 * for f in filter:
26760 * if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f) # <<<<<<<<<<<<<<
26761 *
26762 * # check: format fields are defined
26763 */
26764 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_filter); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 748, __pyx_L1_error)
26765 __Pyx_GOTREF(__pyx_t_1);
26766 __pyx_t_17 = (__Pyx_PySequence_ContainsTF(__pyx_v_f, __pyx_t_1, Py_NE)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 748, __pyx_L1_error)
26767 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26768 if (__pyx_t_17) {
26769 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 748, __pyx_L1_error)
26770 __Pyx_GOTREF(__pyx_t_12);
26771 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_FILTER_NOT_DEFINED); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 748, __pyx_L1_error)
26772 __Pyx_GOTREF(__pyx_t_3);
26773 __pyx_t_9 = NULL;
26774 __pyx_t_4 = 0;
26775 #if CYTHON_UNPACK_METHODS
26776 if (likely(PyMethod_Check(__pyx_t_12))) {
26777 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_12);
26778 if (likely(__pyx_t_9)) {
26779 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_12);
26780 __Pyx_INCREF(__pyx_t_9);
26781 __Pyx_INCREF(function);
26782 __Pyx_DECREF_SET(__pyx_t_12, function);
26783 __pyx_t_4 = 1;
26784 }
26785 }
26786 #endif
26787 {
26788 PyObject *__pyx_callargs[4] = {__pyx_t_9, __pyx_v_line, __pyx_t_3, __pyx_v_f};
26789 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_12, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
26790 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
26791 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
26792 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 748, __pyx_L1_error)
26793 __Pyx_GOTREF(__pyx_t_1);
26794 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26795 }
26796 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26797 }
26798
26799 /* "pysam/libcvcf.pyx":747
26800 *
26801 * # check: all filters are defined
26802 * for f in filter: # <<<<<<<<<<<<<<
26803 * if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f)
26804 *
26805 */
26806 }
26807 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
26808
26809 /* "pysam/libcvcf.pyx":751
26810 *
26811 * # check: format fields are defined
26812 * if self._format: # <<<<<<<<<<<<<<
26813 * for f in format:
26814 * if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
26815 */
26816 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 751, __pyx_L1_error)
26817 __Pyx_GOTREF(__pyx_t_2);
26818 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 751, __pyx_L1_error)
26819 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
26820 if (__pyx_t_17) {
26821
26822 /* "pysam/libcvcf.pyx":752
26823 * # check: format fields are defined
26824 * if self._format:
26825 * for f in format: # <<<<<<<<<<<<<<
26826 * if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
26827 *
26828 */
26829 if (likely(PyList_CheckExact(__pyx_v_format)) || PyTuple_CheckExact(__pyx_v_format)) {
26830 __pyx_t_2 = __pyx_v_format; __Pyx_INCREF(__pyx_t_2);
26831 __pyx_t_6 = 0;
26832 __pyx_t_18 = NULL;
26833 } else {
26834 __pyx_t_6 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_format); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 752, __pyx_L1_error)
26835 __Pyx_GOTREF(__pyx_t_2);
26836 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_2); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 752, __pyx_L1_error)
26837 }
26838 for (;;) {
26839 if (likely(!__pyx_t_18)) {
26840 if (likely(PyList_CheckExact(__pyx_t_2))) {
26841 {
26842 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2);
26843 #if !CYTHON_ASSUME_SAFE_MACROS
26844 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 752, __pyx_L1_error)
26845 #endif
26846 if (__pyx_t_6 >= __pyx_temp) break;
26847 }
26848 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
26849 __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 752, __pyx_L1_error)
26850 #else
26851 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 752, __pyx_L1_error)
26852 __Pyx_GOTREF(__pyx_t_1);
26853 #endif
26854 } else {
26855 {
26856 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_2);
26857 #if !CYTHON_ASSUME_SAFE_MACROS
26858 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 752, __pyx_L1_error)
26859 #endif
26860 if (__pyx_t_6 >= __pyx_temp) break;
26861 }
26862 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
26863 __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 752, __pyx_L1_error)
26864 #else
26865 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 752, __pyx_L1_error)
26866 __Pyx_GOTREF(__pyx_t_1);
26867 #endif
26868 }
26869 } else {
26870 __pyx_t_1 = __pyx_t_18(__pyx_t_2);
26871 if (unlikely(!__pyx_t_1)) {
26872 PyObject* exc_type = PyErr_Occurred();
26873 if (exc_type) {
26874 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
26875 else __PYX_ERR(0, 752, __pyx_L1_error)
26876 }
26877 break;
26878 }
26879 __Pyx_GOTREF(__pyx_t_1);
26880 }
26881 __Pyx_XDECREF_SET(__pyx_v_f, __pyx_t_1);
26882 __pyx_t_1 = 0;
26883
26884 /* "pysam/libcvcf.pyx":753
26885 * if self._format:
26886 * for f in format:
26887 * if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f) # <<<<<<<<<<<<<<
26888 *
26889 * # convert v3.3 alleles
26890 */
26891 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 753, __pyx_L1_error)
26892 __Pyx_GOTREF(__pyx_t_1);
26893 __pyx_t_17 = (__Pyx_PySequence_ContainsTF(__pyx_v_f, __pyx_t_1, Py_NE)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 753, __pyx_L1_error)
26894 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26895 if (__pyx_t_17) {
26896 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 753, __pyx_L1_error)
26897 __Pyx_GOTREF(__pyx_t_12);
26898 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_FORMAT_NOT_DEFINED); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 753, __pyx_L1_error)
26899 __Pyx_GOTREF(__pyx_t_3);
26900 __pyx_t_9 = NULL;
26901 __pyx_t_4 = 0;
26902 #if CYTHON_UNPACK_METHODS
26903 if (likely(PyMethod_Check(__pyx_t_12))) {
26904 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_12);
26905 if (likely(__pyx_t_9)) {
26906 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_12);
26907 __Pyx_INCREF(__pyx_t_9);
26908 __Pyx_INCREF(function);
26909 __Pyx_DECREF_SET(__pyx_t_12, function);
26910 __pyx_t_4 = 1;
26911 }
26912 }
26913 #endif
26914 {
26915 PyObject *__pyx_callargs[4] = {__pyx_t_9, __pyx_v_line, __pyx_t_3, __pyx_v_f};
26916 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_12, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
26917 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
26918 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
26919 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 753, __pyx_L1_error)
26920 __Pyx_GOTREF(__pyx_t_1);
26921 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26922 }
26923 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26924 }
26925
26926 /* "pysam/libcvcf.pyx":752
26927 * # check: format fields are defined
26928 * if self._format:
26929 * for f in format: # <<<<<<<<<<<<<<
26930 * if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
26931 *
26932 */
26933 }
26934 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
26935
26936 /* "pysam/libcvcf.pyx":751
26937 *
26938 * # check: format fields are defined
26939 * if self._format: # <<<<<<<<<<<<<<
26940 * for f in format:
26941 * if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
26942 */
26943 }
26944
26945 /* "pysam/libcvcf.pyx":756
26946 *
26947 * # convert v3.3 alleles
26948 * if self._version == 33: # <<<<<<<<<<<<<<
26949 * if len(ref) != 1: self.error(line,self.V33_BAD_REF)
26950 * newalts = []
26951 */
26952 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_version); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 756, __pyx_L1_error)
26953 __Pyx_GOTREF(__pyx_t_2);
26954 __pyx_t_17 = (__Pyx_PyInt_BoolEqObjC(__pyx_t_2, __pyx_int_33, 33, 0)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 756, __pyx_L1_error)
26955 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
26956 if (__pyx_t_17) {
26957
26958 /* "pysam/libcvcf.pyx":757
26959 * # convert v3.3 alleles
26960 * if self._version == 33:
26961 * if len(ref) != 1: self.error(line,self.V33_BAD_REF) # <<<<<<<<<<<<<<
26962 * newalts = []
26963 * have_deletions = False
26964 */
26965 __pyx_t_6 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 757, __pyx_L1_error)
26966 __pyx_t_17 = (__pyx_t_6 != 1);
26967 if (__pyx_t_17) {
26968 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 757, __pyx_L1_error)
26969 __Pyx_GOTREF(__pyx_t_1);
26970 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_V33_BAD_REF); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 757, __pyx_L1_error)
26971 __Pyx_GOTREF(__pyx_t_12);
26972 __pyx_t_3 = NULL;
26973 __pyx_t_4 = 0;
26974 #if CYTHON_UNPACK_METHODS
26975 if (likely(PyMethod_Check(__pyx_t_1))) {
26976 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_1);
26977 if (likely(__pyx_t_3)) {
26978 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
26979 __Pyx_INCREF(__pyx_t_3);
26980 __Pyx_INCREF(function);
26981 __Pyx_DECREF_SET(__pyx_t_1, function);
26982 __pyx_t_4 = 1;
26983 }
26984 }
26985 #endif
26986 {
26987 PyObject *__pyx_callargs[3] = {__pyx_t_3, __pyx_v_line, __pyx_t_12};
26988 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
26989 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
26990 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
26991 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 757, __pyx_L1_error)
26992 __Pyx_GOTREF(__pyx_t_2);
26993 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
26994 }
26995 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
26996 }
26997
26998 /* "pysam/libcvcf.pyx":758
26999 * if self._version == 33:
27000 * if len(ref) != 1: self.error(line,self.V33_BAD_REF)
27001 * newalts = [] # <<<<<<<<<<<<<<
27002 * have_deletions = False
27003 * for a in alt:
27004 */
27005 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 758, __pyx_L1_error)
27006 __Pyx_GOTREF(__pyx_t_2);
27007 __pyx_v_newalts = ((PyObject*)__pyx_t_2);
27008 __pyx_t_2 = 0;
27009
27010 /* "pysam/libcvcf.pyx":759
27011 * if len(ref) != 1: self.error(line,self.V33_BAD_REF)
27012 * newalts = []
27013 * have_deletions = False # <<<<<<<<<<<<<<
27014 * for a in alt:
27015 * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
27016 */
27017 __pyx_v_have_deletions = 0;
27018
27019 /* "pysam/libcvcf.pyx":760
27020 * newalts = []
27021 * have_deletions = False
27022 * for a in alt: # <<<<<<<<<<<<<<
27023 * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
27024 * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
27025 */
27026 if (likely(PyList_CheckExact(__pyx_v_alt)) || PyTuple_CheckExact(__pyx_v_alt)) {
27027 __pyx_t_2 = __pyx_v_alt; __Pyx_INCREF(__pyx_t_2);
27028 __pyx_t_6 = 0;
27029 __pyx_t_18 = NULL;
27030 } else {
27031 __pyx_t_6 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_alt); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 760, __pyx_L1_error)
27032 __Pyx_GOTREF(__pyx_t_2);
27033 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_2); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 760, __pyx_L1_error)
27034 }
27035 for (;;) {
27036 if (likely(!__pyx_t_18)) {
27037 if (likely(PyList_CheckExact(__pyx_t_2))) {
27038 {
27039 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2);
27040 #if !CYTHON_ASSUME_SAFE_MACROS
27041 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 760, __pyx_L1_error)
27042 #endif
27043 if (__pyx_t_6 >= __pyx_temp) break;
27044 }
27045 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
27046 __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 760, __pyx_L1_error)
27047 #else
27048 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 760, __pyx_L1_error)
27049 __Pyx_GOTREF(__pyx_t_1);
27050 #endif
27051 } else {
27052 {
27053 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_2);
27054 #if !CYTHON_ASSUME_SAFE_MACROS
27055 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 760, __pyx_L1_error)
27056 #endif
27057 if (__pyx_t_6 >= __pyx_temp) break;
27058 }
27059 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
27060 __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 760, __pyx_L1_error)
27061 #else
27062 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 760, __pyx_L1_error)
27063 __Pyx_GOTREF(__pyx_t_1);
27064 #endif
27065 }
27066 } else {
27067 __pyx_t_1 = __pyx_t_18(__pyx_t_2);
27068 if (unlikely(!__pyx_t_1)) {
27069 PyObject* exc_type = PyErr_Occurred();
27070 if (exc_type) {
27071 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
27072 else __PYX_ERR(0, 760, __pyx_L1_error)
27073 }
27074 break;
27075 }
27076 __Pyx_GOTREF(__pyx_t_1);
27077 }
27078 __Pyx_XDECREF_SET(__pyx_v_a, __pyx_t_1);
27079 __pyx_t_1 = 0;
27080
27081 /* "pysam/libcvcf.pyx":761
27082 * have_deletions = False
27083 * for a in alt:
27084 * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference # <<<<<<<<<<<<<<
27085 * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
27086 * elif a.startswith('D'): # allow D<seq> and D<num>
27087 */
27088 __pyx_t_5 = PyObject_Length(__pyx_v_a); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 761, __pyx_L1_error)
27089 __pyx_t_17 = (__pyx_t_5 == 1);
27090 if (__pyx_t_17) {
27091 __pyx_t_1 = __Pyx_PyObject_GetSlice(__pyx_v_ref, 1, 0, NULL, NULL, &__pyx_slice__18, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 761, __pyx_L1_error)
27092 __Pyx_GOTREF(__pyx_t_1);
27093 __pyx_t_12 = PyNumber_Add(__pyx_v_a, __pyx_t_1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 761, __pyx_L1_error)
27094 __Pyx_GOTREF(__pyx_t_12);
27095 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
27096 __Pyx_DECREF_SET(__pyx_v_a, __pyx_t_12);
27097 __pyx_t_12 = 0;
27098 goto __pyx_L58;
27099 }
27100
27101 /* "pysam/libcvcf.pyx":762
27102 * for a in alt:
27103 * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
27104 * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference # <<<<<<<<<<<<<<
27105 * elif a.startswith('D'): # allow D<seq> and D<num>
27106 * have_deletions = True
27107 */
27108 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_a, __pyx_n_s_startswith); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 762, __pyx_L1_error)
27109 __Pyx_GOTREF(__pyx_t_1);
27110 __pyx_t_3 = NULL;
27111 __pyx_t_4 = 0;
27112 #if CYTHON_UNPACK_METHODS
27113 if (likely(PyMethod_Check(__pyx_t_1))) {
27114 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_1);
27115 if (likely(__pyx_t_3)) {
27116 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
27117 __Pyx_INCREF(__pyx_t_3);
27118 __Pyx_INCREF(function);
27119 __Pyx_DECREF_SET(__pyx_t_1, function);
27120 __pyx_t_4 = 1;
27121 }
27122 }
27123 #endif
27124 {
27125 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_n_u_I};
27126 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
27127 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
27128 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 762, __pyx_L1_error)
27129 __Pyx_GOTREF(__pyx_t_12);
27130 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
27131 }
27132 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_12); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 762, __pyx_L1_error)
27133 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
27134 if (__pyx_t_17) {
27135 __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_ref, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 762, __pyx_L1_error)
27136 __Pyx_GOTREF(__pyx_t_12);
27137 __pyx_t_1 = __Pyx_PyObject_GetSlice(__pyx_v_a, 1, 0, NULL, NULL, &__pyx_slice__18, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 762, __pyx_L1_error)
27138 __Pyx_GOTREF(__pyx_t_1);
27139 __pyx_t_3 = PyNumber_Add(__pyx_t_12, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 762, __pyx_L1_error)
27140 __Pyx_GOTREF(__pyx_t_3);
27141 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
27142 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
27143 __pyx_t_1 = __Pyx_PyObject_GetSlice(__pyx_v_ref, 1, 0, NULL, NULL, &__pyx_slice__18, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 762, __pyx_L1_error)
27144 __Pyx_GOTREF(__pyx_t_1);
27145 __pyx_t_12 = PyNumber_Add(__pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 762, __pyx_L1_error)
27146 __Pyx_GOTREF(__pyx_t_12);
27147 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
27148 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
27149 __Pyx_DECREF_SET(__pyx_v_a, __pyx_t_12);
27150 __pyx_t_12 = 0;
27151 goto __pyx_L58;
27152 }
27153
27154 /* "pysam/libcvcf.pyx":763
27155 * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
27156 * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
27157 * elif a.startswith('D'): # allow D<seq> and D<num> # <<<<<<<<<<<<<<
27158 * have_deletions = True
27159 * try:
27160 */
27161 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_a, __pyx_n_s_startswith); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 763, __pyx_L1_error)
27162 __Pyx_GOTREF(__pyx_t_1);
27163 __pyx_t_3 = NULL;
27164 __pyx_t_4 = 0;
27165 #if CYTHON_UNPACK_METHODS
27166 if (likely(PyMethod_Check(__pyx_t_1))) {
27167 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_1);
27168 if (likely(__pyx_t_3)) {
27169 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
27170 __Pyx_INCREF(__pyx_t_3);
27171 __Pyx_INCREF(function);
27172 __Pyx_DECREF_SET(__pyx_t_1, function);
27173 __pyx_t_4 = 1;
27174 }
27175 }
27176 #endif
27177 {
27178 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_n_u_D};
27179 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
27180 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
27181 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 763, __pyx_L1_error)
27182 __Pyx_GOTREF(__pyx_t_12);
27183 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
27184 }
27185 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_12); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 763, __pyx_L1_error)
27186 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
27187 if (__pyx_t_17) {
27188
27189 /* "pysam/libcvcf.pyx":764
27190 * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
27191 * elif a.startswith('D'): # allow D<seq> and D<num>
27192 * have_deletions = True # <<<<<<<<<<<<<<
27193 * try:
27194 * l = int(a[1:]) # throws ValueError if sequence
27195 */
27196 __pyx_v_have_deletions = 1;
27197
27198 /* "pysam/libcvcf.pyx":765
27199 * elif a.startswith('D'): # allow D<seq> and D<num>
27200 * have_deletions = True
27201 * try: # <<<<<<<<<<<<<<
27202 * l = int(a[1:]) # throws ValueError if sequence
27203 * if len(ref) < l: # add to reference if necessary
27204 */
27205 {
27206 __Pyx_PyThreadState_declare
27207 __Pyx_PyThreadState_assign
27208 __Pyx_ExceptionSave(&__pyx_t_13, &__pyx_t_14, &__pyx_t_15);
27209 __Pyx_XGOTREF(__pyx_t_13);
27210 __Pyx_XGOTREF(__pyx_t_14);
27211 __Pyx_XGOTREF(__pyx_t_15);
27212 /*try:*/ {
27213
27214 /* "pysam/libcvcf.pyx":766
27215 * have_deletions = True
27216 * try:
27217 * l = int(a[1:]) # throws ValueError if sequence # <<<<<<<<<<<<<<
27218 * if len(ref) < l: # add to reference if necessary
27219 * addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
27220 */
27221 __pyx_t_12 = __Pyx_PyObject_GetSlice(__pyx_v_a, 1, 0, NULL, NULL, &__pyx_slice__18, 1, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 766, __pyx_L59_error)
27222 __Pyx_GOTREF(__pyx_t_12);
27223 __pyx_t_1 = __Pyx_PyNumber_Int(__pyx_t_12); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 766, __pyx_L59_error)
27224 __Pyx_GOTREF(__pyx_t_1);
27225 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
27226 __Pyx_XDECREF_SET(__pyx_v_l, __pyx_t_1);
27227 __pyx_t_1 = 0;
27228
27229 /* "pysam/libcvcf.pyx":767
27230 * try:
27231 * l = int(a[1:]) # throws ValueError if sequence
27232 * if len(ref) < l: # add to reference if necessary # <<<<<<<<<<<<<<
27233 * addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
27234 * ref += addns
27235 */
27236 __pyx_t_5 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 767, __pyx_L59_error)
27237 __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_5); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 767, __pyx_L59_error)
27238 __Pyx_GOTREF(__pyx_t_1);
27239 __pyx_t_12 = PyObject_RichCompare(__pyx_t_1, __pyx_v_l, Py_LT); __Pyx_XGOTREF(__pyx_t_12); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 767, __pyx_L59_error)
27240 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
27241 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_12); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 767, __pyx_L59_error)
27242 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
27243 if (__pyx_t_17) {
27244
27245 /* "pysam/libcvcf.pyx":768
27246 * l = int(a[1:]) # throws ValueError if sequence
27247 * if len(ref) < l: # add to reference if necessary
27248 * addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference) # <<<<<<<<<<<<<<
27249 * ref += addns
27250 * for i,na in enumerate(newalts): newalts[i] = na+addns
27251 */
27252 __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_get_sequence); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 768, __pyx_L59_error)
27253 __Pyx_GOTREF(__pyx_t_1);
27254 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 768, __pyx_L59_error) }
27255 __pyx_t_5 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 768, __pyx_L59_error)
27256 __pyx_t_3 = PyInt_FromSsize_t(__pyx_t_5); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 768, __pyx_L59_error)
27257 __Pyx_GOTREF(__pyx_t_3);
27258 __pyx_t_9 = PyNumber_Add(__pyx_v_pos, __pyx_t_3); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 768, __pyx_L59_error)
27259 __Pyx_GOTREF(__pyx_t_9);
27260 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
27261 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 768, __pyx_L59_error) }
27262 __pyx_t_3 = PyNumber_Add(__pyx_v_pos, __pyx_v_l); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 768, __pyx_L59_error)
27263 __Pyx_GOTREF(__pyx_t_3);
27264 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_reference_2); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 768, __pyx_L59_error)
27265 __Pyx_GOTREF(__pyx_t_11);
27266 __pyx_t_16 = NULL;
27267 __pyx_t_4 = 0;
27268 #if CYTHON_UNPACK_METHODS
27269 if (unlikely(PyMethod_Check(__pyx_t_1))) {
27270 __pyx_t_16 = PyMethod_GET_SELF(__pyx_t_1);
27271 if (likely(__pyx_t_16)) {
27272 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
27273 __Pyx_INCREF(__pyx_t_16);
27274 __Pyx_INCREF(function);
27275 __Pyx_DECREF_SET(__pyx_t_1, function);
27276 __pyx_t_4 = 1;
27277 }
27278 }
27279 #endif
27280 {
27281 PyObject *__pyx_callargs[5] = {__pyx_t_16, __pyx_v_chrom, __pyx_t_9, __pyx_t_3, __pyx_t_11};
27282 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 4+__pyx_t_4);
27283 __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
27284 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
27285 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
27286 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
27287 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 768, __pyx_L59_error)
27288 __Pyx_GOTREF(__pyx_t_12);
27289 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
27290 }
27291 __Pyx_XDECREF_SET(__pyx_v_addns, __pyx_t_12);
27292 __pyx_t_12 = 0;
27293
27294 /* "pysam/libcvcf.pyx":769
27295 * if len(ref) < l: # add to reference if necessary
27296 * addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
27297 * ref += addns # <<<<<<<<<<<<<<
27298 * for i,na in enumerate(newalts): newalts[i] = na+addns
27299 * a = ref[l:] # new deletion, deleting pos...pos+l
27300 */
27301 __pyx_t_12 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addns); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 769, __pyx_L59_error)
27302 __Pyx_GOTREF(__pyx_t_12);
27303 __Pyx_DECREF_SET(__pyx_v_ref, __pyx_t_12);
27304 __pyx_t_12 = 0;
27305
27306 /* "pysam/libcvcf.pyx":770
27307 * addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
27308 * ref += addns
27309 * for i,na in enumerate(newalts): newalts[i] = na+addns # <<<<<<<<<<<<<<
27310 * a = ref[l:] # new deletion, deleting pos...pos+l
27311 * except ValueError:
27312 */
27313 __Pyx_INCREF(__pyx_int_0);
27314 __pyx_t_12 = __pyx_int_0;
27315 __pyx_t_1 = __pyx_v_newalts; __Pyx_INCREF(__pyx_t_1);
27316 __pyx_t_5 = 0;
27317 for (;;) {
27318 {
27319 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1);
27320 #if !CYTHON_ASSUME_SAFE_MACROS
27321 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 770, __pyx_L59_error)
27322 #endif
27323 if (__pyx_t_5 >= __pyx_temp) break;
27324 }
27325 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
27326 __pyx_t_11 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_11); __pyx_t_5++; if (unlikely((0 < 0))) __PYX_ERR(0, 770, __pyx_L59_error)
27327 #else
27328 __pyx_t_11 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 770, __pyx_L59_error)
27329 __Pyx_GOTREF(__pyx_t_11);
27330 #endif
27331 __Pyx_XDECREF_SET(__pyx_v_na, __pyx_t_11);
27332 __pyx_t_11 = 0;
27333 __Pyx_INCREF(__pyx_t_12);
27334 __Pyx_XDECREF_SET(__pyx_v_i, __pyx_t_12);
27335 __pyx_t_11 = __Pyx_PyInt_AddObjC(__pyx_t_12, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 770, __pyx_L59_error)
27336 __Pyx_GOTREF(__pyx_t_11);
27337 __Pyx_DECREF(__pyx_t_12);
27338 __pyx_t_12 = __pyx_t_11;
27339 __pyx_t_11 = 0;
27340 __pyx_t_11 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 770, __pyx_L59_error)
27341 __Pyx_GOTREF(__pyx_t_11);
27342 if (unlikely((PyObject_SetItem(__pyx_v_newalts, __pyx_v_i, __pyx_t_11) < 0))) __PYX_ERR(0, 770, __pyx_L59_error)
27343 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
27344 }
27345 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
27346 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
27347
27348 /* "pysam/libcvcf.pyx":767
27349 * try:
27350 * l = int(a[1:]) # throws ValueError if sequence
27351 * if len(ref) < l: # add to reference if necessary # <<<<<<<<<<<<<<
27352 * addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
27353 * ref += addns
27354 */
27355 }
27356
27357 /* "pysam/libcvcf.pyx":771
27358 * ref += addns
27359 * for i,na in enumerate(newalts): newalts[i] = na+addns
27360 * a = ref[l:] # new deletion, deleting pos...pos+l # <<<<<<<<<<<<<<
27361 * except ValueError:
27362 * s = a[1:]
27363 */
27364 __pyx_t_12 = __Pyx_PyObject_GetSlice(__pyx_v_ref, 0, 0, &__pyx_v_l, NULL, NULL, 0, 0, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 771, __pyx_L59_error)
27365 __Pyx_GOTREF(__pyx_t_12);
27366 __Pyx_DECREF_SET(__pyx_v_a, __pyx_t_12);
27367 __pyx_t_12 = 0;
27368
27369 /* "pysam/libcvcf.pyx":765
27370 * elif a.startswith('D'): # allow D<seq> and D<num>
27371 * have_deletions = True
27372 * try: # <<<<<<<<<<<<<<
27373 * l = int(a[1:]) # throws ValueError if sequence
27374 * if len(ref) < l: # add to reference if necessary
27375 */
27376 }
27377 __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
27378 __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
27379 __Pyx_XDECREF(__pyx_t_15); __pyx_t_15 = 0;
27380 goto __pyx_L66_try_end;
27381 __pyx_L59_error:;
27382 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
27383 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
27384 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
27385 __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
27386 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
27387 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
27388
27389 /* "pysam/libcvcf.pyx":772
27390 * for i,na in enumerate(newalts): newalts[i] = na+addns
27391 * a = ref[l:] # new deletion, deleting pos...pos+l
27392 * except ValueError: # <<<<<<<<<<<<<<
27393 * s = a[1:]
27394 * if len(ref) < len(s): # add Ns to reference if necessary
27395 */
27396 __pyx_t_21 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_ValueError);
27397 if (__pyx_t_21) {
27398 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
27399 if (__Pyx_GetException(&__pyx_t_12, &__pyx_t_1, &__pyx_t_11) < 0) __PYX_ERR(0, 772, __pyx_L61_except_error)
27400 __Pyx_XGOTREF(__pyx_t_12);
27401 __Pyx_XGOTREF(__pyx_t_1);
27402 __Pyx_XGOTREF(__pyx_t_11);
27403
27404 /* "pysam/libcvcf.pyx":773
27405 * a = ref[l:] # new deletion, deleting pos...pos+l
27406 * except ValueError:
27407 * s = a[1:] # <<<<<<<<<<<<<<
27408 * if len(ref) < len(s): # add Ns to reference if necessary
27409 * addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
27410 */
27411 __pyx_t_3 = __Pyx_PyObject_GetSlice(__pyx_v_a, 1, 0, NULL, NULL, &__pyx_slice__18, 1, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 773, __pyx_L61_except_error)
27412 __Pyx_GOTREF(__pyx_t_3);
27413 __Pyx_XDECREF_SET(__pyx_v_s, __pyx_t_3);
27414 __pyx_t_3 = 0;
27415
27416 /* "pysam/libcvcf.pyx":774
27417 * except ValueError:
27418 * s = a[1:]
27419 * if len(ref) < len(s): # add Ns to reference if necessary # <<<<<<<<<<<<<<
27420 * addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
27421 * if not s.endswith(addns) and addns != 'N'*len(addns):
27422 */
27423 __pyx_t_5 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 774, __pyx_L61_except_error)
27424 __pyx_t_22 = PyObject_Length(__pyx_v_s); if (unlikely(__pyx_t_22 == ((Py_ssize_t)-1))) __PYX_ERR(0, 774, __pyx_L61_except_error)
27425 __pyx_t_17 = (__pyx_t_5 < __pyx_t_22);
27426 if (__pyx_t_17) {
27427
27428 /* "pysam/libcvcf.pyx":775
27429 * s = a[1:]
27430 * if len(ref) < len(s): # add Ns to reference if necessary
27431 * addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference) # <<<<<<<<<<<<<<
27432 * if not s.endswith(addns) and addns != 'N'*len(addns):
27433 * self.error(line,self.V33_UNMATCHED_DELETION,
27434 */
27435 __Pyx_GetModuleGlobalName(__pyx_t_9, __pyx_n_s_get_sequence); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 775, __pyx_L61_except_error)
27436 __Pyx_GOTREF(__pyx_t_9);
27437 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 775, __pyx_L61_except_error) }
27438 __pyx_t_22 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_22 == ((Py_ssize_t)-1))) __PYX_ERR(0, 775, __pyx_L61_except_error)
27439 __pyx_t_16 = PyInt_FromSsize_t(__pyx_t_22); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 775, __pyx_L61_except_error)
27440 __Pyx_GOTREF(__pyx_t_16);
27441 __pyx_t_23 = PyNumber_Add(__pyx_v_pos, __pyx_t_16); if (unlikely(!__pyx_t_23)) __PYX_ERR(0, 775, __pyx_L61_except_error)
27442 __Pyx_GOTREF(__pyx_t_23);
27443 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
27444 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 775, __pyx_L61_except_error) }
27445 __pyx_t_22 = PyObject_Length(__pyx_v_s); if (unlikely(__pyx_t_22 == ((Py_ssize_t)-1))) __PYX_ERR(0, 775, __pyx_L61_except_error)
27446 __pyx_t_16 = PyInt_FromSsize_t(__pyx_t_22); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 775, __pyx_L61_except_error)
27447 __Pyx_GOTREF(__pyx_t_16);
27448 __pyx_t_24 = PyNumber_Add(__pyx_v_pos, __pyx_t_16); if (unlikely(!__pyx_t_24)) __PYX_ERR(0, 775, __pyx_L61_except_error)
27449 __Pyx_GOTREF(__pyx_t_24);
27450 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
27451 __pyx_t_16 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_reference_2); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 775, __pyx_L61_except_error)
27452 __Pyx_GOTREF(__pyx_t_16);
27453 __pyx_t_25 = NULL;
27454 __pyx_t_4 = 0;
27455 #if CYTHON_UNPACK_METHODS
27456 if (unlikely(PyMethod_Check(__pyx_t_9))) {
27457 __pyx_t_25 = PyMethod_GET_SELF(__pyx_t_9);
27458 if (likely(__pyx_t_25)) {
27459 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_9);
27460 __Pyx_INCREF(__pyx_t_25);
27461 __Pyx_INCREF(function);
27462 __Pyx_DECREF_SET(__pyx_t_9, function);
27463 __pyx_t_4 = 1;
27464 }
27465 }
27466 #endif
27467 {
27468 PyObject *__pyx_callargs[5] = {__pyx_t_25, __pyx_v_chrom, __pyx_t_23, __pyx_t_24, __pyx_t_16};
27469 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_4, 4+__pyx_t_4);
27470 __Pyx_XDECREF(__pyx_t_25); __pyx_t_25 = 0;
27471 __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
27472 __Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0;
27473 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
27474 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 775, __pyx_L61_except_error)
27475 __Pyx_GOTREF(__pyx_t_3);
27476 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
27477 }
27478 __Pyx_XDECREF_SET(__pyx_v_addns, __pyx_t_3);
27479 __pyx_t_3 = 0;
27480
27481 /* "pysam/libcvcf.pyx":776
27482 * if len(ref) < len(s): # add Ns to reference if necessary
27483 * addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
27484 * if not s.endswith(addns) and addns != 'N'*len(addns): # <<<<<<<<<<<<<<
27485 * self.error(line,self.V33_UNMATCHED_DELETION,
27486 * "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
27487 */
27488 __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_s, __pyx_n_s_endswith); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 776, __pyx_L61_except_error)
27489 __Pyx_GOTREF(__pyx_t_9);
27490 __pyx_t_16 = NULL;
27491 __pyx_t_4 = 0;
27492 #if CYTHON_UNPACK_METHODS
27493 if (likely(PyMethod_Check(__pyx_t_9))) {
27494 __pyx_t_16 = PyMethod_GET_SELF(__pyx_t_9);
27495 if (likely(__pyx_t_16)) {
27496 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_9);
27497 __Pyx_INCREF(__pyx_t_16);
27498 __Pyx_INCREF(function);
27499 __Pyx_DECREF_SET(__pyx_t_9, function);
27500 __pyx_t_4 = 1;
27501 }
27502 }
27503 #endif
27504 {
27505 PyObject *__pyx_callargs[2] = {__pyx_t_16, __pyx_v_addns};
27506 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
27507 __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
27508 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 776, __pyx_L61_except_error)
27509 __Pyx_GOTREF(__pyx_t_3);
27510 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
27511 }
27512 __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_7 < 0))) __PYX_ERR(0, 776, __pyx_L61_except_error)
27513 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
27514 __pyx_t_26 = (!__pyx_t_7);
27515 if (__pyx_t_26) {
27516 } else {
27517 __pyx_t_17 = __pyx_t_26;
27518 goto __pyx_L75_bool_binop_done;
27519 }
27520 __pyx_t_22 = PyObject_Length(__pyx_v_addns); if (unlikely(__pyx_t_22 == ((Py_ssize_t)-1))) __PYX_ERR(0, 776, __pyx_L61_except_error)
27521 __pyx_t_3 = __Pyx_PySequence_Multiply(__pyx_n_u_N, __pyx_t_22); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 776, __pyx_L61_except_error)
27522 __Pyx_GOTREF(__pyx_t_3);
27523 __pyx_t_26 = (__Pyx_PyUnicode_Equals(__pyx_v_addns, __pyx_t_3, Py_NE)); if (unlikely((__pyx_t_26 < 0))) __PYX_ERR(0, 776, __pyx_L61_except_error)
27524 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
27525 __pyx_t_17 = __pyx_t_26;
27526 __pyx_L75_bool_binop_done:;
27527 if (__pyx_t_17) {
27528
27529 /* "pysam/libcvcf.pyx":777
27530 * addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
27531 * if not s.endswith(addns) and addns != 'N'*len(addns):
27532 * self.error(line,self.V33_UNMATCHED_DELETION, # <<<<<<<<<<<<<<
27533 * "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
27534 * ref += addns
27535 */
27536 __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 777, __pyx_L61_except_error)
27537 __Pyx_GOTREF(__pyx_t_9);
27538 __pyx_t_16 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_V33_UNMATCHED_DELETION); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 777, __pyx_L61_except_error)
27539 __Pyx_GOTREF(__pyx_t_16);
27540
27541 /* "pysam/libcvcf.pyx":778
27542 * if not s.endswith(addns) and addns != 'N'*len(addns):
27543 * self.error(line,self.V33_UNMATCHED_DELETION,
27544 * "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference))) # <<<<<<<<<<<<<<
27545 * ref += addns
27546 * for i,na in enumerate(newalts): newalts[i] = na+addns
27547 */
27548 __pyx_t_24 = PyTuple_New(5); if (unlikely(!__pyx_t_24)) __PYX_ERR(0, 778, __pyx_L61_except_error)
27549 __Pyx_GOTREF(__pyx_t_24);
27550 __pyx_t_22 = 0;
27551 __pyx_t_10 = 127;
27552 __Pyx_INCREF(__pyx_kp_u_deletion_is);
27553 __pyx_t_22 += 13;
27554 __Pyx_GIVEREF(__pyx_kp_u_deletion_is);
27555 PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_kp_u_deletion_is);
27556 __pyx_t_23 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_a), __pyx_empty_unicode); if (unlikely(!__pyx_t_23)) __PYX_ERR(0, 778, __pyx_L61_except_error)
27557 __Pyx_GOTREF(__pyx_t_23);
27558 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_23) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_23) : __pyx_t_10;
27559 __pyx_t_22 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_23);
27560 __Pyx_GIVEREF(__pyx_t_23);
27561 PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_23);
27562 __pyx_t_23 = 0;
27563 __Pyx_INCREF(__pyx_kp_u_reference_is_2);
27564 __pyx_t_22 += 15;
27565 __Pyx_GIVEREF(__pyx_kp_u_reference_is_2);
27566 PyTuple_SET_ITEM(__pyx_t_24, 2, __pyx_kp_u_reference_is_2);
27567 __Pyx_GetModuleGlobalName(__pyx_t_25, __pyx_n_s_get_sequence); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 778, __pyx_L61_except_error)
27568 __Pyx_GOTREF(__pyx_t_25);
27569 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 778, __pyx_L61_except_error) }
27570 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 778, __pyx_L61_except_error) }
27571 __pyx_t_5 = PyObject_Length(__pyx_v_s); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 778, __pyx_L61_except_error)
27572 __pyx_t_27 = PyInt_FromSsize_t(__pyx_t_5); if (unlikely(!__pyx_t_27)) __PYX_ERR(0, 778, __pyx_L61_except_error)
27573 __Pyx_GOTREF(__pyx_t_27);
27574 __pyx_t_28 = PyNumber_Add(__pyx_v_pos, __pyx_t_27); if (unlikely(!__pyx_t_28)) __PYX_ERR(0, 778, __pyx_L61_except_error)
27575 __Pyx_GOTREF(__pyx_t_28);
27576 __Pyx_DECREF(__pyx_t_27); __pyx_t_27 = 0;
27577 __pyx_t_27 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_reference_2); if (unlikely(!__pyx_t_27)) __PYX_ERR(0, 778, __pyx_L61_except_error)
27578 __Pyx_GOTREF(__pyx_t_27);
27579 __pyx_t_29 = NULL;
27580 __pyx_t_4 = 0;
27581 #if CYTHON_UNPACK_METHODS
27582 if (unlikely(PyMethod_Check(__pyx_t_25))) {
27583 __pyx_t_29 = PyMethod_GET_SELF(__pyx_t_25);
27584 if (likely(__pyx_t_29)) {
27585 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_25);
27586 __Pyx_INCREF(__pyx_t_29);
27587 __Pyx_INCREF(function);
27588 __Pyx_DECREF_SET(__pyx_t_25, function);
27589 __pyx_t_4 = 1;
27590 }
27591 }
27592 #endif
27593 {
27594 PyObject *__pyx_callargs[5] = {__pyx_t_29, __pyx_v_chrom, __pyx_v_pos, __pyx_t_28, __pyx_t_27};
27595 __pyx_t_23 = __Pyx_PyObject_FastCall(__pyx_t_25, __pyx_callargs+1-__pyx_t_4, 4+__pyx_t_4);
27596 __Pyx_XDECREF(__pyx_t_29); __pyx_t_29 = 0;
27597 __Pyx_DECREF(__pyx_t_28); __pyx_t_28 = 0;
27598 __Pyx_DECREF(__pyx_t_27); __pyx_t_27 = 0;
27599 if (unlikely(!__pyx_t_23)) __PYX_ERR(0, 778, __pyx_L61_except_error)
27600 __Pyx_GOTREF(__pyx_t_23);
27601 __Pyx_DECREF(__pyx_t_25); __pyx_t_25 = 0;
27602 }
27603 __pyx_t_25 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_23), __pyx_empty_unicode); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 778, __pyx_L61_except_error)
27604 __Pyx_GOTREF(__pyx_t_25);
27605 __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
27606 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_25) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_25) : __pyx_t_10;
27607 __pyx_t_22 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_25);
27608 __Pyx_GIVEREF(__pyx_t_25);
27609 PyTuple_SET_ITEM(__pyx_t_24, 3, __pyx_t_25);
27610 __pyx_t_25 = 0;
27611 __Pyx_INCREF(__pyx_kp_u__8);
27612 __pyx_t_22 += 1;
27613 __Pyx_GIVEREF(__pyx_kp_u__8);
27614 PyTuple_SET_ITEM(__pyx_t_24, 4, __pyx_kp_u__8);
27615 __pyx_t_25 = __Pyx_PyUnicode_Join(__pyx_t_24, 5, __pyx_t_22, __pyx_t_10); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 778, __pyx_L61_except_error)
27616 __Pyx_GOTREF(__pyx_t_25);
27617 __Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0;
27618 __pyx_t_24 = NULL;
27619 __pyx_t_4 = 0;
27620 #if CYTHON_UNPACK_METHODS
27621 if (likely(PyMethod_Check(__pyx_t_9))) {
27622 __pyx_t_24 = PyMethod_GET_SELF(__pyx_t_9);
27623 if (likely(__pyx_t_24)) {
27624 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_9);
27625 __Pyx_INCREF(__pyx_t_24);
27626 __Pyx_INCREF(function);
27627 __Pyx_DECREF_SET(__pyx_t_9, function);
27628 __pyx_t_4 = 1;
27629 }
27630 }
27631 #endif
27632 {
27633 PyObject *__pyx_callargs[4] = {__pyx_t_24, __pyx_v_line, __pyx_t_16, __pyx_t_25};
27634 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
27635 __Pyx_XDECREF(__pyx_t_24); __pyx_t_24 = 0;
27636 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
27637 __Pyx_DECREF(__pyx_t_25); __pyx_t_25 = 0;
27638 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 777, __pyx_L61_except_error)
27639 __Pyx_GOTREF(__pyx_t_3);
27640 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
27641 }
27642 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
27643
27644 /* "pysam/libcvcf.pyx":776
27645 * if len(ref) < len(s): # add Ns to reference if necessary
27646 * addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
27647 * if not s.endswith(addns) and addns != 'N'*len(addns): # <<<<<<<<<<<<<<
27648 * self.error(line,self.V33_UNMATCHED_DELETION,
27649 * "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
27650 */
27651 }
27652
27653 /* "pysam/libcvcf.pyx":779
27654 * self.error(line,self.V33_UNMATCHED_DELETION,
27655 * "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
27656 * ref += addns # <<<<<<<<<<<<<<
27657 * for i,na in enumerate(newalts): newalts[i] = na+addns
27658 * a = ref[len(s):] # new deletion, deleting from pos
27659 */
27660 __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addns); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 779, __pyx_L61_except_error)
27661 __Pyx_GOTREF(__pyx_t_3);
27662 __Pyx_DECREF_SET(__pyx_v_ref, __pyx_t_3);
27663 __pyx_t_3 = 0;
27664
27665 /* "pysam/libcvcf.pyx":780
27666 * "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
27667 * ref += addns
27668 * for i,na in enumerate(newalts): newalts[i] = na+addns # <<<<<<<<<<<<<<
27669 * a = ref[len(s):] # new deletion, deleting from pos
27670 * else:
27671 */
27672 __Pyx_INCREF(__pyx_int_0);
27673 __pyx_t_3 = __pyx_int_0;
27674 __pyx_t_9 = __pyx_v_newalts; __Pyx_INCREF(__pyx_t_9);
27675 __pyx_t_22 = 0;
27676 for (;;) {
27677 {
27678 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_9);
27679 #if !CYTHON_ASSUME_SAFE_MACROS
27680 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 780, __pyx_L61_except_error)
27681 #endif
27682 if (__pyx_t_22 >= __pyx_temp) break;
27683 }
27684 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
27685 __pyx_t_25 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_22); __Pyx_INCREF(__pyx_t_25); __pyx_t_22++; if (unlikely((0 < 0))) __PYX_ERR(0, 780, __pyx_L61_except_error)
27686 #else
27687 __pyx_t_25 = __Pyx_PySequence_ITEM(__pyx_t_9, __pyx_t_22); __pyx_t_22++; if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 780, __pyx_L61_except_error)
27688 __Pyx_GOTREF(__pyx_t_25);
27689 #endif
27690 __Pyx_XDECREF_SET(__pyx_v_na, __pyx_t_25);
27691 __pyx_t_25 = 0;
27692 __Pyx_INCREF(__pyx_t_3);
27693 __Pyx_XDECREF_SET(__pyx_v_i, __pyx_t_3);
27694 __pyx_t_25 = __Pyx_PyInt_AddObjC(__pyx_t_3, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 780, __pyx_L61_except_error)
27695 __Pyx_GOTREF(__pyx_t_25);
27696 __Pyx_DECREF(__pyx_t_3);
27697 __pyx_t_3 = __pyx_t_25;
27698 __pyx_t_25 = 0;
27699 __pyx_t_25 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 780, __pyx_L61_except_error)
27700 __Pyx_GOTREF(__pyx_t_25);
27701 if (unlikely((PyObject_SetItem(__pyx_v_newalts, __pyx_v_i, __pyx_t_25) < 0))) __PYX_ERR(0, 780, __pyx_L61_except_error)
27702 __Pyx_DECREF(__pyx_t_25); __pyx_t_25 = 0;
27703 }
27704 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
27705 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
27706
27707 /* "pysam/libcvcf.pyx":774
27708 * except ValueError:
27709 * s = a[1:]
27710 * if len(ref) < len(s): # add Ns to reference if necessary # <<<<<<<<<<<<<<
27711 * addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
27712 * if not s.endswith(addns) and addns != 'N'*len(addns):
27713 */
27714 }
27715
27716 /* "pysam/libcvcf.pyx":781
27717 * ref += addns
27718 * for i,na in enumerate(newalts): newalts[i] = na+addns
27719 * a = ref[len(s):] # new deletion, deleting from pos # <<<<<<<<<<<<<<
27720 * else:
27721 * self.error(line,self.V33_BAD_ALLELE)
27722 */
27723 __pyx_t_22 = PyObject_Length(__pyx_v_s); if (unlikely(__pyx_t_22 == ((Py_ssize_t)-1))) __PYX_ERR(0, 781, __pyx_L61_except_error)
27724 __pyx_t_3 = __Pyx_PyObject_GetSlice(__pyx_v_ref, __pyx_t_22, 0, NULL, NULL, NULL, 1, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 781, __pyx_L61_except_error)
27725 __Pyx_GOTREF(__pyx_t_3);
27726 __Pyx_DECREF_SET(__pyx_v_a, __pyx_t_3);
27727 __pyx_t_3 = 0;
27728 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
27729 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
27730 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
27731 goto __pyx_L60_exception_handled;
27732 }
27733 goto __pyx_L61_except_error;
27734
27735 /* "pysam/libcvcf.pyx":765
27736 * elif a.startswith('D'): # allow D<seq> and D<num>
27737 * have_deletions = True
27738 * try: # <<<<<<<<<<<<<<
27739 * l = int(a[1:]) # throws ValueError if sequence
27740 * if len(ref) < l: # add to reference if necessary
27741 */
27742 __pyx_L61_except_error:;
27743 __Pyx_XGIVEREF(__pyx_t_13);
27744 __Pyx_XGIVEREF(__pyx_t_14);
27745 __Pyx_XGIVEREF(__pyx_t_15);
27746 __Pyx_ExceptionReset(__pyx_t_13, __pyx_t_14, __pyx_t_15);
27747 goto __pyx_L1_error;
27748 __pyx_L60_exception_handled:;
27749 __Pyx_XGIVEREF(__pyx_t_13);
27750 __Pyx_XGIVEREF(__pyx_t_14);
27751 __Pyx_XGIVEREF(__pyx_t_15);
27752 __Pyx_ExceptionReset(__pyx_t_13, __pyx_t_14, __pyx_t_15);
27753 __pyx_L66_try_end:;
27754 }
27755
27756 /* "pysam/libcvcf.pyx":763
27757 * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
27758 * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
27759 * elif a.startswith('D'): # allow D<seq> and D<num> # <<<<<<<<<<<<<<
27760 * have_deletions = True
27761 * try:
27762 */
27763 goto __pyx_L58;
27764 }
27765
27766 /* "pysam/libcvcf.pyx":783
27767 * a = ref[len(s):] # new deletion, deleting from pos
27768 * else:
27769 * self.error(line,self.V33_BAD_ALLELE) # <<<<<<<<<<<<<<
27770 * newalts.append(a)
27771 * alt = newalts
27772 */
27773 /*else*/ {
27774 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 783, __pyx_L1_error)
27775 __Pyx_GOTREF(__pyx_t_1);
27776 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_V33_BAD_ALLELE); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 783, __pyx_L1_error)
27777 __Pyx_GOTREF(__pyx_t_12);
27778 __pyx_t_3 = NULL;
27779 __pyx_t_4 = 0;
27780 #if CYTHON_UNPACK_METHODS
27781 if (likely(PyMethod_Check(__pyx_t_1))) {
27782 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_1);
27783 if (likely(__pyx_t_3)) {
27784 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
27785 __Pyx_INCREF(__pyx_t_3);
27786 __Pyx_INCREF(function);
27787 __Pyx_DECREF_SET(__pyx_t_1, function);
27788 __pyx_t_4 = 1;
27789 }
27790 }
27791 #endif
27792 {
27793 PyObject *__pyx_callargs[3] = {__pyx_t_3, __pyx_v_line, __pyx_t_12};
27794 __pyx_t_11 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
27795 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
27796 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
27797 if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 783, __pyx_L1_error)
27798 __Pyx_GOTREF(__pyx_t_11);
27799 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
27800 }
27801 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
27802 }
27803 __pyx_L58:;
27804
27805 /* "pysam/libcvcf.pyx":784
27806 * else:
27807 * self.error(line,self.V33_BAD_ALLELE)
27808 * newalts.append(a) # <<<<<<<<<<<<<<
27809 * alt = newalts
27810 * # deletion alleles exist, add dummy 1st reference allele, and account for leading base
27811 */
27812 __pyx_t_8 = __Pyx_PyList_Append(__pyx_v_newalts, __pyx_v_a); if (unlikely(__pyx_t_8 == ((int)-1))) __PYX_ERR(0, 784, __pyx_L1_error)
27813
27814 /* "pysam/libcvcf.pyx":760
27815 * newalts = []
27816 * have_deletions = False
27817 * for a in alt: # <<<<<<<<<<<<<<
27818 * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
27819 * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
27820 */
27821 }
27822 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
27823
27824 /* "pysam/libcvcf.pyx":785
27825 * self.error(line,self.V33_BAD_ALLELE)
27826 * newalts.append(a)
27827 * alt = newalts # <<<<<<<<<<<<<<
27828 * # deletion alleles exist, add dummy 1st reference allele, and account for leading base
27829 * if have_deletions:
27830 */
27831 __Pyx_INCREF(__pyx_v_newalts);
27832 __Pyx_DECREF_SET(__pyx_v_alt, __pyx_v_newalts);
27833
27834 /* "pysam/libcvcf.pyx":787
27835 * alt = newalts
27836 * # deletion alleles exist, add dummy 1st reference allele, and account for leading base
27837 * if have_deletions: # <<<<<<<<<<<<<<
27838 * if pos == 0:
27839 * # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
27840 */
27841 if (__pyx_v_have_deletions) {
27842
27843 /* "pysam/libcvcf.pyx":788
27844 * # deletion alleles exist, add dummy 1st reference allele, and account for leading base
27845 * if have_deletions:
27846 * if pos == 0: # <<<<<<<<<<<<<<
27847 * # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
27848 * addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
27849 */
27850 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 788, __pyx_L1_error) }
27851 __pyx_t_17 = (__Pyx_PyInt_BoolEqObjC(__pyx_v_pos, __pyx_int_0, 0, 0)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 788, __pyx_L1_error)
27852 if (__pyx_t_17) {
27853
27854 /* "pysam/libcvcf.pyx":790
27855 * if pos == 0:
27856 * # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
27857 * addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference) # <<<<<<<<<<<<<<
27858 * ref += addn
27859 * alt = [allele+addn for allele in alt]
27860 */
27861 __Pyx_GetModuleGlobalName(__pyx_t_11, __pyx_n_s_get_sequence); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 790, __pyx_L1_error)
27862 __Pyx_GOTREF(__pyx_t_11);
27863 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 790, __pyx_L1_error) }
27864 __pyx_t_6 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 790, __pyx_L1_error)
27865 __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_6); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 790, __pyx_L1_error)
27866 __Pyx_GOTREF(__pyx_t_1);
27867 __pyx_t_12 = PyNumber_Add(__pyx_v_pos, __pyx_t_1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 790, __pyx_L1_error)
27868 __Pyx_GOTREF(__pyx_t_12);
27869 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
27870 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 790, __pyx_L1_error) }
27871 __pyx_t_6 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 790, __pyx_L1_error)
27872 __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_6); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 790, __pyx_L1_error)
27873 __Pyx_GOTREF(__pyx_t_1);
27874 __pyx_t_3 = PyNumber_Add(__pyx_v_pos, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 790, __pyx_L1_error)
27875 __Pyx_GOTREF(__pyx_t_3);
27876 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
27877 __pyx_t_1 = __Pyx_PyInt_AddObjC(__pyx_t_3, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 790, __pyx_L1_error)
27878 __Pyx_GOTREF(__pyx_t_1);
27879 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
27880 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_reference_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 790, __pyx_L1_error)
27881 __Pyx_GOTREF(__pyx_t_3);
27882 __pyx_t_9 = NULL;
27883 __pyx_t_4 = 0;
27884 #if CYTHON_UNPACK_METHODS
27885 if (unlikely(PyMethod_Check(__pyx_t_11))) {
27886 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_11);
27887 if (likely(__pyx_t_9)) {
27888 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
27889 __Pyx_INCREF(__pyx_t_9);
27890 __Pyx_INCREF(function);
27891 __Pyx_DECREF_SET(__pyx_t_11, function);
27892 __pyx_t_4 = 1;
27893 }
27894 }
27895 #endif
27896 {
27897 PyObject *__pyx_callargs[5] = {__pyx_t_9, __pyx_v_chrom, __pyx_t_12, __pyx_t_1, __pyx_t_3};
27898 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_11, __pyx_callargs+1-__pyx_t_4, 4+__pyx_t_4);
27899 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
27900 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
27901 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
27902 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
27903 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 790, __pyx_L1_error)
27904 __Pyx_GOTREF(__pyx_t_2);
27905 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
27906 }
27907 __pyx_v_addn = __pyx_t_2;
27908 __pyx_t_2 = 0;
27909
27910 /* "pysam/libcvcf.pyx":791
27911 * # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
27912 * addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
27913 * ref += addn # <<<<<<<<<<<<<<
27914 * alt = [allele+addn for allele in alt]
27915 * else:
27916 */
27917 __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addn); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 791, __pyx_L1_error)
27918 __Pyx_GOTREF(__pyx_t_2);
27919 __Pyx_DECREF_SET(__pyx_v_ref, __pyx_t_2);
27920 __pyx_t_2 = 0;
27921
27922 /* "pysam/libcvcf.pyx":792
27923 * addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
27924 * ref += addn
27925 * alt = [allele+addn for allele in alt] # <<<<<<<<<<<<<<
27926 * else:
27927 * addn = get_sequence(chrom,pos-1,pos,self._reference)
27928 */
27929 { /* enter inner scope */
27930 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 792, __pyx_L85_error)
27931 __Pyx_GOTREF(__pyx_t_2);
27932 if (likely(PyList_CheckExact(__pyx_v_alt)) || PyTuple_CheckExact(__pyx_v_alt)) {
27933 __pyx_t_11 = __pyx_v_alt; __Pyx_INCREF(__pyx_t_11);
27934 __pyx_t_6 = 0;
27935 __pyx_t_18 = NULL;
27936 } else {
27937 __pyx_t_6 = -1; __pyx_t_11 = PyObject_GetIter(__pyx_v_alt); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 792, __pyx_L85_error)
27938 __Pyx_GOTREF(__pyx_t_11);
27939 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_11); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 792, __pyx_L85_error)
27940 }
27941 for (;;) {
27942 if (likely(!__pyx_t_18)) {
27943 if (likely(PyList_CheckExact(__pyx_t_11))) {
27944 {
27945 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_11);
27946 #if !CYTHON_ASSUME_SAFE_MACROS
27947 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 792, __pyx_L85_error)
27948 #endif
27949 if (__pyx_t_6 >= __pyx_temp) break;
27950 }
27951 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
27952 __pyx_t_3 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_6); __Pyx_INCREF(__pyx_t_3); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 792, __pyx_L85_error)
27953 #else
27954 __pyx_t_3 = __Pyx_PySequence_ITEM(__pyx_t_11, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 792, __pyx_L85_error)
27955 __Pyx_GOTREF(__pyx_t_3);
27956 #endif
27957 } else {
27958 {
27959 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_11);
27960 #if !CYTHON_ASSUME_SAFE_MACROS
27961 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 792, __pyx_L85_error)
27962 #endif
27963 if (__pyx_t_6 >= __pyx_temp) break;
27964 }
27965 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
27966 __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_6); __Pyx_INCREF(__pyx_t_3); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 792, __pyx_L85_error)
27967 #else
27968 __pyx_t_3 = __Pyx_PySequence_ITEM(__pyx_t_11, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 792, __pyx_L85_error)
27969 __Pyx_GOTREF(__pyx_t_3);
27970 #endif
27971 }
27972 } else {
27973 __pyx_t_3 = __pyx_t_18(__pyx_t_11);
27974 if (unlikely(!__pyx_t_3)) {
27975 PyObject* exc_type = PyErr_Occurred();
27976 if (exc_type) {
27977 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
27978 else __PYX_ERR(0, 792, __pyx_L85_error)
27979 }
27980 break;
27981 }
27982 __Pyx_GOTREF(__pyx_t_3);
27983 }
27984 __Pyx_XDECREF_SET(__pyx_8genexpr3__pyx_v_allele, __pyx_t_3);
27985 __pyx_t_3 = 0;
27986 __pyx_t_3 = PyNumber_Add(__pyx_8genexpr3__pyx_v_allele, __pyx_v_addn); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 792, __pyx_L85_error)
27987 __Pyx_GOTREF(__pyx_t_3);
27988 if (unlikely(__Pyx_ListComp_Append(__pyx_t_2, (PyObject*)__pyx_t_3))) __PYX_ERR(0, 792, __pyx_L85_error)
27989 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
27990 }
27991 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
27992 __Pyx_XDECREF(__pyx_8genexpr3__pyx_v_allele); __pyx_8genexpr3__pyx_v_allele = 0;
27993 goto __pyx_L89_exit_scope;
27994 __pyx_L85_error:;
27995 __Pyx_XDECREF(__pyx_8genexpr3__pyx_v_allele); __pyx_8genexpr3__pyx_v_allele = 0;
27996 goto __pyx_L1_error;
27997 __pyx_L89_exit_scope:;
27998 } /* exit inner scope */
27999 __Pyx_DECREF_SET(__pyx_v_alt, __pyx_t_2);
28000 __pyx_t_2 = 0;
28001
28002 /* "pysam/libcvcf.pyx":788
28003 * # deletion alleles exist, add dummy 1st reference allele, and account for leading base
28004 * if have_deletions:
28005 * if pos == 0: # <<<<<<<<<<<<<<
28006 * # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
28007 * addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
28008 */
28009 goto __pyx_L82;
28010 }
28011
28012 /* "pysam/libcvcf.pyx":794
28013 * alt = [allele+addn for allele in alt]
28014 * else:
28015 * addn = get_sequence(chrom,pos-1,pos,self._reference) # <<<<<<<<<<<<<<
28016 * ref = addn + ref
28017 * alt = [addn + allele for allele in alt]
28018 */
28019 /*else*/ {
28020 __Pyx_GetModuleGlobalName(__pyx_t_11, __pyx_n_s_get_sequence); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 794, __pyx_L1_error)
28021 __Pyx_GOTREF(__pyx_t_11);
28022 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 794, __pyx_L1_error) }
28023 __pyx_t_3 = __Pyx_PyInt_SubtractObjC(__pyx_v_pos, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 794, __pyx_L1_error)
28024 __Pyx_GOTREF(__pyx_t_3);
28025 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 794, __pyx_L1_error) }
28026 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_reference_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 794, __pyx_L1_error)
28027 __Pyx_GOTREF(__pyx_t_1);
28028 __pyx_t_12 = NULL;
28029 __pyx_t_4 = 0;
28030 #if CYTHON_UNPACK_METHODS
28031 if (unlikely(PyMethod_Check(__pyx_t_11))) {
28032 __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_11);
28033 if (likely(__pyx_t_12)) {
28034 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
28035 __Pyx_INCREF(__pyx_t_12);
28036 __Pyx_INCREF(function);
28037 __Pyx_DECREF_SET(__pyx_t_11, function);
28038 __pyx_t_4 = 1;
28039 }
28040 }
28041 #endif
28042 {
28043 PyObject *__pyx_callargs[5] = {__pyx_t_12, __pyx_v_chrom, __pyx_t_3, __pyx_v_pos, __pyx_t_1};
28044 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_11, __pyx_callargs+1-__pyx_t_4, 4+__pyx_t_4);
28045 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
28046 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
28047 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
28048 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 794, __pyx_L1_error)
28049 __Pyx_GOTREF(__pyx_t_2);
28050 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28051 }
28052 __pyx_v_addn = __pyx_t_2;
28053 __pyx_t_2 = 0;
28054
28055 /* "pysam/libcvcf.pyx":795
28056 * else:
28057 * addn = get_sequence(chrom,pos-1,pos,self._reference)
28058 * ref = addn + ref # <<<<<<<<<<<<<<
28059 * alt = [addn + allele for allele in alt]
28060 * pos -= 1
28061 */
28062 __pyx_t_2 = PyNumber_Add(__pyx_v_addn, __pyx_v_ref); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 795, __pyx_L1_error)
28063 __Pyx_GOTREF(__pyx_t_2);
28064 __Pyx_DECREF_SET(__pyx_v_ref, __pyx_t_2);
28065 __pyx_t_2 = 0;
28066
28067 /* "pysam/libcvcf.pyx":796
28068 * addn = get_sequence(chrom,pos-1,pos,self._reference)
28069 * ref = addn + ref
28070 * alt = [addn + allele for allele in alt] # <<<<<<<<<<<<<<
28071 * pos -= 1
28072 * else:
28073 */
28074 { /* enter inner scope */
28075 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 796, __pyx_L92_error)
28076 __Pyx_GOTREF(__pyx_t_2);
28077 if (likely(PyList_CheckExact(__pyx_v_alt)) || PyTuple_CheckExact(__pyx_v_alt)) {
28078 __pyx_t_11 = __pyx_v_alt; __Pyx_INCREF(__pyx_t_11);
28079 __pyx_t_6 = 0;
28080 __pyx_t_18 = NULL;
28081 } else {
28082 __pyx_t_6 = -1; __pyx_t_11 = PyObject_GetIter(__pyx_v_alt); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 796, __pyx_L92_error)
28083 __Pyx_GOTREF(__pyx_t_11);
28084 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_11); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 796, __pyx_L92_error)
28085 }
28086 for (;;) {
28087 if (likely(!__pyx_t_18)) {
28088 if (likely(PyList_CheckExact(__pyx_t_11))) {
28089 {
28090 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_11);
28091 #if !CYTHON_ASSUME_SAFE_MACROS
28092 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 796, __pyx_L92_error)
28093 #endif
28094 if (__pyx_t_6 >= __pyx_temp) break;
28095 }
28096 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
28097 __pyx_t_1 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 796, __pyx_L92_error)
28098 #else
28099 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_11, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 796, __pyx_L92_error)
28100 __Pyx_GOTREF(__pyx_t_1);
28101 #endif
28102 } else {
28103 {
28104 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_11);
28105 #if !CYTHON_ASSUME_SAFE_MACROS
28106 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 796, __pyx_L92_error)
28107 #endif
28108 if (__pyx_t_6 >= __pyx_temp) break;
28109 }
28110 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
28111 __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 796, __pyx_L92_error)
28112 #else
28113 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_11, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 796, __pyx_L92_error)
28114 __Pyx_GOTREF(__pyx_t_1);
28115 #endif
28116 }
28117 } else {
28118 __pyx_t_1 = __pyx_t_18(__pyx_t_11);
28119 if (unlikely(!__pyx_t_1)) {
28120 PyObject* exc_type = PyErr_Occurred();
28121 if (exc_type) {
28122 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
28123 else __PYX_ERR(0, 796, __pyx_L92_error)
28124 }
28125 break;
28126 }
28127 __Pyx_GOTREF(__pyx_t_1);
28128 }
28129 __Pyx_XDECREF_SET(__pyx_8genexpr4__pyx_v_allele, __pyx_t_1);
28130 __pyx_t_1 = 0;
28131 __pyx_t_1 = PyNumber_Add(__pyx_v_addn, __pyx_8genexpr4__pyx_v_allele); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 796, __pyx_L92_error)
28132 __Pyx_GOTREF(__pyx_t_1);
28133 if (unlikely(__Pyx_ListComp_Append(__pyx_t_2, (PyObject*)__pyx_t_1))) __PYX_ERR(0, 796, __pyx_L92_error)
28134 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
28135 }
28136 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28137 __Pyx_XDECREF(__pyx_8genexpr4__pyx_v_allele); __pyx_8genexpr4__pyx_v_allele = 0;
28138 goto __pyx_L96_exit_scope;
28139 __pyx_L92_error:;
28140 __Pyx_XDECREF(__pyx_8genexpr4__pyx_v_allele); __pyx_8genexpr4__pyx_v_allele = 0;
28141 goto __pyx_L1_error;
28142 __pyx_L96_exit_scope:;
28143 } /* exit inner scope */
28144 __Pyx_DECREF_SET(__pyx_v_alt, __pyx_t_2);
28145 __pyx_t_2 = 0;
28146
28147 /* "pysam/libcvcf.pyx":797
28148 * ref = addn + ref
28149 * alt = [addn + allele for allele in alt]
28150 * pos -= 1 # <<<<<<<<<<<<<<
28151 * else:
28152 * # format v4.0 -- just check for nucleotides
28153 */
28154 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 797, __pyx_L1_error) }
28155 __pyx_t_2 = __Pyx_PyInt_SubtractObjC(__pyx_v_pos, __pyx_int_1, 1, 1, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 797, __pyx_L1_error)
28156 __Pyx_GOTREF(__pyx_t_2);
28157 __Pyx_XDECREF_SET(__pyx_v_pos, __pyx_t_2);
28158 __pyx_t_2 = 0;
28159 }
28160 __pyx_L82:;
28161
28162 /* "pysam/libcvcf.pyx":787
28163 * alt = newalts
28164 * # deletion alleles exist, add dummy 1st reference allele, and account for leading base
28165 * if have_deletions: # <<<<<<<<<<<<<<
28166 * if pos == 0:
28167 * # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
28168 */
28169 }
28170
28171 /* "pysam/libcvcf.pyx":756
28172 *
28173 * # convert v3.3 alleles
28174 * if self._version == 33: # <<<<<<<<<<<<<<
28175 * if len(ref) != 1: self.error(line,self.V33_BAD_REF)
28176 * newalts = []
28177 */
28178 goto __pyx_L54;
28179 }
28180
28181 /* "pysam/libcvcf.pyx":800
28182 * else:
28183 * # format v4.0 -- just check for nucleotides
28184 * for allele in alt: # <<<<<<<<<<<<<<
28185 * if not alleleRegEx.match(allele):
28186 * self.error(line,self.V40_BAD_ALLELE,allele)
28187 */
28188 /*else*/ {
28189 if (likely(PyList_CheckExact(__pyx_v_alt)) || PyTuple_CheckExact(__pyx_v_alt)) {
28190 __pyx_t_2 = __pyx_v_alt; __Pyx_INCREF(__pyx_t_2);
28191 __pyx_t_6 = 0;
28192 __pyx_t_18 = NULL;
28193 } else {
28194 __pyx_t_6 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_alt); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 800, __pyx_L1_error)
28195 __Pyx_GOTREF(__pyx_t_2);
28196 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_2); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 800, __pyx_L1_error)
28197 }
28198 for (;;) {
28199 if (likely(!__pyx_t_18)) {
28200 if (likely(PyList_CheckExact(__pyx_t_2))) {
28201 {
28202 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2);
28203 #if !CYTHON_ASSUME_SAFE_MACROS
28204 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 800, __pyx_L1_error)
28205 #endif
28206 if (__pyx_t_6 >= __pyx_temp) break;
28207 }
28208 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
28209 __pyx_t_11 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_11); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 800, __pyx_L1_error)
28210 #else
28211 __pyx_t_11 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 800, __pyx_L1_error)
28212 __Pyx_GOTREF(__pyx_t_11);
28213 #endif
28214 } else {
28215 {
28216 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_2);
28217 #if !CYTHON_ASSUME_SAFE_MACROS
28218 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 800, __pyx_L1_error)
28219 #endif
28220 if (__pyx_t_6 >= __pyx_temp) break;
28221 }
28222 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
28223 __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_11); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 800, __pyx_L1_error)
28224 #else
28225 __pyx_t_11 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 800, __pyx_L1_error)
28226 __Pyx_GOTREF(__pyx_t_11);
28227 #endif
28228 }
28229 } else {
28230 __pyx_t_11 = __pyx_t_18(__pyx_t_2);
28231 if (unlikely(!__pyx_t_11)) {
28232 PyObject* exc_type = PyErr_Occurred();
28233 if (exc_type) {
28234 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
28235 else __PYX_ERR(0, 800, __pyx_L1_error)
28236 }
28237 break;
28238 }
28239 __Pyx_GOTREF(__pyx_t_11);
28240 }
28241 __Pyx_XDECREF_SET(__pyx_v_allele, __pyx_t_11);
28242 __pyx_t_11 = 0;
28243
28244 /* "pysam/libcvcf.pyx":801
28245 * # format v4.0 -- just check for nucleotides
28246 * for allele in alt:
28247 * if not alleleRegEx.match(allele): # <<<<<<<<<<<<<<
28248 * self.error(line,self.V40_BAD_ALLELE,allele)
28249 *
28250 */
28251 __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_alleleRegEx); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 801, __pyx_L1_error)
28252 __Pyx_GOTREF(__pyx_t_1);
28253 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_match); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 801, __pyx_L1_error)
28254 __Pyx_GOTREF(__pyx_t_3);
28255 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
28256 __pyx_t_1 = NULL;
28257 __pyx_t_4 = 0;
28258 #if CYTHON_UNPACK_METHODS
28259 if (unlikely(PyMethod_Check(__pyx_t_3))) {
28260 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_3);
28261 if (likely(__pyx_t_1)) {
28262 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
28263 __Pyx_INCREF(__pyx_t_1);
28264 __Pyx_INCREF(function);
28265 __Pyx_DECREF_SET(__pyx_t_3, function);
28266 __pyx_t_4 = 1;
28267 }
28268 }
28269 #endif
28270 {
28271 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_v_allele};
28272 __pyx_t_11 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
28273 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
28274 if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 801, __pyx_L1_error)
28275 __Pyx_GOTREF(__pyx_t_11);
28276 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
28277 }
28278 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_11); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 801, __pyx_L1_error)
28279 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28280 __pyx_t_26 = (!__pyx_t_17);
28281 if (__pyx_t_26) {
28282
28283 /* "pysam/libcvcf.pyx":802
28284 * for allele in alt:
28285 * if not alleleRegEx.match(allele):
28286 * self.error(line,self.V40_BAD_ALLELE,allele) # <<<<<<<<<<<<<<
28287 *
28288 * # check for leading nucleotide in indel calls
28289 */
28290 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 802, __pyx_L1_error)
28291 __Pyx_GOTREF(__pyx_t_3);
28292 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_V40_BAD_ALLELE); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 802, __pyx_L1_error)
28293 __Pyx_GOTREF(__pyx_t_1);
28294 __pyx_t_12 = NULL;
28295 __pyx_t_4 = 0;
28296 #if CYTHON_UNPACK_METHODS
28297 if (likely(PyMethod_Check(__pyx_t_3))) {
28298 __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_3);
28299 if (likely(__pyx_t_12)) {
28300 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
28301 __Pyx_INCREF(__pyx_t_12);
28302 __Pyx_INCREF(function);
28303 __Pyx_DECREF_SET(__pyx_t_3, function);
28304 __pyx_t_4 = 1;
28305 }
28306 }
28307 #endif
28308 {
28309 PyObject *__pyx_callargs[4] = {__pyx_t_12, __pyx_v_line, __pyx_t_1, __pyx_v_allele};
28310 __pyx_t_11 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
28311 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
28312 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
28313 if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 802, __pyx_L1_error)
28314 __Pyx_GOTREF(__pyx_t_11);
28315 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
28316 }
28317 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28318
28319 /* "pysam/libcvcf.pyx":801
28320 * # format v4.0 -- just check for nucleotides
28321 * for allele in alt:
28322 * if not alleleRegEx.match(allele): # <<<<<<<<<<<<<<
28323 * self.error(line,self.V40_BAD_ALLELE,allele)
28324 *
28325 */
28326 }
28327
28328 /* "pysam/libcvcf.pyx":800
28329 * else:
28330 * # format v4.0 -- just check for nucleotides
28331 * for allele in alt: # <<<<<<<<<<<<<<
28332 * if not alleleRegEx.match(allele):
28333 * self.error(line,self.V40_BAD_ALLELE,allele)
28334 */
28335 }
28336 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
28337 }
28338 __pyx_L54:;
28339
28340 /* "pysam/libcvcf.pyx":805
28341 *
28342 * # check for leading nucleotide in indel calls
28343 * for allele in alt: # <<<<<<<<<<<<<<
28344 * if len(allele) != len(ref):
28345 * if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
28346 */
28347 if (likely(PyList_CheckExact(__pyx_v_alt)) || PyTuple_CheckExact(__pyx_v_alt)) {
28348 __pyx_t_2 = __pyx_v_alt; __Pyx_INCREF(__pyx_t_2);
28349 __pyx_t_6 = 0;
28350 __pyx_t_18 = NULL;
28351 } else {
28352 __pyx_t_6 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_alt); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 805, __pyx_L1_error)
28353 __Pyx_GOTREF(__pyx_t_2);
28354 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_2); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 805, __pyx_L1_error)
28355 }
28356 for (;;) {
28357 if (likely(!__pyx_t_18)) {
28358 if (likely(PyList_CheckExact(__pyx_t_2))) {
28359 {
28360 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2);
28361 #if !CYTHON_ASSUME_SAFE_MACROS
28362 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 805, __pyx_L1_error)
28363 #endif
28364 if (__pyx_t_6 >= __pyx_temp) break;
28365 }
28366 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
28367 __pyx_t_11 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_11); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 805, __pyx_L1_error)
28368 #else
28369 __pyx_t_11 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 805, __pyx_L1_error)
28370 __Pyx_GOTREF(__pyx_t_11);
28371 #endif
28372 } else {
28373 {
28374 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_2);
28375 #if !CYTHON_ASSUME_SAFE_MACROS
28376 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 805, __pyx_L1_error)
28377 #endif
28378 if (__pyx_t_6 >= __pyx_temp) break;
28379 }
28380 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
28381 __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_11); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 805, __pyx_L1_error)
28382 #else
28383 __pyx_t_11 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 805, __pyx_L1_error)
28384 __Pyx_GOTREF(__pyx_t_11);
28385 #endif
28386 }
28387 } else {
28388 __pyx_t_11 = __pyx_t_18(__pyx_t_2);
28389 if (unlikely(!__pyx_t_11)) {
28390 PyObject* exc_type = PyErr_Occurred();
28391 if (exc_type) {
28392 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
28393 else __PYX_ERR(0, 805, __pyx_L1_error)
28394 }
28395 break;
28396 }
28397 __Pyx_GOTREF(__pyx_t_11);
28398 }
28399 __Pyx_XDECREF_SET(__pyx_v_allele, __pyx_t_11);
28400 __pyx_t_11 = 0;
28401
28402 /* "pysam/libcvcf.pyx":806
28403 * # check for leading nucleotide in indel calls
28404 * for allele in alt:
28405 * if len(allele) != len(ref): # <<<<<<<<<<<<<<
28406 * if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
28407 * if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
28408 */
28409 __pyx_t_22 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_22 == ((Py_ssize_t)-1))) __PYX_ERR(0, 806, __pyx_L1_error)
28410 __pyx_t_5 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 806, __pyx_L1_error)
28411 __pyx_t_26 = (__pyx_t_22 != __pyx_t_5);
28412 if (__pyx_t_26) {
28413
28414 /* "pysam/libcvcf.pyx":807
28415 * for allele in alt:
28416 * if len(allele) != len(ref):
28417 * if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE) # <<<<<<<<<<<<<<
28418 * if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
28419 * self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
28420 */
28421 __pyx_t_5 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 807, __pyx_L1_error)
28422 __pyx_t_26 = (__pyx_t_5 == 0);
28423 if (__pyx_t_26) {
28424 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 807, __pyx_L1_error)
28425 __Pyx_GOTREF(__pyx_t_3);
28426 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_ZERO_LENGTH_ALLELE); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 807, __pyx_L1_error)
28427 __Pyx_GOTREF(__pyx_t_1);
28428 __pyx_t_12 = NULL;
28429 __pyx_t_4 = 0;
28430 #if CYTHON_UNPACK_METHODS
28431 if (likely(PyMethod_Check(__pyx_t_3))) {
28432 __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_3);
28433 if (likely(__pyx_t_12)) {
28434 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
28435 __Pyx_INCREF(__pyx_t_12);
28436 __Pyx_INCREF(function);
28437 __Pyx_DECREF_SET(__pyx_t_3, function);
28438 __pyx_t_4 = 1;
28439 }
28440 }
28441 #endif
28442 {
28443 PyObject *__pyx_callargs[3] = {__pyx_t_12, __pyx_v_line, __pyx_t_1};
28444 __pyx_t_11 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
28445 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
28446 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
28447 if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 807, __pyx_L1_error)
28448 __Pyx_GOTREF(__pyx_t_11);
28449 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
28450 }
28451 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28452 }
28453
28454 /* "pysam/libcvcf.pyx":808
28455 * if len(allele) != len(ref):
28456 * if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
28457 * if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper(): # <<<<<<<<<<<<<<
28458 * self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
28459 *
28460 */
28461 __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_ref, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 808, __pyx_L1_error)
28462 __Pyx_GOTREF(__pyx_t_3);
28463 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_upper); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 808, __pyx_L1_error)
28464 __Pyx_GOTREF(__pyx_t_1);
28465 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
28466 __pyx_t_3 = NULL;
28467 __pyx_t_4 = 0;
28468 #if CYTHON_UNPACK_METHODS
28469 if (likely(PyMethod_Check(__pyx_t_1))) {
28470 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_1);
28471 if (likely(__pyx_t_3)) {
28472 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
28473 __Pyx_INCREF(__pyx_t_3);
28474 __Pyx_INCREF(function);
28475 __Pyx_DECREF_SET(__pyx_t_1, function);
28476 __pyx_t_4 = 1;
28477 }
28478 }
28479 #endif
28480 {
28481 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
28482 __pyx_t_11 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
28483 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
28484 if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 808, __pyx_L1_error)
28485 __Pyx_GOTREF(__pyx_t_11);
28486 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
28487 }
28488 __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_allele, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 808, __pyx_L1_error)
28489 __Pyx_GOTREF(__pyx_t_3);
28490 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_upper); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 808, __pyx_L1_error)
28491 __Pyx_GOTREF(__pyx_t_12);
28492 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
28493 __pyx_t_3 = NULL;
28494 __pyx_t_4 = 0;
28495 #if CYTHON_UNPACK_METHODS
28496 if (likely(PyMethod_Check(__pyx_t_12))) {
28497 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_12);
28498 if (likely(__pyx_t_3)) {
28499 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_12);
28500 __Pyx_INCREF(__pyx_t_3);
28501 __Pyx_INCREF(function);
28502 __Pyx_DECREF_SET(__pyx_t_12, function);
28503 __pyx_t_4 = 1;
28504 }
28505 }
28506 #endif
28507 {
28508 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
28509 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_12, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
28510 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
28511 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 808, __pyx_L1_error)
28512 __Pyx_GOTREF(__pyx_t_1);
28513 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
28514 }
28515 __pyx_t_12 = PyObject_RichCompare(__pyx_t_11, __pyx_t_1, Py_NE); __Pyx_XGOTREF(__pyx_t_12); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 808, __pyx_L1_error)
28516 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28517 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
28518 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_12); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 808, __pyx_L1_error)
28519 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
28520 if (__pyx_t_17) {
28521 } else {
28522 __pyx_t_26 = __pyx_t_17;
28523 goto __pyx_L106_bool_binop_done;
28524 }
28525 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_ref, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 808, __pyx_L1_error)
28526 __Pyx_GOTREF(__pyx_t_1);
28527 __pyx_t_11 = __Pyx_GetItemInt(__pyx_v_allele, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 808, __pyx_L1_error)
28528 __Pyx_GOTREF(__pyx_t_11);
28529 __pyx_t_3 = PyNumber_Add(__pyx_t_1, __pyx_t_11); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 808, __pyx_L1_error)
28530 __Pyx_GOTREF(__pyx_t_3);
28531 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
28532 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28533 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_upper); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 808, __pyx_L1_error)
28534 __Pyx_GOTREF(__pyx_t_11);
28535 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
28536 __pyx_t_3 = NULL;
28537 __pyx_t_4 = 0;
28538 #if CYTHON_UNPACK_METHODS
28539 if (likely(PyMethod_Check(__pyx_t_11))) {
28540 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_11);
28541 if (likely(__pyx_t_3)) {
28542 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
28543 __Pyx_INCREF(__pyx_t_3);
28544 __Pyx_INCREF(function);
28545 __Pyx_DECREF_SET(__pyx_t_11, function);
28546 __pyx_t_4 = 1;
28547 }
28548 }
28549 #endif
28550 {
28551 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
28552 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_11, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
28553 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
28554 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 808, __pyx_L1_error)
28555 __Pyx_GOTREF(__pyx_t_12);
28556 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28557 }
28558 __pyx_t_17 = (__Pyx_PySequence_ContainsTF(__pyx_n_u_N, __pyx_t_12, Py_NE)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 808, __pyx_L1_error)
28559 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
28560 __pyx_t_26 = __pyx_t_17;
28561 __pyx_L106_bool_binop_done:;
28562 if (__pyx_t_26) {
28563
28564 /* "pysam/libcvcf.pyx":809
28565 * if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
28566 * if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
28567 * self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE) # <<<<<<<<<<<<<<
28568 *
28569 * # trim trailing bases in alleles
28570 */
28571 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 809, __pyx_L1_error)
28572 __Pyx_GOTREF(__pyx_t_11);
28573 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_MISSING_INDEL_ALLELE_REF_BASE); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 809, __pyx_L1_error)
28574 __Pyx_GOTREF(__pyx_t_3);
28575 __pyx_t_1 = NULL;
28576 __pyx_t_4 = 0;
28577 #if CYTHON_UNPACK_METHODS
28578 if (likely(PyMethod_Check(__pyx_t_11))) {
28579 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_11);
28580 if (likely(__pyx_t_1)) {
28581 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
28582 __Pyx_INCREF(__pyx_t_1);
28583 __Pyx_INCREF(function);
28584 __Pyx_DECREF_SET(__pyx_t_11, function);
28585 __pyx_t_4 = 1;
28586 }
28587 }
28588 #endif
28589 {
28590 PyObject *__pyx_callargs[3] = {__pyx_t_1, __pyx_v_line, __pyx_t_3};
28591 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_11, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
28592 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
28593 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
28594 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 809, __pyx_L1_error)
28595 __Pyx_GOTREF(__pyx_t_12);
28596 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28597 }
28598 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
28599
28600 /* "pysam/libcvcf.pyx":808
28601 * if len(allele) != len(ref):
28602 * if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
28603 * if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper(): # <<<<<<<<<<<<<<
28604 * self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
28605 *
28606 */
28607 }
28608
28609 /* "pysam/libcvcf.pyx":806
28610 * # check for leading nucleotide in indel calls
28611 * for allele in alt:
28612 * if len(allele) != len(ref): # <<<<<<<<<<<<<<
28613 * if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
28614 * if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
28615 */
28616 }
28617
28618 /* "pysam/libcvcf.pyx":805
28619 *
28620 * # check for leading nucleotide in indel calls
28621 * for allele in alt: # <<<<<<<<<<<<<<
28622 * if len(allele) != len(ref):
28623 * if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
28624 */
28625 }
28626 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
28627
28628 /* "pysam/libcvcf.pyx":821
28629 *
28630 * # left-align alleles, if a reference is available
28631 * if self._leftalign and self._reference: # <<<<<<<<<<<<<<
28632 * while left < pos:
28633 * movable = True
28634 */
28635 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_leftalign_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 821, __pyx_L1_error)
28636 __Pyx_GOTREF(__pyx_t_2);
28637 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 821, __pyx_L1_error)
28638 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
28639 if (__pyx_t_17) {
28640 } else {
28641 __pyx_t_26 = __pyx_t_17;
28642 goto __pyx_L110_bool_binop_done;
28643 }
28644 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_reference_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 821, __pyx_L1_error)
28645 __Pyx_GOTREF(__pyx_t_2);
28646 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 821, __pyx_L1_error)
28647 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
28648 __pyx_t_26 = __pyx_t_17;
28649 __pyx_L110_bool_binop_done:;
28650 if (__pyx_t_26) {
28651
28652 /* "pysam/libcvcf.pyx":822
28653 * # left-align alleles, if a reference is available
28654 * if self._leftalign and self._reference:
28655 * while left < pos: # <<<<<<<<<<<<<<
28656 * movable = True
28657 * for allele in alt:
28658 */
28659 while (1) {
28660 if (unlikely(!__pyx_v_left)) { __Pyx_RaiseUnboundLocalError("left"); __PYX_ERR(0, 822, __pyx_L1_error) }
28661 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 822, __pyx_L1_error) }
28662 __pyx_t_2 = PyObject_RichCompare(__pyx_v_left, __pyx_v_pos, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 822, __pyx_L1_error)
28663 __pyx_t_26 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_26 < 0))) __PYX_ERR(0, 822, __pyx_L1_error)
28664 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
28665 if (!__pyx_t_26) break;
28666
28667 /* "pysam/libcvcf.pyx":823
28668 * if self._leftalign and self._reference:
28669 * while left < pos:
28670 * movable = True # <<<<<<<<<<<<<<
28671 * for allele in alt:
28672 * if len(allele) > len(ref):
28673 */
28674 __pyx_v_movable = 1;
28675
28676 /* "pysam/libcvcf.pyx":824
28677 * while left < pos:
28678 * movable = True
28679 * for allele in alt: # <<<<<<<<<<<<<<
28680 * if len(allele) > len(ref):
28681 * longest, shortest = allele, ref
28682 */
28683 if (likely(PyList_CheckExact(__pyx_v_alt)) || PyTuple_CheckExact(__pyx_v_alt)) {
28684 __pyx_t_2 = __pyx_v_alt; __Pyx_INCREF(__pyx_t_2);
28685 __pyx_t_6 = 0;
28686 __pyx_t_18 = NULL;
28687 } else {
28688 __pyx_t_6 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_alt); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 824, __pyx_L1_error)
28689 __Pyx_GOTREF(__pyx_t_2);
28690 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_2); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 824, __pyx_L1_error)
28691 }
28692 for (;;) {
28693 if (likely(!__pyx_t_18)) {
28694 if (likely(PyList_CheckExact(__pyx_t_2))) {
28695 {
28696 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2);
28697 #if !CYTHON_ASSUME_SAFE_MACROS
28698 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 824, __pyx_L1_error)
28699 #endif
28700 if (__pyx_t_6 >= __pyx_temp) break;
28701 }
28702 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
28703 __pyx_t_12 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_12); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 824, __pyx_L1_error)
28704 #else
28705 __pyx_t_12 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 824, __pyx_L1_error)
28706 __Pyx_GOTREF(__pyx_t_12);
28707 #endif
28708 } else {
28709 {
28710 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_2);
28711 #if !CYTHON_ASSUME_SAFE_MACROS
28712 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 824, __pyx_L1_error)
28713 #endif
28714 if (__pyx_t_6 >= __pyx_temp) break;
28715 }
28716 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
28717 __pyx_t_12 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_12); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 824, __pyx_L1_error)
28718 #else
28719 __pyx_t_12 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 824, __pyx_L1_error)
28720 __Pyx_GOTREF(__pyx_t_12);
28721 #endif
28722 }
28723 } else {
28724 __pyx_t_12 = __pyx_t_18(__pyx_t_2);
28725 if (unlikely(!__pyx_t_12)) {
28726 PyObject* exc_type = PyErr_Occurred();
28727 if (exc_type) {
28728 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
28729 else __PYX_ERR(0, 824, __pyx_L1_error)
28730 }
28731 break;
28732 }
28733 __Pyx_GOTREF(__pyx_t_12);
28734 }
28735 __Pyx_XDECREF_SET(__pyx_v_allele, __pyx_t_12);
28736 __pyx_t_12 = 0;
28737
28738 /* "pysam/libcvcf.pyx":825
28739 * movable = True
28740 * for allele in alt:
28741 * if len(allele) > len(ref): # <<<<<<<<<<<<<<
28742 * longest, shortest = allele, ref
28743 * else:
28744 */
28745 __pyx_t_5 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 825, __pyx_L1_error)
28746 __pyx_t_22 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_22 == ((Py_ssize_t)-1))) __PYX_ERR(0, 825, __pyx_L1_error)
28747 __pyx_t_26 = (__pyx_t_5 > __pyx_t_22);
28748 if (__pyx_t_26) {
28749
28750 /* "pysam/libcvcf.pyx":826
28751 * for allele in alt:
28752 * if len(allele) > len(ref):
28753 * longest, shortest = allele, ref # <<<<<<<<<<<<<<
28754 * else:
28755 * longest, shortest = ref, allele
28756 */
28757 __pyx_t_12 = __pyx_v_allele;
28758 __Pyx_INCREF(__pyx_t_12);
28759 __pyx_t_11 = __pyx_v_ref;
28760 __Pyx_INCREF(__pyx_t_11);
28761 __Pyx_XDECREF_SET(__pyx_v_longest, __pyx_t_12);
28762 __pyx_t_12 = 0;
28763 __Pyx_XDECREF_SET(__pyx_v_shortest, __pyx_t_11);
28764 __pyx_t_11 = 0;
28765
28766 /* "pysam/libcvcf.pyx":825
28767 * movable = True
28768 * for allele in alt:
28769 * if len(allele) > len(ref): # <<<<<<<<<<<<<<
28770 * longest, shortest = allele, ref
28771 * else:
28772 */
28773 goto __pyx_L116;
28774 }
28775
28776 /* "pysam/libcvcf.pyx":828
28777 * longest, shortest = allele, ref
28778 * else:
28779 * longest, shortest = ref, allele # <<<<<<<<<<<<<<
28780 * if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
28781 * movable = False
28782 */
28783 /*else*/ {
28784 __pyx_t_11 = __pyx_v_ref;
28785 __Pyx_INCREF(__pyx_t_11);
28786 __pyx_t_12 = __pyx_v_allele;
28787 __Pyx_INCREF(__pyx_t_12);
28788 __Pyx_XDECREF_SET(__pyx_v_longest, __pyx_t_11);
28789 __pyx_t_11 = 0;
28790 __Pyx_XDECREF_SET(__pyx_v_shortest, __pyx_t_12);
28791 __pyx_t_12 = 0;
28792 }
28793 __pyx_L116:;
28794
28795 /* "pysam/libcvcf.pyx":829
28796 * else:
28797 * longest, shortest = ref, allele
28798 * if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): # <<<<<<<<<<<<<<
28799 * movable = False
28800 * if longest[-1].upper() != longest[len(shortest)-1].upper():
28801 */
28802 __pyx_t_22 = PyObject_Length(__pyx_v_longest); if (unlikely(__pyx_t_22 == ((Py_ssize_t)-1))) __PYX_ERR(0, 829, __pyx_L1_error)
28803 __pyx_t_5 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 829, __pyx_L1_error)
28804 __pyx_t_17 = (__pyx_t_22 == __pyx_t_5);
28805 if (!__pyx_t_17) {
28806 } else {
28807 __pyx_t_26 = __pyx_t_17;
28808 goto __pyx_L118_bool_binop_done;
28809 }
28810 __pyx_t_5 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 829, __pyx_L1_error)
28811 __pyx_t_11 = __Pyx_PyObject_GetSlice(__pyx_v_longest, 0, __pyx_t_5, NULL, NULL, NULL, 0, 1, 1); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 829, __pyx_L1_error)
28812 __Pyx_GOTREF(__pyx_t_11);
28813 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_11, __pyx_n_s_upper); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 829, __pyx_L1_error)
28814 __Pyx_GOTREF(__pyx_t_3);
28815 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28816 __pyx_t_11 = NULL;
28817 __pyx_t_4 = 0;
28818 #if CYTHON_UNPACK_METHODS
28819 if (likely(PyMethod_Check(__pyx_t_3))) {
28820 __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_3);
28821 if (likely(__pyx_t_11)) {
28822 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
28823 __Pyx_INCREF(__pyx_t_11);
28824 __Pyx_INCREF(function);
28825 __Pyx_DECREF_SET(__pyx_t_3, function);
28826 __pyx_t_4 = 1;
28827 }
28828 }
28829 #endif
28830 {
28831 PyObject *__pyx_callargs[2] = {__pyx_t_11, NULL};
28832 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
28833 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
28834 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 829, __pyx_L1_error)
28835 __Pyx_GOTREF(__pyx_t_12);
28836 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
28837 }
28838 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_shortest, __pyx_n_s_upper); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 829, __pyx_L1_error)
28839 __Pyx_GOTREF(__pyx_t_11);
28840 __pyx_t_1 = NULL;
28841 __pyx_t_4 = 0;
28842 #if CYTHON_UNPACK_METHODS
28843 if (likely(PyMethod_Check(__pyx_t_11))) {
28844 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_11);
28845 if (likely(__pyx_t_1)) {
28846 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
28847 __Pyx_INCREF(__pyx_t_1);
28848 __Pyx_INCREF(function);
28849 __Pyx_DECREF_SET(__pyx_t_11, function);
28850 __pyx_t_4 = 1;
28851 }
28852 }
28853 #endif
28854 {
28855 PyObject *__pyx_callargs[2] = {__pyx_t_1, NULL};
28856 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_11, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
28857 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
28858 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 829, __pyx_L1_error)
28859 __Pyx_GOTREF(__pyx_t_3);
28860 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28861 }
28862 __pyx_t_11 = PyObject_RichCompare(__pyx_t_12, __pyx_t_3, Py_NE); __Pyx_XGOTREF(__pyx_t_11); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 829, __pyx_L1_error)
28863 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
28864 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
28865 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_11); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 829, __pyx_L1_error)
28866 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28867 __pyx_t_26 = __pyx_t_17;
28868 __pyx_L118_bool_binop_done:;
28869 if (__pyx_t_26) {
28870
28871 /* "pysam/libcvcf.pyx":830
28872 * longest, shortest = ref, allele
28873 * if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
28874 * movable = False # <<<<<<<<<<<<<<
28875 * if longest[-1].upper() != longest[len(shortest)-1].upper():
28876 * movable = False
28877 */
28878 __pyx_v_movable = 0;
28879
28880 /* "pysam/libcvcf.pyx":829
28881 * else:
28882 * longest, shortest = ref, allele
28883 * if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): # <<<<<<<<<<<<<<
28884 * movable = False
28885 * if longest[-1].upper() != longest[len(shortest)-1].upper():
28886 */
28887 }
28888
28889 /* "pysam/libcvcf.pyx":831
28890 * if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
28891 * movable = False
28892 * if longest[-1].upper() != longest[len(shortest)-1].upper(): # <<<<<<<<<<<<<<
28893 * movable = False
28894 * if not movable:
28895 */
28896 __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_longest, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 831, __pyx_L1_error)
28897 __Pyx_GOTREF(__pyx_t_3);
28898 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_upper); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 831, __pyx_L1_error)
28899 __Pyx_GOTREF(__pyx_t_12);
28900 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
28901 __pyx_t_3 = NULL;
28902 __pyx_t_4 = 0;
28903 #if CYTHON_UNPACK_METHODS
28904 if (likely(PyMethod_Check(__pyx_t_12))) {
28905 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_12);
28906 if (likely(__pyx_t_3)) {
28907 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_12);
28908 __Pyx_INCREF(__pyx_t_3);
28909 __Pyx_INCREF(function);
28910 __Pyx_DECREF_SET(__pyx_t_12, function);
28911 __pyx_t_4 = 1;
28912 }
28913 }
28914 #endif
28915 {
28916 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
28917 __pyx_t_11 = __Pyx_PyObject_FastCall(__pyx_t_12, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
28918 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
28919 if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 831, __pyx_L1_error)
28920 __Pyx_GOTREF(__pyx_t_11);
28921 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
28922 }
28923 __pyx_t_5 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 831, __pyx_L1_error)
28924 __pyx_t_22 = (__pyx_t_5 - 1);
28925 __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_longest, __pyx_t_22, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 831, __pyx_L1_error)
28926 __Pyx_GOTREF(__pyx_t_3);
28927 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_upper); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 831, __pyx_L1_error)
28928 __Pyx_GOTREF(__pyx_t_1);
28929 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
28930 __pyx_t_3 = NULL;
28931 __pyx_t_4 = 0;
28932 #if CYTHON_UNPACK_METHODS
28933 if (likely(PyMethod_Check(__pyx_t_1))) {
28934 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_1);
28935 if (likely(__pyx_t_3)) {
28936 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
28937 __Pyx_INCREF(__pyx_t_3);
28938 __Pyx_INCREF(function);
28939 __Pyx_DECREF_SET(__pyx_t_1, function);
28940 __pyx_t_4 = 1;
28941 }
28942 }
28943 #endif
28944 {
28945 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
28946 __pyx_t_12 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
28947 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
28948 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 831, __pyx_L1_error)
28949 __Pyx_GOTREF(__pyx_t_12);
28950 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
28951 }
28952 __pyx_t_1 = PyObject_RichCompare(__pyx_t_11, __pyx_t_12, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 831, __pyx_L1_error)
28953 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
28954 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
28955 __pyx_t_26 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_26 < 0))) __PYX_ERR(0, 831, __pyx_L1_error)
28956 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
28957 if (__pyx_t_26) {
28958
28959 /* "pysam/libcvcf.pyx":832
28960 * movable = False
28961 * if longest[-1].upper() != longest[len(shortest)-1].upper():
28962 * movable = False # <<<<<<<<<<<<<<
28963 * if not movable:
28964 * break
28965 */
28966 __pyx_v_movable = 0;
28967
28968 /* "pysam/libcvcf.pyx":831
28969 * if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
28970 * movable = False
28971 * if longest[-1].upper() != longest[len(shortest)-1].upper(): # <<<<<<<<<<<<<<
28972 * movable = False
28973 * if not movable:
28974 */
28975 }
28976
28977 /* "pysam/libcvcf.pyx":824
28978 * while left < pos:
28979 * movable = True
28980 * for allele in alt: # <<<<<<<<<<<<<<
28981 * if len(allele) > len(ref):
28982 * longest, shortest = allele, ref
28983 */
28984 }
28985 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
28986
28987 /* "pysam/libcvcf.pyx":833
28988 * if longest[-1].upper() != longest[len(shortest)-1].upper():
28989 * movable = False
28990 * if not movable: # <<<<<<<<<<<<<<
28991 * break
28992 * ref = ref[:-1]
28993 */
28994 __pyx_t_26 = (!__pyx_v_movable);
28995 if (__pyx_t_26) {
28996
28997 /* "pysam/libcvcf.pyx":834
28998 * movable = False
28999 * if not movable:
29000 * break # <<<<<<<<<<<<<<
29001 * ref = ref[:-1]
29002 * alt = [allele[:-1] for allele in alt]
29003 */
29004 goto __pyx_L113_break;
29005
29006 /* "pysam/libcvcf.pyx":833
29007 * if longest[-1].upper() != longest[len(shortest)-1].upper():
29008 * movable = False
29009 * if not movable: # <<<<<<<<<<<<<<
29010 * break
29011 * ref = ref[:-1]
29012 */
29013 }
29014
29015 /* "pysam/libcvcf.pyx":835
29016 * if not movable:
29017 * break
29018 * ref = ref[:-1] # <<<<<<<<<<<<<<
29019 * alt = [allele[:-1] for allele in alt]
29020 * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
29021 */
29022 __pyx_t_2 = __Pyx_PyObject_GetSlice(__pyx_v_ref, 0, -1L, NULL, NULL, &__pyx_slice__28, 0, 1, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 835, __pyx_L1_error)
29023 __Pyx_GOTREF(__pyx_t_2);
29024 __Pyx_DECREF_SET(__pyx_v_ref, __pyx_t_2);
29025 __pyx_t_2 = 0;
29026
29027 /* "pysam/libcvcf.pyx":836
29028 * break
29029 * ref = ref[:-1]
29030 * alt = [allele[:-1] for allele in alt] # <<<<<<<<<<<<<<
29031 * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
29032 * ref = faref_leftflank[pos-left-1] + ref
29033 */
29034 { /* enter inner scope */
29035 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 836, __pyx_L125_error)
29036 __Pyx_GOTREF(__pyx_t_2);
29037 if (likely(PyList_CheckExact(__pyx_v_alt)) || PyTuple_CheckExact(__pyx_v_alt)) {
29038 __pyx_t_1 = __pyx_v_alt; __Pyx_INCREF(__pyx_t_1);
29039 __pyx_t_6 = 0;
29040 __pyx_t_18 = NULL;
29041 } else {
29042 __pyx_t_6 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_alt); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 836, __pyx_L125_error)
29043 __Pyx_GOTREF(__pyx_t_1);
29044 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 836, __pyx_L125_error)
29045 }
29046 for (;;) {
29047 if (likely(!__pyx_t_18)) {
29048 if (likely(PyList_CheckExact(__pyx_t_1))) {
29049 {
29050 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1);
29051 #if !CYTHON_ASSUME_SAFE_MACROS
29052 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 836, __pyx_L125_error)
29053 #endif
29054 if (__pyx_t_6 >= __pyx_temp) break;
29055 }
29056 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
29057 __pyx_t_12 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_6); __Pyx_INCREF(__pyx_t_12); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 836, __pyx_L125_error)
29058 #else
29059 __pyx_t_12 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 836, __pyx_L125_error)
29060 __Pyx_GOTREF(__pyx_t_12);
29061 #endif
29062 } else {
29063 {
29064 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1);
29065 #if !CYTHON_ASSUME_SAFE_MACROS
29066 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 836, __pyx_L125_error)
29067 #endif
29068 if (__pyx_t_6 >= __pyx_temp) break;
29069 }
29070 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
29071 __pyx_t_12 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_6); __Pyx_INCREF(__pyx_t_12); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 836, __pyx_L125_error)
29072 #else
29073 __pyx_t_12 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 836, __pyx_L125_error)
29074 __Pyx_GOTREF(__pyx_t_12);
29075 #endif
29076 }
29077 } else {
29078 __pyx_t_12 = __pyx_t_18(__pyx_t_1);
29079 if (unlikely(!__pyx_t_12)) {
29080 PyObject* exc_type = PyErr_Occurred();
29081 if (exc_type) {
29082 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
29083 else __PYX_ERR(0, 836, __pyx_L125_error)
29084 }
29085 break;
29086 }
29087 __Pyx_GOTREF(__pyx_t_12);
29088 }
29089 __Pyx_XDECREF_SET(__pyx_8genexpr5__pyx_v_allele, __pyx_t_12);
29090 __pyx_t_12 = 0;
29091 __pyx_t_12 = __Pyx_PyObject_GetSlice(__pyx_8genexpr5__pyx_v_allele, 0, -1L, NULL, NULL, &__pyx_slice__28, 0, 1, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 836, __pyx_L125_error)
29092 __Pyx_GOTREF(__pyx_t_12);
29093 if (unlikely(__Pyx_ListComp_Append(__pyx_t_2, (PyObject*)__pyx_t_12))) __PYX_ERR(0, 836, __pyx_L125_error)
29094 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
29095 }
29096 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
29097 __Pyx_XDECREF(__pyx_8genexpr5__pyx_v_allele); __pyx_8genexpr5__pyx_v_allele = 0;
29098 goto __pyx_L129_exit_scope;
29099 __pyx_L125_error:;
29100 __Pyx_XDECREF(__pyx_8genexpr5__pyx_v_allele); __pyx_8genexpr5__pyx_v_allele = 0;
29101 goto __pyx_L1_error;
29102 __pyx_L129_exit_scope:;
29103 } /* exit inner scope */
29104 __Pyx_DECREF_SET(__pyx_v_alt, __pyx_t_2);
29105 __pyx_t_2 = 0;
29106
29107 /* "pysam/libcvcf.pyx":837
29108 * ref = ref[:-1]
29109 * alt = [allele[:-1] for allele in alt]
29110 * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: # <<<<<<<<<<<<<<
29111 * ref = faref_leftflank[pos-left-1] + ref
29112 * alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
29113 */
29114 { /* enter inner scope */
29115 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 837, __pyx_L135_error)
29116 __Pyx_GOTREF(__pyx_t_2);
29117 if (likely(PyList_CheckExact(__pyx_v_alt)) || PyTuple_CheckExact(__pyx_v_alt)) {
29118 __pyx_t_1 = __pyx_v_alt; __Pyx_INCREF(__pyx_t_1);
29119 __pyx_t_6 = 0;
29120 __pyx_t_18 = NULL;
29121 } else {
29122 __pyx_t_6 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_alt); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 837, __pyx_L135_error)
29123 __Pyx_GOTREF(__pyx_t_1);
29124 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 837, __pyx_L135_error)
29125 }
29126 for (;;) {
29127 if (likely(!__pyx_t_18)) {
29128 if (likely(PyList_CheckExact(__pyx_t_1))) {
29129 {
29130 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1);
29131 #if !CYTHON_ASSUME_SAFE_MACROS
29132 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 837, __pyx_L135_error)
29133 #endif
29134 if (__pyx_t_6 >= __pyx_temp) break;
29135 }
29136 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
29137 __pyx_t_12 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_6); __Pyx_INCREF(__pyx_t_12); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 837, __pyx_L135_error)
29138 #else
29139 __pyx_t_12 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 837, __pyx_L135_error)
29140 __Pyx_GOTREF(__pyx_t_12);
29141 #endif
29142 } else {
29143 {
29144 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1);
29145 #if !CYTHON_ASSUME_SAFE_MACROS
29146 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 837, __pyx_L135_error)
29147 #endif
29148 if (__pyx_t_6 >= __pyx_temp) break;
29149 }
29150 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
29151 __pyx_t_12 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_6); __Pyx_INCREF(__pyx_t_12); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 837, __pyx_L135_error)
29152 #else
29153 __pyx_t_12 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 837, __pyx_L135_error)
29154 __Pyx_GOTREF(__pyx_t_12);
29155 #endif
29156 }
29157 } else {
29158 __pyx_t_12 = __pyx_t_18(__pyx_t_1);
29159 if (unlikely(!__pyx_t_12)) {
29160 PyObject* exc_type = PyErr_Occurred();
29161 if (exc_type) {
29162 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
29163 else __PYX_ERR(0, 837, __pyx_L135_error)
29164 }
29165 break;
29166 }
29167 __Pyx_GOTREF(__pyx_t_12);
29168 }
29169 __Pyx_XDECREF_SET(__pyx_8genexpr6__pyx_v_allele, __pyx_t_12);
29170 __pyx_t_12 = 0;
29171 __pyx_t_22 = PyObject_Length(__pyx_8genexpr6__pyx_v_allele); if (unlikely(__pyx_t_22 == ((Py_ssize_t)-1))) __PYX_ERR(0, 837, __pyx_L135_error)
29172 __pyx_t_12 = PyInt_FromSsize_t(__pyx_t_22); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 837, __pyx_L135_error)
29173 __Pyx_GOTREF(__pyx_t_12);
29174 if (unlikely(__Pyx_ListComp_Append(__pyx_t_2, (PyObject*)__pyx_t_12))) __PYX_ERR(0, 837, __pyx_L135_error)
29175 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
29176 }
29177 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
29178 __Pyx_XDECREF(__pyx_8genexpr6__pyx_v_allele); __pyx_8genexpr6__pyx_v_allele = 0;
29179 goto __pyx_L139_exit_scope;
29180 __pyx_L135_error:;
29181 __Pyx_XDECREF(__pyx_8genexpr6__pyx_v_allele); __pyx_8genexpr6__pyx_v_allele = 0;
29182 goto __pyx_L1_error;
29183 __pyx_L139_exit_scope:;
29184 } /* exit inner scope */
29185 __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_min, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 837, __pyx_L1_error)
29186 __Pyx_GOTREF(__pyx_t_1);
29187 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29188 __pyx_t_17 = (__Pyx_PyInt_BoolEqObjC(__pyx_t_1, __pyx_int_0, 0, 0)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 837, __pyx_L1_error)
29189 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
29190 if (!__pyx_t_17) {
29191 } else {
29192 __pyx_t_26 = __pyx_t_17;
29193 goto __pyx_L131_bool_binop_done;
29194 }
29195 __pyx_t_6 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 837, __pyx_L1_error)
29196 __pyx_t_17 = (__pyx_t_6 == 0);
29197 __pyx_t_26 = __pyx_t_17;
29198 __pyx_L131_bool_binop_done:;
29199 if (__pyx_t_26) {
29200
29201 /* "pysam/libcvcf.pyx":838
29202 * alt = [allele[:-1] for allele in alt]
29203 * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
29204 * ref = faref_leftflank[pos-left-1] + ref # <<<<<<<<<<<<<<
29205 * alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
29206 * pos -= 1
29207 */
29208 if (unlikely(!__pyx_v_faref_leftflank)) { __Pyx_RaiseUnboundLocalError("faref_leftflank"); __PYX_ERR(0, 838, __pyx_L1_error) }
29209 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 838, __pyx_L1_error) }
29210 if (unlikely(!__pyx_v_left)) { __Pyx_RaiseUnboundLocalError("left"); __PYX_ERR(0, 838, __pyx_L1_error) }
29211 __pyx_t_1 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 838, __pyx_L1_error)
29212 __Pyx_GOTREF(__pyx_t_1);
29213 __pyx_t_2 = __Pyx_PyInt_SubtractObjC(__pyx_t_1, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 838, __pyx_L1_error)
29214 __Pyx_GOTREF(__pyx_t_2);
29215 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
29216 __pyx_t_1 = __Pyx_PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 838, __pyx_L1_error)
29217 __Pyx_GOTREF(__pyx_t_1);
29218 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29219 __pyx_t_2 = PyNumber_Add(__pyx_t_1, __pyx_v_ref); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 838, __pyx_L1_error)
29220 __Pyx_GOTREF(__pyx_t_2);
29221 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
29222 __Pyx_DECREF_SET(__pyx_v_ref, __pyx_t_2);
29223 __pyx_t_2 = 0;
29224
29225 /* "pysam/libcvcf.pyx":839
29226 * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
29227 * ref = faref_leftflank[pos-left-1] + ref
29228 * alt = [faref_leftflank[pos-left-1] + allele for allele in alt] # <<<<<<<<<<<<<<
29229 * pos -= 1
29230 *
29231 */
29232 { /* enter inner scope */
29233 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 839, __pyx_L142_error)
29234 __Pyx_GOTREF(__pyx_t_2);
29235 if (likely(PyList_CheckExact(__pyx_v_alt)) || PyTuple_CheckExact(__pyx_v_alt)) {
29236 __pyx_t_1 = __pyx_v_alt; __Pyx_INCREF(__pyx_t_1);
29237 __pyx_t_6 = 0;
29238 __pyx_t_18 = NULL;
29239 } else {
29240 __pyx_t_6 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_alt); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 839, __pyx_L142_error)
29241 __Pyx_GOTREF(__pyx_t_1);
29242 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 839, __pyx_L142_error)
29243 }
29244 for (;;) {
29245 if (likely(!__pyx_t_18)) {
29246 if (likely(PyList_CheckExact(__pyx_t_1))) {
29247 {
29248 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1);
29249 #if !CYTHON_ASSUME_SAFE_MACROS
29250 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 839, __pyx_L142_error)
29251 #endif
29252 if (__pyx_t_6 >= __pyx_temp) break;
29253 }
29254 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
29255 __pyx_t_12 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_6); __Pyx_INCREF(__pyx_t_12); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 839, __pyx_L142_error)
29256 #else
29257 __pyx_t_12 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 839, __pyx_L142_error)
29258 __Pyx_GOTREF(__pyx_t_12);
29259 #endif
29260 } else {
29261 {
29262 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1);
29263 #if !CYTHON_ASSUME_SAFE_MACROS
29264 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 839, __pyx_L142_error)
29265 #endif
29266 if (__pyx_t_6 >= __pyx_temp) break;
29267 }
29268 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
29269 __pyx_t_12 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_6); __Pyx_INCREF(__pyx_t_12); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 839, __pyx_L142_error)
29270 #else
29271 __pyx_t_12 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 839, __pyx_L142_error)
29272 __Pyx_GOTREF(__pyx_t_12);
29273 #endif
29274 }
29275 } else {
29276 __pyx_t_12 = __pyx_t_18(__pyx_t_1);
29277 if (unlikely(!__pyx_t_12)) {
29278 PyObject* exc_type = PyErr_Occurred();
29279 if (exc_type) {
29280 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
29281 else __PYX_ERR(0, 839, __pyx_L142_error)
29282 }
29283 break;
29284 }
29285 __Pyx_GOTREF(__pyx_t_12);
29286 }
29287 __Pyx_XDECREF_SET(__pyx_8genexpr7__pyx_v_allele, __pyx_t_12);
29288 __pyx_t_12 = 0;
29289 if (unlikely(!__pyx_v_faref_leftflank)) { __Pyx_RaiseUnboundLocalError("faref_leftflank"); __PYX_ERR(0, 839, __pyx_L142_error) }
29290 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 839, __pyx_L142_error) }
29291 if (unlikely(!__pyx_v_left)) { __Pyx_RaiseUnboundLocalError("left"); __PYX_ERR(0, 839, __pyx_L142_error) }
29292 __pyx_t_12 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 839, __pyx_L142_error)
29293 __Pyx_GOTREF(__pyx_t_12);
29294 __pyx_t_11 = __Pyx_PyInt_SubtractObjC(__pyx_t_12, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 839, __pyx_L142_error)
29295 __Pyx_GOTREF(__pyx_t_11);
29296 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
29297 __pyx_t_12 = __Pyx_PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_11); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 839, __pyx_L142_error)
29298 __Pyx_GOTREF(__pyx_t_12);
29299 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29300 __pyx_t_11 = PyNumber_Add(__pyx_t_12, __pyx_8genexpr7__pyx_v_allele); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 839, __pyx_L142_error)
29301 __Pyx_GOTREF(__pyx_t_11);
29302 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
29303 if (unlikely(__Pyx_ListComp_Append(__pyx_t_2, (PyObject*)__pyx_t_11))) __PYX_ERR(0, 839, __pyx_L142_error)
29304 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29305 }
29306 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
29307 __Pyx_XDECREF(__pyx_8genexpr7__pyx_v_allele); __pyx_8genexpr7__pyx_v_allele = 0;
29308 goto __pyx_L146_exit_scope;
29309 __pyx_L142_error:;
29310 __Pyx_XDECREF(__pyx_8genexpr7__pyx_v_allele); __pyx_8genexpr7__pyx_v_allele = 0;
29311 goto __pyx_L1_error;
29312 __pyx_L146_exit_scope:;
29313 } /* exit inner scope */
29314 __Pyx_DECREF_SET(__pyx_v_alt, __pyx_t_2);
29315 __pyx_t_2 = 0;
29316
29317 /* "pysam/libcvcf.pyx":840
29318 * ref = faref_leftflank[pos-left-1] + ref
29319 * alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
29320 * pos -= 1 # <<<<<<<<<<<<<<
29321 *
29322 * # parse sample columns
29323 */
29324 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 840, __pyx_L1_error) }
29325 __pyx_t_2 = __Pyx_PyInt_SubtractObjC(__pyx_v_pos, __pyx_int_1, 1, 1, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 840, __pyx_L1_error)
29326 __Pyx_GOTREF(__pyx_t_2);
29327 __Pyx_XDECREF_SET(__pyx_v_pos, __pyx_t_2);
29328 __pyx_t_2 = 0;
29329
29330 /* "pysam/libcvcf.pyx":837
29331 * ref = ref[:-1]
29332 * alt = [allele[:-1] for allele in alt]
29333 * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: # <<<<<<<<<<<<<<
29334 * ref = faref_leftflank[pos-left-1] + ref
29335 * alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
29336 */
29337 }
29338 }
29339 __pyx_L113_break:;
29340
29341 /* "pysam/libcvcf.pyx":821
29342 *
29343 * # left-align alleles, if a reference is available
29344 * if self._leftalign and self._reference: # <<<<<<<<<<<<<<
29345 * while left < pos:
29346 * movable = True
29347 */
29348 }
29349
29350 /* "pysam/libcvcf.pyx":843
29351 *
29352 * # parse sample columns
29353 * samples = [] # <<<<<<<<<<<<<<
29354 * for sample in cols[9:]:
29355 * dict = {}
29356 */
29357 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 843, __pyx_L1_error)
29358 __Pyx_GOTREF(__pyx_t_2);
29359 __pyx_v_samples = ((PyObject*)__pyx_t_2);
29360 __pyx_t_2 = 0;
29361
29362 /* "pysam/libcvcf.pyx":844
29363 * # parse sample columns
29364 * samples = []
29365 * for sample in cols[9:]: # <<<<<<<<<<<<<<
29366 * dict = {}
29367 * values = sample.split(':')
29368 */
29369 __pyx_t_2 = __Pyx_PyObject_GetSlice(__pyx_v_cols, 9, 0, NULL, NULL, &__pyx_slice__26, 1, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 844, __pyx_L1_error)
29370 __Pyx_GOTREF(__pyx_t_2);
29371 if (likely(PyList_CheckExact(__pyx_t_2)) || PyTuple_CheckExact(__pyx_t_2)) {
29372 __pyx_t_1 = __pyx_t_2; __Pyx_INCREF(__pyx_t_1);
29373 __pyx_t_6 = 0;
29374 __pyx_t_18 = NULL;
29375 } else {
29376 __pyx_t_6 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 844, __pyx_L1_error)
29377 __Pyx_GOTREF(__pyx_t_1);
29378 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 844, __pyx_L1_error)
29379 }
29380 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29381 for (;;) {
29382 if (likely(!__pyx_t_18)) {
29383 if (likely(PyList_CheckExact(__pyx_t_1))) {
29384 {
29385 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1);
29386 #if !CYTHON_ASSUME_SAFE_MACROS
29387 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 844, __pyx_L1_error)
29388 #endif
29389 if (__pyx_t_6 >= __pyx_temp) break;
29390 }
29391 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
29392 __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_6); __Pyx_INCREF(__pyx_t_2); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 844, __pyx_L1_error)
29393 #else
29394 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 844, __pyx_L1_error)
29395 __Pyx_GOTREF(__pyx_t_2);
29396 #endif
29397 } else {
29398 {
29399 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1);
29400 #if !CYTHON_ASSUME_SAFE_MACROS
29401 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 844, __pyx_L1_error)
29402 #endif
29403 if (__pyx_t_6 >= __pyx_temp) break;
29404 }
29405 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
29406 __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_6); __Pyx_INCREF(__pyx_t_2); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 844, __pyx_L1_error)
29407 #else
29408 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 844, __pyx_L1_error)
29409 __Pyx_GOTREF(__pyx_t_2);
29410 #endif
29411 }
29412 } else {
29413 __pyx_t_2 = __pyx_t_18(__pyx_t_1);
29414 if (unlikely(!__pyx_t_2)) {
29415 PyObject* exc_type = PyErr_Occurred();
29416 if (exc_type) {
29417 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
29418 else __PYX_ERR(0, 844, __pyx_L1_error)
29419 }
29420 break;
29421 }
29422 __Pyx_GOTREF(__pyx_t_2);
29423 }
29424 __Pyx_XDECREF_SET(__pyx_v_sample, __pyx_t_2);
29425 __pyx_t_2 = 0;
29426
29427 /* "pysam/libcvcf.pyx":845
29428 * samples = []
29429 * for sample in cols[9:]:
29430 * dict = {} # <<<<<<<<<<<<<<
29431 * values = sample.split(':')
29432 * if len(values) > len(format):
29433 */
29434 __pyx_t_2 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 845, __pyx_L1_error)
29435 __Pyx_GOTREF(__pyx_t_2);
29436 __Pyx_XDECREF_SET(__pyx_v_dict, ((PyObject*)__pyx_t_2));
29437 __pyx_t_2 = 0;
29438
29439 /* "pysam/libcvcf.pyx":846
29440 * for sample in cols[9:]:
29441 * dict = {}
29442 * values = sample.split(':') # <<<<<<<<<<<<<<
29443 * if len(values) > len(format):
29444 * self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
29445 */
29446 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_sample, __pyx_n_s_split); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 846, __pyx_L1_error)
29447 __Pyx_GOTREF(__pyx_t_11);
29448 __pyx_t_12 = NULL;
29449 __pyx_t_4 = 0;
29450 #if CYTHON_UNPACK_METHODS
29451 if (likely(PyMethod_Check(__pyx_t_11))) {
29452 __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_11);
29453 if (likely(__pyx_t_12)) {
29454 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
29455 __Pyx_INCREF(__pyx_t_12);
29456 __Pyx_INCREF(function);
29457 __Pyx_DECREF_SET(__pyx_t_11, function);
29458 __pyx_t_4 = 1;
29459 }
29460 }
29461 #endif
29462 {
29463 PyObject *__pyx_callargs[2] = {__pyx_t_12, __pyx_kp_u__3};
29464 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_11, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
29465 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
29466 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 846, __pyx_L1_error)
29467 __Pyx_GOTREF(__pyx_t_2);
29468 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29469 }
29470 __Pyx_XDECREF_SET(__pyx_v_values, __pyx_t_2);
29471 __pyx_t_2 = 0;
29472
29473 /* "pysam/libcvcf.pyx":847
29474 * dict = {}
29475 * values = sample.split(':')
29476 * if len(values) > len(format): # <<<<<<<<<<<<<<
29477 * self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
29478 * for idx in range(len(format)):
29479 */
29480 __pyx_t_22 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_22 == ((Py_ssize_t)-1))) __PYX_ERR(0, 847, __pyx_L1_error)
29481 __pyx_t_5 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 847, __pyx_L1_error)
29482 __pyx_t_26 = (__pyx_t_22 > __pyx_t_5);
29483 if (__pyx_t_26) {
29484
29485 /* "pysam/libcvcf.pyx":848
29486 * values = sample.split(':')
29487 * if len(values) > len(format):
29488 * self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format))) # <<<<<<<<<<<<<<
29489 * for idx in range(len(format)):
29490 * expected = self.get_expected(format[idx], self._format, alt)
29491 */
29492 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 848, __pyx_L1_error)
29493 __Pyx_GOTREF(__pyx_t_11);
29494 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_BAD_NUMBER_OF_VALUES); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 848, __pyx_L1_error)
29495 __Pyx_GOTREF(__pyx_t_12);
29496 __pyx_t_3 = PyTuple_New(7); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 848, __pyx_L1_error)
29497 __Pyx_GOTREF(__pyx_t_3);
29498 __pyx_t_5 = 0;
29499 __pyx_t_10 = 127;
29500 __Pyx_INCREF(__pyx_kp_u_found);
29501 __pyx_t_5 += 7;
29502 __Pyx_GIVEREF(__pyx_kp_u_found);
29503 PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_kp_u_found);
29504 __pyx_t_22 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_22 == ((Py_ssize_t)-1))) __PYX_ERR(0, 848, __pyx_L1_error)
29505 __pyx_t_9 = __Pyx_PyUnicode_From_Py_ssize_t(__pyx_t_22, 0, ' ', 'd'); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 848, __pyx_L1_error)
29506 __Pyx_GOTREF(__pyx_t_9);
29507 __pyx_t_5 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_9);
29508 __Pyx_GIVEREF(__pyx_t_9);
29509 PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_9);
29510 __pyx_t_9 = 0;
29511 __Pyx_INCREF(__pyx_kp_u_values_in_element);
29512 __pyx_t_5 += 19;
29513 __Pyx_GIVEREF(__pyx_kp_u_values_in_element);
29514 PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_kp_u_values_in_element);
29515 __pyx_t_9 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_sample), __pyx_empty_unicode); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 848, __pyx_L1_error)
29516 __Pyx_GOTREF(__pyx_t_9);
29517 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_9) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_9) : __pyx_t_10;
29518 __pyx_t_5 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_9);
29519 __Pyx_GIVEREF(__pyx_t_9);
29520 PyTuple_SET_ITEM(__pyx_t_3, 3, __pyx_t_9);
29521 __pyx_t_9 = 0;
29522 __Pyx_INCREF(__pyx_kp_u_expected);
29523 __pyx_t_5 += 11;
29524 __Pyx_GIVEREF(__pyx_kp_u_expected);
29525 PyTuple_SET_ITEM(__pyx_t_3, 4, __pyx_kp_u_expected);
29526 __pyx_t_22 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_22 == ((Py_ssize_t)-1))) __PYX_ERR(0, 848, __pyx_L1_error)
29527 __pyx_t_9 = __Pyx_PyUnicode_From_Py_ssize_t(__pyx_t_22, 0, ' ', 'd'); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 848, __pyx_L1_error)
29528 __Pyx_GOTREF(__pyx_t_9);
29529 __pyx_t_5 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_9);
29530 __Pyx_GIVEREF(__pyx_t_9);
29531 PyTuple_SET_ITEM(__pyx_t_3, 5, __pyx_t_9);
29532 __pyx_t_9 = 0;
29533 __Pyx_INCREF(__pyx_kp_u__8);
29534 __pyx_t_5 += 1;
29535 __Pyx_GIVEREF(__pyx_kp_u__8);
29536 PyTuple_SET_ITEM(__pyx_t_3, 6, __pyx_kp_u__8);
29537 __pyx_t_9 = __Pyx_PyUnicode_Join(__pyx_t_3, 7, __pyx_t_5, __pyx_t_10); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 848, __pyx_L1_error)
29538 __Pyx_GOTREF(__pyx_t_9);
29539 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
29540 __pyx_t_3 = NULL;
29541 __pyx_t_4 = 0;
29542 #if CYTHON_UNPACK_METHODS
29543 if (likely(PyMethod_Check(__pyx_t_11))) {
29544 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_11);
29545 if (likely(__pyx_t_3)) {
29546 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
29547 __Pyx_INCREF(__pyx_t_3);
29548 __Pyx_INCREF(function);
29549 __Pyx_DECREF_SET(__pyx_t_11, function);
29550 __pyx_t_4 = 1;
29551 }
29552 }
29553 #endif
29554 {
29555 PyObject *__pyx_callargs[4] = {__pyx_t_3, __pyx_v_line, __pyx_t_12, __pyx_t_9};
29556 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_11, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
29557 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
29558 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
29559 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
29560 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 848, __pyx_L1_error)
29561 __Pyx_GOTREF(__pyx_t_2);
29562 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29563 }
29564 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29565
29566 /* "pysam/libcvcf.pyx":847
29567 * dict = {}
29568 * values = sample.split(':')
29569 * if len(values) > len(format): # <<<<<<<<<<<<<<
29570 * self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
29571 * for idx in range(len(format)):
29572 */
29573 }
29574
29575 /* "pysam/libcvcf.pyx":849
29576 * if len(values) > len(format):
29577 * self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
29578 * for idx in range(len(format)): # <<<<<<<<<<<<<<
29579 * expected = self.get_expected(format[idx], self._format, alt)
29580 * if idx < len(values): value = values[idx]
29581 */
29582 __pyx_t_5 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 849, __pyx_L1_error)
29583 __pyx_t_22 = __pyx_t_5;
29584 for (__pyx_t_30 = 0; __pyx_t_30 < __pyx_t_22; __pyx_t_30+=1) {
29585 __pyx_v_idx = __pyx_t_30;
29586
29587 /* "pysam/libcvcf.pyx":850
29588 * self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
29589 * for idx in range(len(format)):
29590 * expected = self.get_expected(format[idx], self._format, alt) # <<<<<<<<<<<<<<
29591 * if idx < len(values): value = values[idx]
29592 * else:
29593 */
29594 __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_get_expected); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 850, __pyx_L1_error)
29595 __Pyx_GOTREF(__pyx_t_11);
29596 __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 850, __pyx_L1_error)
29597 __Pyx_GOTREF(__pyx_t_9);
29598 __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_2); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 850, __pyx_L1_error)
29599 __Pyx_GOTREF(__pyx_t_12);
29600 __pyx_t_3 = NULL;
29601 __pyx_t_4 = 0;
29602 #if CYTHON_UNPACK_METHODS
29603 if (likely(PyMethod_Check(__pyx_t_11))) {
29604 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_11);
29605 if (likely(__pyx_t_3)) {
29606 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
29607 __Pyx_INCREF(__pyx_t_3);
29608 __Pyx_INCREF(function);
29609 __Pyx_DECREF_SET(__pyx_t_11, function);
29610 __pyx_t_4 = 1;
29611 }
29612 }
29613 #endif
29614 {
29615 PyObject *__pyx_callargs[4] = {__pyx_t_3, __pyx_t_9, __pyx_t_12, __pyx_v_alt};
29616 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_11, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
29617 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
29618 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
29619 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
29620 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 850, __pyx_L1_error)
29621 __Pyx_GOTREF(__pyx_t_2);
29622 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29623 }
29624 __Pyx_XDECREF_SET(__pyx_v_expected, __pyx_t_2);
29625 __pyx_t_2 = 0;
29626
29627 /* "pysam/libcvcf.pyx":851
29628 * for idx in range(len(format)):
29629 * expected = self.get_expected(format[idx], self._format, alt)
29630 * if idx < len(values): value = values[idx] # <<<<<<<<<<<<<<
29631 * else:
29632 * if expected == -1: value = "."
29633 */
29634 __pyx_t_31 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_31 == ((Py_ssize_t)-1))) __PYX_ERR(0, 851, __pyx_L1_error)
29635 __pyx_t_26 = (__pyx_v_idx < __pyx_t_31);
29636 if (__pyx_t_26) {
29637 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_values, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 851, __pyx_L1_error)
29638 __Pyx_GOTREF(__pyx_t_2);
29639 __Pyx_XDECREF_SET(__pyx_v_value, __pyx_t_2);
29640 __pyx_t_2 = 0;
29641 goto __pyx_L152;
29642 }
29643
29644 /* "pysam/libcvcf.pyx":853
29645 * if idx < len(values): value = values[idx]
29646 * else:
29647 * if expected == -1: value = "." # <<<<<<<<<<<<<<
29648 * else: value = ",".join(["."]*expected)
29649 *
29650 */
29651 /*else*/ {
29652 __pyx_t_26 = (__Pyx_PyInt_BoolEqObjC(__pyx_v_expected, __pyx_int_neg_1, -1L, 0)); if (unlikely((__pyx_t_26 < 0))) __PYX_ERR(0, 853, __pyx_L1_error)
29653 if (__pyx_t_26) {
29654 __Pyx_INCREF(__pyx_kp_u__5);
29655 __Pyx_XDECREF_SET(__pyx_v_value, __pyx_kp_u__5);
29656 goto __pyx_L153;
29657 }
29658
29659 /* "pysam/libcvcf.pyx":854
29660 * else:
29661 * if expected == -1: value = "."
29662 * else: value = ",".join(["."]*expected) # <<<<<<<<<<<<<<
29663 *
29664 * dict[format[idx]] = self.parse_formatdata(format[idx],
29665 */
29666 /*else*/ {
29667 __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 854, __pyx_L1_error)
29668 __Pyx_GOTREF(__pyx_t_2);
29669 __Pyx_INCREF(__pyx_kp_u__5);
29670 __Pyx_GIVEREF(__pyx_kp_u__5);
29671 if (__Pyx_PyList_SET_ITEM(__pyx_t_2, 0, __pyx_kp_u__5)) __PYX_ERR(0, 854, __pyx_L1_error);
29672 { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_v_expected); if (unlikely(!__pyx_temp)) __PYX_ERR(0, 854, __pyx_L1_error)
29673 __Pyx_GOTREF(__pyx_temp);
29674 __Pyx_DECREF(__pyx_t_2);
29675 __pyx_t_2 = __pyx_temp;
29676 }
29677 __pyx_t_11 = PyUnicode_Join(__pyx_kp_u__2, __pyx_t_2); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 854, __pyx_L1_error)
29678 __Pyx_GOTREF(__pyx_t_11);
29679 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29680 __Pyx_XDECREF_SET(__pyx_v_value, __pyx_t_11);
29681 __pyx_t_11 = 0;
29682 }
29683 __pyx_L153:;
29684 }
29685 __pyx_L152:;
29686
29687 /* "pysam/libcvcf.pyx":856
29688 * else: value = ",".join(["."]*expected)
29689 *
29690 * dict[format[idx]] = self.parse_formatdata(format[idx], # <<<<<<<<<<<<<<
29691 * value,
29692 * self._format,
29693 */
29694 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parse_formatdata); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 856, __pyx_L1_error)
29695 __Pyx_GOTREF(__pyx_t_2);
29696 __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 856, __pyx_L1_error)
29697 __Pyx_GOTREF(__pyx_t_12);
29698
29699 /* "pysam/libcvcf.pyx":858
29700 * dict[format[idx]] = self.parse_formatdata(format[idx],
29701 * value,
29702 * self._format, # <<<<<<<<<<<<<<
29703 * line)
29704 * if expected != -1 and len(dict[format[idx]]) != expected:
29705 */
29706 __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 858, __pyx_L1_error)
29707 __Pyx_GOTREF(__pyx_t_9);
29708
29709 /* "pysam/libcvcf.pyx":859
29710 * value,
29711 * self._format,
29712 * line) # <<<<<<<<<<<<<<
29713 * if expected != -1 and len(dict[format[idx]]) != expected:
29714 * self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
29715 */
29716 __pyx_t_3 = NULL;
29717 __pyx_t_4 = 0;
29718 #if CYTHON_UNPACK_METHODS
29719 if (likely(PyMethod_Check(__pyx_t_2))) {
29720 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
29721 if (likely(__pyx_t_3)) {
29722 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
29723 __Pyx_INCREF(__pyx_t_3);
29724 __Pyx_INCREF(function);
29725 __Pyx_DECREF_SET(__pyx_t_2, function);
29726 __pyx_t_4 = 1;
29727 }
29728 }
29729 #endif
29730 {
29731 PyObject *__pyx_callargs[5] = {__pyx_t_3, __pyx_t_12, __pyx_v_value, __pyx_t_9, __pyx_v_line};
29732 __pyx_t_11 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 4+__pyx_t_4);
29733 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
29734 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
29735 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
29736 if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 856, __pyx_L1_error)
29737 __Pyx_GOTREF(__pyx_t_11);
29738 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29739 }
29740
29741 /* "pysam/libcvcf.pyx":856
29742 * else: value = ",".join(["."]*expected)
29743 *
29744 * dict[format[idx]] = self.parse_formatdata(format[idx], # <<<<<<<<<<<<<<
29745 * value,
29746 * self._format,
29747 */
29748 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 856, __pyx_L1_error)
29749 __Pyx_GOTREF(__pyx_t_2);
29750 if (unlikely((PyDict_SetItem(__pyx_v_dict, __pyx_t_2, __pyx_t_11) < 0))) __PYX_ERR(0, 856, __pyx_L1_error)
29751 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29752 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29753
29754 /* "pysam/libcvcf.pyx":860
29755 * self._format,
29756 * line)
29757 * if expected != -1 and len(dict[format[idx]]) != expected: # <<<<<<<<<<<<<<
29758 * self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
29759 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
29760 */
29761 __pyx_t_17 = (__Pyx_PyInt_BoolNeObjC(__pyx_v_expected, __pyx_int_neg_1, -1L, 0)); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 860, __pyx_L1_error)
29762 if (__pyx_t_17) {
29763 } else {
29764 __pyx_t_26 = __pyx_t_17;
29765 goto __pyx_L155_bool_binop_done;
29766 }
29767 __pyx_t_11 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 860, __pyx_L1_error)
29768 __Pyx_GOTREF(__pyx_t_11);
29769 __pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_dict, __pyx_t_11); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 860, __pyx_L1_error)
29770 __Pyx_GOTREF(__pyx_t_2);
29771 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29772 __pyx_t_31 = PyObject_Length(__pyx_t_2); if (unlikely(__pyx_t_31 == ((Py_ssize_t)-1))) __PYX_ERR(0, 860, __pyx_L1_error)
29773 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29774 __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_31); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 860, __pyx_L1_error)
29775 __Pyx_GOTREF(__pyx_t_2);
29776 __pyx_t_11 = PyObject_RichCompare(__pyx_t_2, __pyx_v_expected, Py_NE); __Pyx_XGOTREF(__pyx_t_11); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 860, __pyx_L1_error)
29777 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29778 __pyx_t_17 = __Pyx_PyObject_IsTrue(__pyx_t_11); if (unlikely((__pyx_t_17 < 0))) __PYX_ERR(0, 860, __pyx_L1_error)
29779 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29780 __pyx_t_26 = __pyx_t_17;
29781 __pyx_L155_bool_binop_done:;
29782 if (__pyx_t_26) {
29783
29784 /* "pysam/libcvcf.pyx":861
29785 * line)
29786 * if expected != -1 and len(dict[format[idx]]) != expected:
29787 * self.error(line,self.BAD_NUMBER_OF_PARAMETERS, # <<<<<<<<<<<<<<
29788 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
29789 * if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
29790 */
29791 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_error); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 861, __pyx_L1_error)
29792 __Pyx_GOTREF(__pyx_t_2);
29793 __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_BAD_NUMBER_OF_PARAMETERS); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 861, __pyx_L1_error)
29794 __Pyx_GOTREF(__pyx_t_9);
29795
29796 /* "pysam/libcvcf.pyx":862
29797 * if expected != -1 and len(dict[format[idx]]) != expected:
29798 * self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
29799 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]])) # <<<<<<<<<<<<<<
29800 * if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
29801 * dict[format[idx]] = dict[format[idx]][:expected]
29802 */
29803 __pyx_t_12 = PyTuple_New(6); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 862, __pyx_L1_error)
29804 __Pyx_GOTREF(__pyx_t_12);
29805 __pyx_t_31 = 0;
29806 __pyx_t_10 = 127;
29807 __Pyx_INCREF(__pyx_kp_u_id);
29808 __pyx_t_31 += 3;
29809 __Pyx_GIVEREF(__pyx_kp_u_id);
29810 PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_kp_u_id);
29811 __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 862, __pyx_L1_error)
29812 __Pyx_GOTREF(__pyx_t_3);
29813 __pyx_t_25 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_3), __pyx_empty_unicode); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 862, __pyx_L1_error)
29814 __Pyx_GOTREF(__pyx_t_25);
29815 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
29816 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_25) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_25) : __pyx_t_10;
29817 __pyx_t_31 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_25);
29818 __Pyx_GIVEREF(__pyx_t_25);
29819 PyTuple_SET_ITEM(__pyx_t_12, 1, __pyx_t_25);
29820 __pyx_t_25 = 0;
29821 __Pyx_INCREF(__pyx_kp_u_expected_2);
29822 __pyx_t_31 += 11;
29823 __Pyx_GIVEREF(__pyx_kp_u_expected_2);
29824 PyTuple_SET_ITEM(__pyx_t_12, 2, __pyx_kp_u_expected_2);
29825 __pyx_t_25 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_expected), __pyx_empty_unicode); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 862, __pyx_L1_error)
29826 __Pyx_GOTREF(__pyx_t_25);
29827 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_25) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_25) : __pyx_t_10;
29828 __pyx_t_31 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_25);
29829 __Pyx_GIVEREF(__pyx_t_25);
29830 PyTuple_SET_ITEM(__pyx_t_12, 3, __pyx_t_25);
29831 __pyx_t_25 = 0;
29832 __Pyx_INCREF(__pyx_kp_u_parameters_got);
29833 __pyx_t_31 += 17;
29834 __Pyx_GIVEREF(__pyx_kp_u_parameters_got);
29835 PyTuple_SET_ITEM(__pyx_t_12, 4, __pyx_kp_u_parameters_got);
29836 __pyx_t_25 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 862, __pyx_L1_error)
29837 __Pyx_GOTREF(__pyx_t_25);
29838 __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_dict, __pyx_t_25); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 862, __pyx_L1_error)
29839 __Pyx_GOTREF(__pyx_t_3);
29840 __Pyx_DECREF(__pyx_t_25); __pyx_t_25 = 0;
29841 __pyx_t_25 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_3), __pyx_empty_unicode); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 862, __pyx_L1_error)
29842 __Pyx_GOTREF(__pyx_t_25);
29843 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
29844 __pyx_t_10 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_25) > __pyx_t_10) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_25) : __pyx_t_10;
29845 __pyx_t_31 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_25);
29846 __Pyx_GIVEREF(__pyx_t_25);
29847 PyTuple_SET_ITEM(__pyx_t_12, 5, __pyx_t_25);
29848 __pyx_t_25 = 0;
29849 __pyx_t_25 = __Pyx_PyUnicode_Join(__pyx_t_12, 6, __pyx_t_31, __pyx_t_10); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 862, __pyx_L1_error)
29850 __Pyx_GOTREF(__pyx_t_25);
29851 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
29852 __pyx_t_12 = NULL;
29853 __pyx_t_4 = 0;
29854 #if CYTHON_UNPACK_METHODS
29855 if (likely(PyMethod_Check(__pyx_t_2))) {
29856 __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_2);
29857 if (likely(__pyx_t_12)) {
29858 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
29859 __Pyx_INCREF(__pyx_t_12);
29860 __Pyx_INCREF(function);
29861 __Pyx_DECREF_SET(__pyx_t_2, function);
29862 __pyx_t_4 = 1;
29863 }
29864 }
29865 #endif
29866 {
29867 PyObject *__pyx_callargs[4] = {__pyx_t_12, __pyx_v_line, __pyx_t_9, __pyx_t_25};
29868 __pyx_t_11 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 3+__pyx_t_4);
29869 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
29870 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
29871 __Pyx_DECREF(__pyx_t_25); __pyx_t_25 = 0;
29872 if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 861, __pyx_L1_error)
29873 __Pyx_GOTREF(__pyx_t_11);
29874 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29875 }
29876 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29877
29878 /* "pysam/libcvcf.pyx":863
29879 * self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
29880 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
29881 * if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]])) # <<<<<<<<<<<<<<
29882 * dict[format[idx]] = dict[format[idx]][:expected]
29883 * samples.append( dict )
29884 */
29885 __pyx_t_11 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 863, __pyx_L1_error)
29886 __Pyx_GOTREF(__pyx_t_11);
29887 __pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_dict, __pyx_t_11); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 863, __pyx_L1_error)
29888 __Pyx_GOTREF(__pyx_t_2);
29889 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29890 __pyx_t_31 = PyObject_Length(__pyx_t_2); if (unlikely(__pyx_t_31 == ((Py_ssize_t)-1))) __PYX_ERR(0, 863, __pyx_L1_error)
29891 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29892 __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_31); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 863, __pyx_L1_error)
29893 __Pyx_GOTREF(__pyx_t_2);
29894 __pyx_t_11 = PyObject_RichCompare(__pyx_t_2, __pyx_v_expected, Py_LT); __Pyx_XGOTREF(__pyx_t_11); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 863, __pyx_L1_error)
29895 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29896 __pyx_t_26 = __Pyx_PyObject_IsTrue(__pyx_t_11); if (unlikely((__pyx_t_26 < 0))) __PYX_ERR(0, 863, __pyx_L1_error)
29897 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29898 if (__pyx_t_26) {
29899 __pyx_t_11 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 863, __pyx_L1_error)
29900 __Pyx_GOTREF(__pyx_t_11);
29901 __pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_dict, __pyx_t_11); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 863, __pyx_L1_error)
29902 __Pyx_GOTREF(__pyx_t_2);
29903 __pyx_t_25 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 863, __pyx_L1_error)
29904 __Pyx_GOTREF(__pyx_t_25);
29905 __pyx_t_9 = __Pyx_PyDict_GetItem(__pyx_v_dict, __pyx_t_25); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 863, __pyx_L1_error)
29906 __Pyx_GOTREF(__pyx_t_9);
29907 __Pyx_DECREF(__pyx_t_25); __pyx_t_25 = 0;
29908 __pyx_t_25 = __Pyx_GetItemInt(__pyx_t_9, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 863, __pyx_L1_error)
29909 __Pyx_GOTREF(__pyx_t_25);
29910 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
29911 __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 863, __pyx_L1_error)
29912 __Pyx_GOTREF(__pyx_t_9);
29913 __pyx_t_12 = __Pyx_PyDict_GetItem(__pyx_v_dict, __pyx_t_9); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 863, __pyx_L1_error)
29914 __Pyx_GOTREF(__pyx_t_12);
29915 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
29916 __pyx_t_31 = PyObject_Length(__pyx_t_12); if (unlikely(__pyx_t_31 == ((Py_ssize_t)-1))) __PYX_ERR(0, 863, __pyx_L1_error)
29917 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
29918 __pyx_t_12 = PyInt_FromSsize_t(__pyx_t_31); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 863, __pyx_L1_error)
29919 __Pyx_GOTREF(__pyx_t_12);
29920 __pyx_t_9 = PyNumber_Subtract(__pyx_v_expected, __pyx_t_12); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 863, __pyx_L1_error)
29921 __Pyx_GOTREF(__pyx_t_9);
29922 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
29923 __pyx_t_12 = PyList_New(1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 863, __pyx_L1_error)
29924 __Pyx_GOTREF(__pyx_t_12);
29925 __Pyx_GIVEREF(__pyx_t_25);
29926 if (__Pyx_PyList_SET_ITEM(__pyx_t_12, 0, __pyx_t_25)) __PYX_ERR(0, 863, __pyx_L1_error);
29927 { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_12, __pyx_t_9); if (unlikely(!__pyx_temp)) __PYX_ERR(0, 863, __pyx_L1_error)
29928 __Pyx_GOTREF(__pyx_temp);
29929 __Pyx_DECREF(__pyx_t_12);
29930 __pyx_t_12 = __pyx_temp;
29931 }
29932 __pyx_t_25 = 0;
29933 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
29934 __pyx_t_9 = PyNumber_InPlaceAdd(__pyx_t_2, __pyx_t_12); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 863, __pyx_L1_error)
29935 __Pyx_GOTREF(__pyx_t_9);
29936 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
29937 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
29938 if (unlikely((PyDict_SetItem(__pyx_v_dict, __pyx_t_11, __pyx_t_9) < 0))) __PYX_ERR(0, 863, __pyx_L1_error)
29939 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
29940 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29941 }
29942
29943 /* "pysam/libcvcf.pyx":864
29944 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
29945 * if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
29946 * dict[format[idx]] = dict[format[idx]][:expected] # <<<<<<<<<<<<<<
29947 * samples.append( dict )
29948 *
29949 */
29950 __pyx_t_11 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 864, __pyx_L1_error)
29951 __Pyx_GOTREF(__pyx_t_11);
29952 __pyx_t_9 = __Pyx_PyDict_GetItem(__pyx_v_dict, __pyx_t_11); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 864, __pyx_L1_error)
29953 __Pyx_GOTREF(__pyx_t_9);
29954 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29955 __pyx_t_11 = __Pyx_PyObject_GetSlice(__pyx_t_9, 0, 0, NULL, &__pyx_v_expected, NULL, 0, 0, 1); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 864, __pyx_L1_error)
29956 __Pyx_GOTREF(__pyx_t_11);
29957 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
29958 __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_format, __pyx_v_idx, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 864, __pyx_L1_error)
29959 __Pyx_GOTREF(__pyx_t_9);
29960 if (unlikely((PyDict_SetItem(__pyx_v_dict, __pyx_t_9, __pyx_t_11) < 0))) __PYX_ERR(0, 864, __pyx_L1_error)
29961 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
29962 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
29963
29964 /* "pysam/libcvcf.pyx":860
29965 * self._format,
29966 * line)
29967 * if expected != -1 and len(dict[format[idx]]) != expected: # <<<<<<<<<<<<<<
29968 * self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
29969 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
29970 */
29971 }
29972 }
29973
29974 /* "pysam/libcvcf.pyx":865
29975 * if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
29976 * dict[format[idx]] = dict[format[idx]][:expected]
29977 * samples.append( dict ) # <<<<<<<<<<<<<<
29978 *
29979 * # done
29980 */
29981 __pyx_t_8 = __Pyx_PyList_Append(__pyx_v_samples, __pyx_v_dict); if (unlikely(__pyx_t_8 == ((int)-1))) __PYX_ERR(0, 865, __pyx_L1_error)
29982
29983 /* "pysam/libcvcf.pyx":844
29984 * # parse sample columns
29985 * samples = []
29986 * for sample in cols[9:]: # <<<<<<<<<<<<<<
29987 * dict = {}
29988 * values = sample.split(':')
29989 */
29990 }
29991 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
29992
29993 /* "pysam/libcvcf.pyx":868
29994 *
29995 * # done
29996 * d = {'chrom':chrom, # <<<<<<<<<<<<<<
29997 * 'pos':pos, # return 0-based position
29998 * 'id':id,
29999 */
30000 __pyx_t_1 = __Pyx_PyDict_NewPresized(9); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 868, __pyx_L1_error)
30001 __Pyx_GOTREF(__pyx_t_1);
30002 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_chrom, __pyx_v_chrom) < 0) __PYX_ERR(0, 868, __pyx_L1_error)
30003
30004 /* "pysam/libcvcf.pyx":869
30005 * # done
30006 * d = {'chrom':chrom,
30007 * 'pos':pos, # return 0-based position # <<<<<<<<<<<<<<
30008 * 'id':id,
30009 * 'ref':ref,
30010 */
30011 if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); __PYX_ERR(0, 869, __pyx_L1_error) }
30012 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_pos, __pyx_v_pos) < 0) __PYX_ERR(0, 868, __pyx_L1_error)
30013
30014 /* "pysam/libcvcf.pyx":870
30015 * d = {'chrom':chrom,
30016 * 'pos':pos, # return 0-based position
30017 * 'id':id, # <<<<<<<<<<<<<<
30018 * 'ref':ref,
30019 * 'alt':alt,
30020 */
30021 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_id_2, __pyx_v_id) < 0) __PYX_ERR(0, 868, __pyx_L1_error)
30022
30023 /* "pysam/libcvcf.pyx":871
30024 * 'pos':pos, # return 0-based position
30025 * 'id':id,
30026 * 'ref':ref, # <<<<<<<<<<<<<<
30027 * 'alt':alt,
30028 * 'qual':qual,
30029 */
30030 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_ref, __pyx_v_ref) < 0) __PYX_ERR(0, 868, __pyx_L1_error)
30031
30032 /* "pysam/libcvcf.pyx":872
30033 * 'id':id,
30034 * 'ref':ref,
30035 * 'alt':alt, # <<<<<<<<<<<<<<
30036 * 'qual':qual,
30037 * 'filter':filter,
30038 */
30039 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_alt, __pyx_v_alt) < 0) __PYX_ERR(0, 868, __pyx_L1_error)
30040
30041 /* "pysam/libcvcf.pyx":873
30042 * 'ref':ref,
30043 * 'alt':alt,
30044 * 'qual':qual, # <<<<<<<<<<<<<<
30045 * 'filter':filter,
30046 * 'info':info,
30047 */
30048 __pyx_t_11 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 873, __pyx_L1_error)
30049 __Pyx_GOTREF(__pyx_t_11);
30050 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_qual, __pyx_t_11) < 0) __PYX_ERR(0, 868, __pyx_L1_error)
30051 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
30052
30053 /* "pysam/libcvcf.pyx":874
30054 * 'alt':alt,
30055 * 'qual':qual,
30056 * 'filter':filter, # <<<<<<<<<<<<<<
30057 * 'info':info,
30058 * 'format':format}
30059 */
30060 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_filter_2, __pyx_v_filter) < 0) __PYX_ERR(0, 868, __pyx_L1_error)
30061
30062 /* "pysam/libcvcf.pyx":875
30063 * 'qual':qual,
30064 * 'filter':filter,
30065 * 'info':info, # <<<<<<<<<<<<<<
30066 * 'format':format}
30067 * for key,value in zip(self._samples,samples):
30068 */
30069 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_info_2, __pyx_v_info) < 0) __PYX_ERR(0, 868, __pyx_L1_error)
30070
30071 /* "pysam/libcvcf.pyx":876
30072 * 'filter':filter,
30073 * 'info':info,
30074 * 'format':format} # <<<<<<<<<<<<<<
30075 * for key,value in zip(self._samples,samples):
30076 * d[key] = value
30077 */
30078 if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_format, __pyx_v_format) < 0) __PYX_ERR(0, 868, __pyx_L1_error)
30079 __pyx_v_d = ((PyObject*)__pyx_t_1);
30080 __pyx_t_1 = 0;
30081
30082 /* "pysam/libcvcf.pyx":877
30083 * 'info':info,
30084 * 'format':format}
30085 * for key,value in zip(self._samples,samples): # <<<<<<<<<<<<<<
30086 * d[key] = value
30087 *
30088 */
30089 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_samples); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 877, __pyx_L1_error)
30090 __Pyx_GOTREF(__pyx_t_1);
30091 __pyx_t_11 = PyTuple_New(2); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 877, __pyx_L1_error)
30092 __Pyx_GOTREF(__pyx_t_11);
30093 __Pyx_GIVEREF(__pyx_t_1);
30094 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_1)) __PYX_ERR(0, 877, __pyx_L1_error);
30095 __Pyx_INCREF(__pyx_v_samples);
30096 __Pyx_GIVEREF(__pyx_v_samples);
30097 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_11, 1, __pyx_v_samples)) __PYX_ERR(0, 877, __pyx_L1_error);
30098 __pyx_t_1 = 0;
30099 __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_zip, __pyx_t_11, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 877, __pyx_L1_error)
30100 __Pyx_GOTREF(__pyx_t_1);
30101 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
30102 if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) {
30103 __pyx_t_11 = __pyx_t_1; __Pyx_INCREF(__pyx_t_11);
30104 __pyx_t_6 = 0;
30105 __pyx_t_18 = NULL;
30106 } else {
30107 __pyx_t_6 = -1; __pyx_t_11 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 877, __pyx_L1_error)
30108 __Pyx_GOTREF(__pyx_t_11);
30109 __pyx_t_18 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_11); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 877, __pyx_L1_error)
30110 }
30111 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
30112 for (;;) {
30113 if (likely(!__pyx_t_18)) {
30114 if (likely(PyList_CheckExact(__pyx_t_11))) {
30115 {
30116 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_11);
30117 #if !CYTHON_ASSUME_SAFE_MACROS
30118 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 877, __pyx_L1_error)
30119 #endif
30120 if (__pyx_t_6 >= __pyx_temp) break;
30121 }
30122 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
30123 __pyx_t_1 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 877, __pyx_L1_error)
30124 #else
30125 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_11, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 877, __pyx_L1_error)
30126 __Pyx_GOTREF(__pyx_t_1);
30127 #endif
30128 } else {
30129 {
30130 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_11);
30131 #if !CYTHON_ASSUME_SAFE_MACROS
30132 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 877, __pyx_L1_error)
30133 #endif
30134 if (__pyx_t_6 >= __pyx_temp) break;
30135 }
30136 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
30137 __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_6); __Pyx_INCREF(__pyx_t_1); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 877, __pyx_L1_error)
30138 #else
30139 __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_11, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 877, __pyx_L1_error)
30140 __Pyx_GOTREF(__pyx_t_1);
30141 #endif
30142 }
30143 } else {
30144 __pyx_t_1 = __pyx_t_18(__pyx_t_11);
30145 if (unlikely(!__pyx_t_1)) {
30146 PyObject* exc_type = PyErr_Occurred();
30147 if (exc_type) {
30148 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
30149 else __PYX_ERR(0, 877, __pyx_L1_error)
30150 }
30151 break;
30152 }
30153 __Pyx_GOTREF(__pyx_t_1);
30154 }
30155 if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
30156 PyObject* sequence = __pyx_t_1;
30157 Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
30158 if (unlikely(size != 2)) {
30159 if (size > 2) __Pyx_RaiseTooManyValuesError(2);
30160 else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
30161 __PYX_ERR(0, 877, __pyx_L1_error)
30162 }
30163 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
30164 if (likely(PyTuple_CheckExact(sequence))) {
30165 __pyx_t_9 = PyTuple_GET_ITEM(sequence, 0);
30166 __pyx_t_12 = PyTuple_GET_ITEM(sequence, 1);
30167 } else {
30168 __pyx_t_9 = PyList_GET_ITEM(sequence, 0);
30169 __pyx_t_12 = PyList_GET_ITEM(sequence, 1);
30170 }
30171 __Pyx_INCREF(__pyx_t_9);
30172 __Pyx_INCREF(__pyx_t_12);
30173 #else
30174 __pyx_t_9 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 877, __pyx_L1_error)
30175 __Pyx_GOTREF(__pyx_t_9);
30176 __pyx_t_12 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 877, __pyx_L1_error)
30177 __Pyx_GOTREF(__pyx_t_12);
30178 #endif
30179 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
30180 } else {
30181 Py_ssize_t index = -1;
30182 __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 877, __pyx_L1_error)
30183 __Pyx_GOTREF(__pyx_t_2);
30184 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
30185 __pyx_t_32 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_2);
30186 index = 0; __pyx_t_9 = __pyx_t_32(__pyx_t_2); if (unlikely(!__pyx_t_9)) goto __pyx_L161_unpacking_failed;
30187 __Pyx_GOTREF(__pyx_t_9);
30188 index = 1; __pyx_t_12 = __pyx_t_32(__pyx_t_2); if (unlikely(!__pyx_t_12)) goto __pyx_L161_unpacking_failed;
30189 __Pyx_GOTREF(__pyx_t_12);
30190 if (__Pyx_IternextUnpackEndCheck(__pyx_t_32(__pyx_t_2), 2) < 0) __PYX_ERR(0, 877, __pyx_L1_error)
30191 __pyx_t_32 = NULL;
30192 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
30193 goto __pyx_L162_unpacking_done;
30194 __pyx_L161_unpacking_failed:;
30195 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
30196 __pyx_t_32 = NULL;
30197 if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
30198 __PYX_ERR(0, 877, __pyx_L1_error)
30199 __pyx_L162_unpacking_done:;
30200 }
30201 __Pyx_XDECREF_SET(__pyx_v_key, __pyx_t_9);
30202 __pyx_t_9 = 0;
30203 __Pyx_XDECREF_SET(__pyx_v_value, __pyx_t_12);
30204 __pyx_t_12 = 0;
30205
30206 /* "pysam/libcvcf.pyx":878
30207 * 'format':format}
30208 * for key,value in zip(self._samples,samples):
30209 * d[key] = value # <<<<<<<<<<<<<<
30210 *
30211 * return d
30212 */
30213 if (unlikely((PyDict_SetItem(__pyx_v_d, __pyx_v_key, __pyx_v_value) < 0))) __PYX_ERR(0, 878, __pyx_L1_error)
30214
30215 /* "pysam/libcvcf.pyx":877
30216 * 'info':info,
30217 * 'format':format}
30218 * for key,value in zip(self._samples,samples): # <<<<<<<<<<<<<<
30219 * d[key] = value
30220 *
30221 */
30222 }
30223 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
30224
30225 /* "pysam/libcvcf.pyx":880
30226 * d[key] = value
30227 *
30228 * return d # <<<<<<<<<<<<<<
30229 *
30230 *
30231 */
30232 __Pyx_XDECREF(__pyx_r);
30233 __Pyx_INCREF(__pyx_v_d);
30234 __pyx_r = __pyx_v_d;
30235 goto __pyx_L0;
30236
30237 /* "pysam/libcvcf.pyx":671
30238 * return False
30239 *
30240 * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<<
30241 * cols = line.split('\t')
30242 * if len(cols) != len(self._samples)+9:
30243 */
30244
30245 /* function exit code */
30246 __pyx_L1_error:;
30247 __Pyx_XDECREF(__pyx_t_1);
30248 __Pyx_XDECREF(__pyx_t_2);
30249 __Pyx_XDECREF(__pyx_t_3);
30250 __Pyx_XDECREF(__pyx_t_9);
30251 __Pyx_XDECREF(__pyx_t_11);
30252 __Pyx_XDECREF(__pyx_t_12);
30253 __Pyx_XDECREF(__pyx_t_16);
30254 __Pyx_XDECREF(__pyx_t_23);
30255 __Pyx_XDECREF(__pyx_t_24);
30256 __Pyx_XDECREF(__pyx_t_25);
30257 __Pyx_XDECREF(__pyx_t_27);
30258 __Pyx_XDECREF(__pyx_t_28);
30259 __Pyx_XDECREF(__pyx_t_29);
30260 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
30261 __pyx_r = NULL;
30262 __pyx_L0:;
30263 __Pyx_XDECREF(__pyx_v_cols);
30264 __Pyx_XDECREF(__pyx_v_chrom);
30265 __Pyx_XDECREF(__pyx_v_pos);
30266 __Pyx_XDECREF(__pyx_v_id);
30267 __Pyx_XDECREF(__pyx_v_ref);
30268 __Pyx_XDECREF(__pyx_v_c);
30269 __Pyx_XDECREF(__pyx_v_left);
30270 __Pyx_XDECREF(__pyx_v_faref_leftflank);
30271 __Pyx_XDECREF(__pyx_v_faref);
30272 __Pyx_XDECREF(__pyx_v_alt);
30273 __Pyx_XDECREF(__pyx_v_filter);
30274 __Pyx_XDECREF(__pyx_v_info);
30275 __Pyx_XDECREF(__pyx_v_blurp);
30276 __Pyx_XDECREF(__pyx_v_elts);
30277 __Pyx_XDECREF(__pyx_v_v);
30278 __Pyx_XDECREF(__pyx_v_format);
30279 __Pyx_XDECREF(__pyx_v_f);
30280 __Pyx_XDECREF(__pyx_v_newalts);
30281 __Pyx_XDECREF(__pyx_v_a);
30282 __Pyx_XDECREF(__pyx_v_l);
30283 __Pyx_XDECREF(__pyx_v_addns);
30284 __Pyx_XDECREF(__pyx_v_i);
30285 __Pyx_XDECREF(__pyx_v_na);
30286 __Pyx_XDECREF(__pyx_v_s);
30287 __Pyx_XDECREF(__pyx_v_addn);
30288 __Pyx_XDECREF(__pyx_v_allele);
30289 __Pyx_XDECREF(__pyx_v_longest);
30290 __Pyx_XDECREF(__pyx_v_shortest);
30291 __Pyx_XDECREF(__pyx_v_samples);
30292 __Pyx_XDECREF(__pyx_v_sample);
30293 __Pyx_XDECREF(__pyx_v_dict);
30294 __Pyx_XDECREF(__pyx_v_values);
30295 __Pyx_XDECREF(__pyx_v_expected);
30296 __Pyx_XDECREF(__pyx_v_value);
30297 __Pyx_XDECREF(__pyx_v_d);
30298 __Pyx_XDECREF(__pyx_v_key);
30299 __Pyx_XDECREF(__pyx_8genexpr3__pyx_v_allele);
30300 __Pyx_XDECREF(__pyx_8genexpr4__pyx_v_allele);
30301 __Pyx_XDECREF(__pyx_8genexpr5__pyx_v_allele);
30302 __Pyx_XDECREF(__pyx_8genexpr6__pyx_v_allele);
30303 __Pyx_XDECREF(__pyx_8genexpr7__pyx_v_allele);
30304 __Pyx_XGIVEREF(__pyx_r);
30305 __Pyx_RefNannyFinishContext();
30306 return __pyx_r;
30307 }
30308
30309 /* "pysam/libcvcf.pyx":883
30310 *
30311 *
30312 * def write_data(self, stream, data): # <<<<<<<<<<<<<<
30313 * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
30314 * for k in required:
30315 */
30316
30317 /* Python wrapper */
30318 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_35write_data(PyObject *__pyx_self,
30319 #if CYTHON_METH_FASTCALL
30320 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
30321 #else
30322 PyObject *__pyx_args, PyObject *__pyx_kwds
30323 #endif
30324 ); /*proto*/
30325 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_34write_data, "VCF.write_data(self, stream, data)");
30326 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_35write_data = {"write_data", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_35write_data, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_34write_data};
30327 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_35write_data(PyObject *__pyx_self,
30328 #if CYTHON_METH_FASTCALL
30329 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
30330 #else
30331 PyObject *__pyx_args, PyObject *__pyx_kwds
30332 #endif
30333 ) {
30334 PyObject *__pyx_v_self = 0;
30335 PyObject *__pyx_v_stream = 0;
30336 PyObject *__pyx_v_data = 0;
30337 #if !CYTHON_METH_FASTCALL
30338 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
30339 #endif
30340 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
30341 PyObject* values[3] = {0,0,0};
30342 int __pyx_lineno = 0;
30343 const char *__pyx_filename = NULL;
30344 int __pyx_clineno = 0;
30345 PyObject *__pyx_r = 0;
30346 __Pyx_RefNannyDeclarations
30347 __Pyx_RefNannySetupContext("write_data (wrapper)", 0);
30348 #if !CYTHON_METH_FASTCALL
30349 #if CYTHON_ASSUME_SAFE_MACROS
30350 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
30351 #else
30352 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
30353 #endif
30354 #endif
30355 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
30356 {
30357 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_stream,&__pyx_n_s_data,0};
30358 if (__pyx_kwds) {
30359 Py_ssize_t kw_args;
30360 switch (__pyx_nargs) {
30361 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
30362 CYTHON_FALLTHROUGH;
30363 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
30364 CYTHON_FALLTHROUGH;
30365 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
30366 CYTHON_FALLTHROUGH;
30367 case 0: break;
30368 default: goto __pyx_L5_argtuple_error;
30369 }
30370 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
30371 switch (__pyx_nargs) {
30372 case 0:
30373 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
30374 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
30375 kw_args--;
30376 }
30377 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 883, __pyx_L3_error)
30378 else goto __pyx_L5_argtuple_error;
30379 CYTHON_FALLTHROUGH;
30380 case 1:
30381 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_stream)) != 0)) {
30382 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
30383 kw_args--;
30384 }
30385 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 883, __pyx_L3_error)
30386 else {
30387 __Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, 1); __PYX_ERR(0, 883, __pyx_L3_error)
30388 }
30389 CYTHON_FALLTHROUGH;
30390 case 2:
30391 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_data)) != 0)) {
30392 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
30393 kw_args--;
30394 }
30395 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 883, __pyx_L3_error)
30396 else {
30397 __Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, 2); __PYX_ERR(0, 883, __pyx_L3_error)
30398 }
30399 }
30400 if (unlikely(kw_args > 0)) {
30401 const Py_ssize_t kwd_pos_args = __pyx_nargs;
30402 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "write_data") < 0)) __PYX_ERR(0, 883, __pyx_L3_error)
30403 }
30404 } else if (unlikely(__pyx_nargs != 3)) {
30405 goto __pyx_L5_argtuple_error;
30406 } else {
30407 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
30408 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
30409 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
30410 }
30411 __pyx_v_self = values[0];
30412 __pyx_v_stream = values[1];
30413 __pyx_v_data = values[2];
30414 }
30415 goto __pyx_L6_skip;
30416 __pyx_L5_argtuple_error:;
30417 __Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 883, __pyx_L3_error)
30418 __pyx_L6_skip:;
30419 goto __pyx_L4_argument_unpacking_done;
30420 __pyx_L3_error:;
30421 {
30422 Py_ssize_t __pyx_temp;
30423 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
30424 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
30425 }
30426 }
30427 __Pyx_AddTraceback("pysam.libcvcf.VCF.write_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
30428 __Pyx_RefNannyFinishContext();
30429 return NULL;
30430 __pyx_L4_argument_unpacking_done:;
30431 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_34write_data(__pyx_self, __pyx_v_self, __pyx_v_stream, __pyx_v_data);
30432
30433 /* function exit code */
30434 {
30435 Py_ssize_t __pyx_temp;
30436 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
30437 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
30438 }
30439 }
30440 __Pyx_RefNannyFinishContext();
30441 return __pyx_r;
30442 }
30443
30444 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_data) {
30445 PyObject *__pyx_v_required = NULL;
30446 PyObject *__pyx_v_k = NULL;
30447 PyObject *__pyx_v_alt = NULL;
30448 PyObject *__pyx_v_filter = NULL;
30449 PyObject *__pyx_v_qual = NULL;
30450 PyObject *__pyx_v_output = NULL;
30451 PyObject *__pyx_v_s = NULL;
30452 PyObject *__pyx_r = NULL;
30453 __Pyx_RefNannyDeclarations
30454 PyObject *__pyx_t_1 = NULL;
30455 PyObject *__pyx_t_2 = NULL;
30456 PyObject *__pyx_t_3 = NULL;
30457 Py_ssize_t __pyx_t_4;
30458 PyObject *(*__pyx_t_5)(PyObject *);
30459 int __pyx_t_6;
30460 PyObject *__pyx_t_7 = NULL;
30461 PyObject *__pyx_t_8 = NULL;
30462 PyObject *__pyx_t_9 = NULL;
30463 PyObject *__pyx_t_10 = NULL;
30464 PyObject *__pyx_t_11 = NULL;
30465 PyObject *__pyx_t_12 = NULL;
30466 int __pyx_t_13;
30467 unsigned int __pyx_t_14;
30468 int __pyx_lineno = 0;
30469 const char *__pyx_filename = NULL;
30470 int __pyx_clineno = 0;
30471 __Pyx_RefNannySetupContext("write_data", 1);
30472
30473 /* "pysam/libcvcf.pyx":884
30474 *
30475 * def write_data(self, stream, data):
30476 * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples # <<<<<<<<<<<<<<
30477 * for k in required:
30478 * if k not in data: raise ValueError("Required key %s not found in data" % str(k))
30479 */
30480 __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 884, __pyx_L1_error)
30481 __Pyx_GOTREF(__pyx_t_1);
30482 __Pyx_INCREF(__pyx_n_u_chrom);
30483 __Pyx_GIVEREF(__pyx_n_u_chrom);
30484 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_u_chrom)) __PYX_ERR(0, 884, __pyx_L1_error);
30485 __Pyx_INCREF(__pyx_n_u_pos);
30486 __Pyx_GIVEREF(__pyx_n_u_pos);
30487 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 1, __pyx_n_u_pos)) __PYX_ERR(0, 884, __pyx_L1_error);
30488 __Pyx_INCREF(__pyx_n_u_id_2);
30489 __Pyx_GIVEREF(__pyx_n_u_id_2);
30490 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 2, __pyx_n_u_id_2)) __PYX_ERR(0, 884, __pyx_L1_error);
30491 __Pyx_INCREF(__pyx_n_u_ref);
30492 __Pyx_GIVEREF(__pyx_n_u_ref);
30493 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 3, __pyx_n_u_ref)) __PYX_ERR(0, 884, __pyx_L1_error);
30494 __Pyx_INCREF(__pyx_n_u_alt);
30495 __Pyx_GIVEREF(__pyx_n_u_alt);
30496 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 4, __pyx_n_u_alt)) __PYX_ERR(0, 884, __pyx_L1_error);
30497 __Pyx_INCREF(__pyx_n_u_qual);
30498 __Pyx_GIVEREF(__pyx_n_u_qual);
30499 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 5, __pyx_n_u_qual)) __PYX_ERR(0, 884, __pyx_L1_error);
30500 __Pyx_INCREF(__pyx_n_u_filter_2);
30501 __Pyx_GIVEREF(__pyx_n_u_filter_2);
30502 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 6, __pyx_n_u_filter_2)) __PYX_ERR(0, 884, __pyx_L1_error);
30503 __Pyx_INCREF(__pyx_n_u_info_2);
30504 __Pyx_GIVEREF(__pyx_n_u_info_2);
30505 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 7, __pyx_n_u_info_2)) __PYX_ERR(0, 884, __pyx_L1_error);
30506 __Pyx_INCREF(__pyx_n_u_format);
30507 __Pyx_GIVEREF(__pyx_n_u_format);
30508 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 8, __pyx_n_u_format)) __PYX_ERR(0, 884, __pyx_L1_error);
30509 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_samples); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 884, __pyx_L1_error)
30510 __Pyx_GOTREF(__pyx_t_2);
30511 __pyx_t_3 = PyNumber_Add(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 884, __pyx_L1_error)
30512 __Pyx_GOTREF(__pyx_t_3);
30513 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
30514 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
30515 __pyx_v_required = __pyx_t_3;
30516 __pyx_t_3 = 0;
30517
30518 /* "pysam/libcvcf.pyx":885
30519 * def write_data(self, stream, data):
30520 * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
30521 * for k in required: # <<<<<<<<<<<<<<
30522 * if k not in data: raise ValueError("Required key %s not found in data" % str(k))
30523 * if data['alt'] == []: alt = "."
30524 */
30525 if (likely(PyList_CheckExact(__pyx_v_required)) || PyTuple_CheckExact(__pyx_v_required)) {
30526 __pyx_t_3 = __pyx_v_required; __Pyx_INCREF(__pyx_t_3);
30527 __pyx_t_4 = 0;
30528 __pyx_t_5 = NULL;
30529 } else {
30530 __pyx_t_4 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_required); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 885, __pyx_L1_error)
30531 __Pyx_GOTREF(__pyx_t_3);
30532 __pyx_t_5 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_3); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 885, __pyx_L1_error)
30533 }
30534 for (;;) {
30535 if (likely(!__pyx_t_5)) {
30536 if (likely(PyList_CheckExact(__pyx_t_3))) {
30537 {
30538 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_3);
30539 #if !CYTHON_ASSUME_SAFE_MACROS
30540 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 885, __pyx_L1_error)
30541 #endif
30542 if (__pyx_t_4 >= __pyx_temp) break;
30543 }
30544 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
30545 __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 885, __pyx_L1_error)
30546 #else
30547 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 885, __pyx_L1_error)
30548 __Pyx_GOTREF(__pyx_t_2);
30549 #endif
30550 } else {
30551 {
30552 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_3);
30553 #if !CYTHON_ASSUME_SAFE_MACROS
30554 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 885, __pyx_L1_error)
30555 #endif
30556 if (__pyx_t_4 >= __pyx_temp) break;
30557 }
30558 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
30559 __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 885, __pyx_L1_error)
30560 #else
30561 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 885, __pyx_L1_error)
30562 __Pyx_GOTREF(__pyx_t_2);
30563 #endif
30564 }
30565 } else {
30566 __pyx_t_2 = __pyx_t_5(__pyx_t_3);
30567 if (unlikely(!__pyx_t_2)) {
30568 PyObject* exc_type = PyErr_Occurred();
30569 if (exc_type) {
30570 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
30571 else __PYX_ERR(0, 885, __pyx_L1_error)
30572 }
30573 break;
30574 }
30575 __Pyx_GOTREF(__pyx_t_2);
30576 }
30577 __Pyx_XDECREF_SET(__pyx_v_k, __pyx_t_2);
30578 __pyx_t_2 = 0;
30579
30580 /* "pysam/libcvcf.pyx":886
30581 * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
30582 * for k in required:
30583 * if k not in data: raise ValueError("Required key %s not found in data" % str(k)) # <<<<<<<<<<<<<<
30584 * if data['alt'] == []: alt = "."
30585 * else: alt = ",".join(data['alt'])
30586 */
30587 __pyx_t_6 = (__Pyx_PySequence_ContainsTF(__pyx_v_k, __pyx_v_data, Py_NE)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 886, __pyx_L1_error)
30588 if (unlikely(__pyx_t_6)) {
30589 __pyx_t_2 = __Pyx_PyObject_Unicode(__pyx_v_k); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 886, __pyx_L1_error)
30590 __Pyx_GOTREF(__pyx_t_2);
30591 __pyx_t_1 = PyUnicode_Format(__pyx_kp_u_Required_key_s_not_found_in_data, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 886, __pyx_L1_error)
30592 __Pyx_GOTREF(__pyx_t_1);
30593 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
30594 __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 886, __pyx_L1_error)
30595 __Pyx_GOTREF(__pyx_t_2);
30596 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
30597 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
30598 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
30599 __PYX_ERR(0, 886, __pyx_L1_error)
30600 }
30601
30602 /* "pysam/libcvcf.pyx":885
30603 * def write_data(self, stream, data):
30604 * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
30605 * for k in required: # <<<<<<<<<<<<<<
30606 * if k not in data: raise ValueError("Required key %s not found in data" % str(k))
30607 * if data['alt'] == []: alt = "."
30608 */
30609 }
30610 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
30611
30612 /* "pysam/libcvcf.pyx":887
30613 * for k in required:
30614 * if k not in data: raise ValueError("Required key %s not found in data" % str(k))
30615 * if data['alt'] == []: alt = "." # <<<<<<<<<<<<<<
30616 * else: alt = ",".join(data['alt'])
30617 * if data['filter'] == None: filter = "."
30618 */
30619 __pyx_t_3 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_alt); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 887, __pyx_L1_error)
30620 __Pyx_GOTREF(__pyx_t_3);
30621 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 887, __pyx_L1_error)
30622 __Pyx_GOTREF(__pyx_t_2);
30623 __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 887, __pyx_L1_error)
30624 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
30625 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
30626 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 887, __pyx_L1_error)
30627 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
30628 if (__pyx_t_6) {
30629 __Pyx_INCREF(__pyx_kp_u__5);
30630 __pyx_v_alt = __pyx_kp_u__5;
30631 goto __pyx_L7;
30632 }
30633
30634 /* "pysam/libcvcf.pyx":888
30635 * if k not in data: raise ValueError("Required key %s not found in data" % str(k))
30636 * if data['alt'] == []: alt = "."
30637 * else: alt = ",".join(data['alt']) # <<<<<<<<<<<<<<
30638 * if data['filter'] == None: filter = "."
30639 * elif data['filter'] == []:
30640 */
30641 /*else*/ {
30642 __pyx_t_1 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_alt); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 888, __pyx_L1_error)
30643 __Pyx_GOTREF(__pyx_t_1);
30644 __pyx_t_2 = PyUnicode_Join(__pyx_kp_u__2, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 888, __pyx_L1_error)
30645 __Pyx_GOTREF(__pyx_t_2);
30646 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
30647 __pyx_v_alt = ((PyObject*)__pyx_t_2);
30648 __pyx_t_2 = 0;
30649 }
30650 __pyx_L7:;
30651
30652 /* "pysam/libcvcf.pyx":889
30653 * if data['alt'] == []: alt = "."
30654 * else: alt = ",".join(data['alt'])
30655 * if data['filter'] == None: filter = "." # <<<<<<<<<<<<<<
30656 * elif data['filter'] == []:
30657 * if self._version == 33: filter = "0"
30658 */
30659 __pyx_t_2 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_filter_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 889, __pyx_L1_error)
30660 __Pyx_GOTREF(__pyx_t_2);
30661 __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 889, __pyx_L1_error)
30662 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
30663 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 889, __pyx_L1_error)
30664 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
30665 if (__pyx_t_6) {
30666 __Pyx_INCREF(__pyx_kp_u__5);
30667 __pyx_v_filter = __pyx_kp_u__5;
30668 goto __pyx_L8;
30669 }
30670
30671 /* "pysam/libcvcf.pyx":890
30672 * else: alt = ",".join(data['alt'])
30673 * if data['filter'] == None: filter = "."
30674 * elif data['filter'] == []: # <<<<<<<<<<<<<<
30675 * if self._version == 33: filter = "0"
30676 * else: filter = "PASS"
30677 */
30678 __pyx_t_1 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_filter_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 890, __pyx_L1_error)
30679 __Pyx_GOTREF(__pyx_t_1);
30680 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 890, __pyx_L1_error)
30681 __Pyx_GOTREF(__pyx_t_2);
30682 __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 890, __pyx_L1_error)
30683 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
30684 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
30685 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 890, __pyx_L1_error)
30686 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
30687 if (__pyx_t_6) {
30688
30689 /* "pysam/libcvcf.pyx":891
30690 * if data['filter'] == None: filter = "."
30691 * elif data['filter'] == []:
30692 * if self._version == 33: filter = "0" # <<<<<<<<<<<<<<
30693 * else: filter = "PASS"
30694 * else: filter = ';'.join(data['filter'])
30695 */
30696 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_version); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 891, __pyx_L1_error)
30697 __Pyx_GOTREF(__pyx_t_3);
30698 __pyx_t_6 = (__Pyx_PyInt_BoolEqObjC(__pyx_t_3, __pyx_int_33, 33, 0)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 891, __pyx_L1_error)
30699 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
30700 if (__pyx_t_6) {
30701 __Pyx_INCREF(__pyx_kp_u_0);
30702 __pyx_v_filter = __pyx_kp_u_0;
30703 goto __pyx_L9;
30704 }
30705
30706 /* "pysam/libcvcf.pyx":892
30707 * elif data['filter'] == []:
30708 * if self._version == 33: filter = "0"
30709 * else: filter = "PASS" # <<<<<<<<<<<<<<
30710 * else: filter = ';'.join(data['filter'])
30711 * if data['qual'] == -1: qual = "."
30712 */
30713 /*else*/ {
30714 __Pyx_INCREF(__pyx_n_u_PASS);
30715 __pyx_v_filter = __pyx_n_u_PASS;
30716 }
30717 __pyx_L9:;
30718
30719 /* "pysam/libcvcf.pyx":890
30720 * else: alt = ",".join(data['alt'])
30721 * if data['filter'] == None: filter = "."
30722 * elif data['filter'] == []: # <<<<<<<<<<<<<<
30723 * if self._version == 33: filter = "0"
30724 * else: filter = "PASS"
30725 */
30726 goto __pyx_L8;
30727 }
30728
30729 /* "pysam/libcvcf.pyx":893
30730 * if self._version == 33: filter = "0"
30731 * else: filter = "PASS"
30732 * else: filter = ';'.join(data['filter']) # <<<<<<<<<<<<<<
30733 * if data['qual'] == -1: qual = "."
30734 * else: qual = str(data['qual'])
30735 */
30736 /*else*/ {
30737 __pyx_t_3 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_filter_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 893, __pyx_L1_error)
30738 __Pyx_GOTREF(__pyx_t_3);
30739 __pyx_t_2 = PyUnicode_Join(__pyx_kp_u__6, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 893, __pyx_L1_error)
30740 __Pyx_GOTREF(__pyx_t_2);
30741 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
30742 __pyx_v_filter = ((PyObject*)__pyx_t_2);
30743 __pyx_t_2 = 0;
30744 }
30745 __pyx_L8:;
30746
30747 /* "pysam/libcvcf.pyx":894
30748 * else: filter = "PASS"
30749 * else: filter = ';'.join(data['filter'])
30750 * if data['qual'] == -1: qual = "." # <<<<<<<<<<<<<<
30751 * else: qual = str(data['qual'])
30752 *
30753 */
30754 __pyx_t_2 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_qual); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 894, __pyx_L1_error)
30755 __Pyx_GOTREF(__pyx_t_2);
30756 __pyx_t_6 = (__Pyx_PyInt_BoolEqObjC(__pyx_t_2, __pyx_int_neg_1, -1L, 0)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 894, __pyx_L1_error)
30757 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
30758 if (__pyx_t_6) {
30759 __Pyx_INCREF(__pyx_kp_u__5);
30760 __pyx_v_qual = __pyx_kp_u__5;
30761 goto __pyx_L10;
30762 }
30763
30764 /* "pysam/libcvcf.pyx":895
30765 * else: filter = ';'.join(data['filter'])
30766 * if data['qual'] == -1: qual = "."
30767 * else: qual = str(data['qual']) # <<<<<<<<<<<<<<
30768 *
30769 * output = [data['chrom'],
30770 */
30771 /*else*/ {
30772 __pyx_t_2 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_qual); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 895, __pyx_L1_error)
30773 __Pyx_GOTREF(__pyx_t_2);
30774 __pyx_t_3 = __Pyx_PyObject_Unicode(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 895, __pyx_L1_error)
30775 __Pyx_GOTREF(__pyx_t_3);
30776 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
30777 __pyx_v_qual = __pyx_t_3;
30778 __pyx_t_3 = 0;
30779 }
30780 __pyx_L10:;
30781
30782 /* "pysam/libcvcf.pyx":897
30783 * else: qual = str(data['qual'])
30784 *
30785 * output = [data['chrom'], # <<<<<<<<<<<<<<
30786 * str(data['pos']+1), # change to 1-based position
30787 * data['id'],
30788 */
30789 __pyx_t_3 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_chrom); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 897, __pyx_L1_error)
30790 __Pyx_GOTREF(__pyx_t_3);
30791
30792 /* "pysam/libcvcf.pyx":898
30793 *
30794 * output = [data['chrom'],
30795 * str(data['pos']+1), # change to 1-based position # <<<<<<<<<<<<<<
30796 * data['id'],
30797 * data['ref'],
30798 */
30799 __pyx_t_2 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_pos); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 898, __pyx_L1_error)
30800 __Pyx_GOTREF(__pyx_t_2);
30801 __pyx_t_1 = __Pyx_PyInt_AddObjC(__pyx_t_2, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 898, __pyx_L1_error)
30802 __Pyx_GOTREF(__pyx_t_1);
30803 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
30804 __pyx_t_2 = __Pyx_PyObject_Unicode(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 898, __pyx_L1_error)
30805 __Pyx_GOTREF(__pyx_t_2);
30806 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
30807
30808 /* "pysam/libcvcf.pyx":899
30809 * output = [data['chrom'],
30810 * str(data['pos']+1), # change to 1-based position
30811 * data['id'], # <<<<<<<<<<<<<<
30812 * data['ref'],
30813 * alt,
30814 */
30815 __pyx_t_1 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_id_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 899, __pyx_L1_error)
30816 __Pyx_GOTREF(__pyx_t_1);
30817
30818 /* "pysam/libcvcf.pyx":900
30819 * str(data['pos']+1), # change to 1-based position
30820 * data['id'],
30821 * data['ref'], # <<<<<<<<<<<<<<
30822 * alt,
30823 * qual,
30824 */
30825 __pyx_t_7 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_ref); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 900, __pyx_L1_error)
30826 __Pyx_GOTREF(__pyx_t_7);
30827
30828 /* "pysam/libcvcf.pyx":904
30829 * qual,
30830 * filter,
30831 * self.format_formatdata( # <<<<<<<<<<<<<<
30832 * data['info'], self._info, separator=";"),
30833 * self.format_formatdata(
30834 */
30835 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_formatdata); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 904, __pyx_L1_error)
30836 __Pyx_GOTREF(__pyx_t_8);
30837
30838 /* "pysam/libcvcf.pyx":905
30839 * filter,
30840 * self.format_formatdata(
30841 * data['info'], self._info, separator=";"), # <<<<<<<<<<<<<<
30842 * self.format_formatdata(
30843 * data['format'], self._format, value=False)]
30844 */
30845 __pyx_t_9 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_info_2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 905, __pyx_L1_error)
30846 __Pyx_GOTREF(__pyx_t_9);
30847 __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_info); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 905, __pyx_L1_error)
30848 __Pyx_GOTREF(__pyx_t_10);
30849
30850 /* "pysam/libcvcf.pyx":904
30851 * qual,
30852 * filter,
30853 * self.format_formatdata( # <<<<<<<<<<<<<<
30854 * data['info'], self._info, separator=";"),
30855 * self.format_formatdata(
30856 */
30857 __pyx_t_11 = PyTuple_New(2); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 904, __pyx_L1_error)
30858 __Pyx_GOTREF(__pyx_t_11);
30859 __Pyx_GIVEREF(__pyx_t_9);
30860 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_9)) __PYX_ERR(0, 904, __pyx_L1_error);
30861 __Pyx_GIVEREF(__pyx_t_10);
30862 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_11, 1, __pyx_t_10)) __PYX_ERR(0, 904, __pyx_L1_error);
30863 __pyx_t_9 = 0;
30864 __pyx_t_10 = 0;
30865
30866 /* "pysam/libcvcf.pyx":905
30867 * filter,
30868 * self.format_formatdata(
30869 * data['info'], self._info, separator=";"), # <<<<<<<<<<<<<<
30870 * self.format_formatdata(
30871 * data['format'], self._format, value=False)]
30872 */
30873 __pyx_t_10 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 905, __pyx_L1_error)
30874 __Pyx_GOTREF(__pyx_t_10);
30875 if (PyDict_SetItem(__pyx_t_10, __pyx_n_s_separator, __pyx_kp_u__6) < 0) __PYX_ERR(0, 905, __pyx_L1_error)
30876
30877 /* "pysam/libcvcf.pyx":904
30878 * qual,
30879 * filter,
30880 * self.format_formatdata( # <<<<<<<<<<<<<<
30881 * data['info'], self._info, separator=";"),
30882 * self.format_formatdata(
30883 */
30884 __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_t_11, __pyx_t_10); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 904, __pyx_L1_error)
30885 __Pyx_GOTREF(__pyx_t_9);
30886 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
30887 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
30888 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
30889
30890 /* "pysam/libcvcf.pyx":906
30891 * self.format_formatdata(
30892 * data['info'], self._info, separator=";"),
30893 * self.format_formatdata( # <<<<<<<<<<<<<<
30894 * data['format'], self._format, value=False)]
30895 *
30896 */
30897 __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_formatdata); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 906, __pyx_L1_error)
30898 __Pyx_GOTREF(__pyx_t_10);
30899
30900 /* "pysam/libcvcf.pyx":907
30901 * data['info'], self._info, separator=";"),
30902 * self.format_formatdata(
30903 * data['format'], self._format, value=False)] # <<<<<<<<<<<<<<
30904 *
30905 * for s in self._samples:
30906 */
30907 __pyx_t_11 = __Pyx_PyObject_Dict_GetItem(__pyx_v_data, __pyx_n_u_format); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 907, __pyx_L1_error)
30908 __Pyx_GOTREF(__pyx_t_11);
30909 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 907, __pyx_L1_error)
30910 __Pyx_GOTREF(__pyx_t_8);
30911
30912 /* "pysam/libcvcf.pyx":906
30913 * self.format_formatdata(
30914 * data['info'], self._info, separator=";"),
30915 * self.format_formatdata( # <<<<<<<<<<<<<<
30916 * data['format'], self._format, value=False)]
30917 *
30918 */
30919 __pyx_t_12 = PyTuple_New(2); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 906, __pyx_L1_error)
30920 __Pyx_GOTREF(__pyx_t_12);
30921 __Pyx_GIVEREF(__pyx_t_11);
30922 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_t_11)) __PYX_ERR(0, 906, __pyx_L1_error);
30923 __Pyx_GIVEREF(__pyx_t_8);
30924 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_12, 1, __pyx_t_8)) __PYX_ERR(0, 906, __pyx_L1_error);
30925 __pyx_t_11 = 0;
30926 __pyx_t_8 = 0;
30927
30928 /* "pysam/libcvcf.pyx":907
30929 * data['info'], self._info, separator=";"),
30930 * self.format_formatdata(
30931 * data['format'], self._format, value=False)] # <<<<<<<<<<<<<<
30932 *
30933 * for s in self._samples:
30934 */
30935 __pyx_t_8 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 907, __pyx_L1_error)
30936 __Pyx_GOTREF(__pyx_t_8);
30937 if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_value, Py_False) < 0) __PYX_ERR(0, 907, __pyx_L1_error)
30938
30939 /* "pysam/libcvcf.pyx":906
30940 * self.format_formatdata(
30941 * data['info'], self._info, separator=";"),
30942 * self.format_formatdata( # <<<<<<<<<<<<<<
30943 * data['format'], self._format, value=False)]
30944 *
30945 */
30946 __pyx_t_11 = __Pyx_PyObject_Call(__pyx_t_10, __pyx_t_12, __pyx_t_8); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 906, __pyx_L1_error)
30947 __Pyx_GOTREF(__pyx_t_11);
30948 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
30949 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
30950 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
30951
30952 /* "pysam/libcvcf.pyx":897
30953 * else: qual = str(data['qual'])
30954 *
30955 * output = [data['chrom'], # <<<<<<<<<<<<<<
30956 * str(data['pos']+1), # change to 1-based position
30957 * data['id'],
30958 */
30959 __pyx_t_8 = PyList_New(9); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 897, __pyx_L1_error)
30960 __Pyx_GOTREF(__pyx_t_8);
30961 __Pyx_GIVEREF(__pyx_t_3);
30962 if (__Pyx_PyList_SET_ITEM(__pyx_t_8, 0, __pyx_t_3)) __PYX_ERR(0, 897, __pyx_L1_error);
30963 __Pyx_GIVEREF(__pyx_t_2);
30964 if (__Pyx_PyList_SET_ITEM(__pyx_t_8, 1, __pyx_t_2)) __PYX_ERR(0, 897, __pyx_L1_error);
30965 __Pyx_GIVEREF(__pyx_t_1);
30966 if (__Pyx_PyList_SET_ITEM(__pyx_t_8, 2, __pyx_t_1)) __PYX_ERR(0, 897, __pyx_L1_error);
30967 __Pyx_GIVEREF(__pyx_t_7);
30968 if (__Pyx_PyList_SET_ITEM(__pyx_t_8, 3, __pyx_t_7)) __PYX_ERR(0, 897, __pyx_L1_error);
30969 __Pyx_INCREF(__pyx_v_alt);
30970 __Pyx_GIVEREF(__pyx_v_alt);
30971 if (__Pyx_PyList_SET_ITEM(__pyx_t_8, 4, __pyx_v_alt)) __PYX_ERR(0, 897, __pyx_L1_error);
30972 __Pyx_INCREF(__pyx_v_qual);
30973 __Pyx_GIVEREF(__pyx_v_qual);
30974 if (__Pyx_PyList_SET_ITEM(__pyx_t_8, 5, __pyx_v_qual)) __PYX_ERR(0, 897, __pyx_L1_error);
30975 __Pyx_INCREF(__pyx_v_filter);
30976 __Pyx_GIVEREF(__pyx_v_filter);
30977 if (__Pyx_PyList_SET_ITEM(__pyx_t_8, 6, __pyx_v_filter)) __PYX_ERR(0, 897, __pyx_L1_error);
30978 __Pyx_GIVEREF(__pyx_t_9);
30979 if (__Pyx_PyList_SET_ITEM(__pyx_t_8, 7, __pyx_t_9)) __PYX_ERR(0, 897, __pyx_L1_error);
30980 __Pyx_GIVEREF(__pyx_t_11);
30981 if (__Pyx_PyList_SET_ITEM(__pyx_t_8, 8, __pyx_t_11)) __PYX_ERR(0, 897, __pyx_L1_error);
30982 __pyx_t_3 = 0;
30983 __pyx_t_2 = 0;
30984 __pyx_t_1 = 0;
30985 __pyx_t_7 = 0;
30986 __pyx_t_9 = 0;
30987 __pyx_t_11 = 0;
30988 __pyx_v_output = ((PyObject*)__pyx_t_8);
30989 __pyx_t_8 = 0;
30990
30991 /* "pysam/libcvcf.pyx":909
30992 * data['format'], self._format, value=False)]
30993 *
30994 * for s in self._samples: # <<<<<<<<<<<<<<
30995 * output.append(self.format_formatdata(
30996 * data[s], self._format, key=False))
30997 */
30998 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_samples); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 909, __pyx_L1_error)
30999 __Pyx_GOTREF(__pyx_t_8);
31000 if (likely(PyList_CheckExact(__pyx_t_8)) || PyTuple_CheckExact(__pyx_t_8)) {
31001 __pyx_t_11 = __pyx_t_8; __Pyx_INCREF(__pyx_t_11);
31002 __pyx_t_4 = 0;
31003 __pyx_t_5 = NULL;
31004 } else {
31005 __pyx_t_4 = -1; __pyx_t_11 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 909, __pyx_L1_error)
31006 __Pyx_GOTREF(__pyx_t_11);
31007 __pyx_t_5 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_11); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 909, __pyx_L1_error)
31008 }
31009 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
31010 for (;;) {
31011 if (likely(!__pyx_t_5)) {
31012 if (likely(PyList_CheckExact(__pyx_t_11))) {
31013 {
31014 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_11);
31015 #if !CYTHON_ASSUME_SAFE_MACROS
31016 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 909, __pyx_L1_error)
31017 #endif
31018 if (__pyx_t_4 >= __pyx_temp) break;
31019 }
31020 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
31021 __pyx_t_8 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 909, __pyx_L1_error)
31022 #else
31023 __pyx_t_8 = __Pyx_PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 909, __pyx_L1_error)
31024 __Pyx_GOTREF(__pyx_t_8);
31025 #endif
31026 } else {
31027 {
31028 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_11);
31029 #if !CYTHON_ASSUME_SAFE_MACROS
31030 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 909, __pyx_L1_error)
31031 #endif
31032 if (__pyx_t_4 >= __pyx_temp) break;
31033 }
31034 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
31035 __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 909, __pyx_L1_error)
31036 #else
31037 __pyx_t_8 = __Pyx_PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 909, __pyx_L1_error)
31038 __Pyx_GOTREF(__pyx_t_8);
31039 #endif
31040 }
31041 } else {
31042 __pyx_t_8 = __pyx_t_5(__pyx_t_11);
31043 if (unlikely(!__pyx_t_8)) {
31044 PyObject* exc_type = PyErr_Occurred();
31045 if (exc_type) {
31046 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
31047 else __PYX_ERR(0, 909, __pyx_L1_error)
31048 }
31049 break;
31050 }
31051 __Pyx_GOTREF(__pyx_t_8);
31052 }
31053 __Pyx_XDECREF_SET(__pyx_v_s, __pyx_t_8);
31054 __pyx_t_8 = 0;
31055
31056 /* "pysam/libcvcf.pyx":910
31057 *
31058 * for s in self._samples:
31059 * output.append(self.format_formatdata( # <<<<<<<<<<<<<<
31060 * data[s], self._format, key=False))
31061 *
31062 */
31063 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_formatdata); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 910, __pyx_L1_error)
31064 __Pyx_GOTREF(__pyx_t_8);
31065
31066 /* "pysam/libcvcf.pyx":911
31067 * for s in self._samples:
31068 * output.append(self.format_formatdata(
31069 * data[s], self._format, key=False)) # <<<<<<<<<<<<<<
31070 *
31071 * stream.write( "\t".join(output) + "\n" )
31072 */
31073 __pyx_t_9 = __Pyx_PyObject_GetItem(__pyx_v_data, __pyx_v_s); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 911, __pyx_L1_error)
31074 __Pyx_GOTREF(__pyx_t_9);
31075 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_2); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 911, __pyx_L1_error)
31076 __Pyx_GOTREF(__pyx_t_7);
31077
31078 /* "pysam/libcvcf.pyx":910
31079 *
31080 * for s in self._samples:
31081 * output.append(self.format_formatdata( # <<<<<<<<<<<<<<
31082 * data[s], self._format, key=False))
31083 *
31084 */
31085 __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 910, __pyx_L1_error)
31086 __Pyx_GOTREF(__pyx_t_1);
31087 __Pyx_GIVEREF(__pyx_t_9);
31088 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9)) __PYX_ERR(0, 910, __pyx_L1_error);
31089 __Pyx_GIVEREF(__pyx_t_7);
31090 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_7)) __PYX_ERR(0, 910, __pyx_L1_error);
31091 __pyx_t_9 = 0;
31092 __pyx_t_7 = 0;
31093
31094 /* "pysam/libcvcf.pyx":911
31095 * for s in self._samples:
31096 * output.append(self.format_formatdata(
31097 * data[s], self._format, key=False)) # <<<<<<<<<<<<<<
31098 *
31099 * stream.write( "\t".join(output) + "\n" )
31100 */
31101 __pyx_t_7 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 911, __pyx_L1_error)
31102 __Pyx_GOTREF(__pyx_t_7);
31103 if (PyDict_SetItem(__pyx_t_7, __pyx_n_s_key, Py_False) < 0) __PYX_ERR(0, 911, __pyx_L1_error)
31104
31105 /* "pysam/libcvcf.pyx":910
31106 *
31107 * for s in self._samples:
31108 * output.append(self.format_formatdata( # <<<<<<<<<<<<<<
31109 * data[s], self._format, key=False))
31110 *
31111 */
31112 __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_t_1, __pyx_t_7); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 910, __pyx_L1_error)
31113 __Pyx_GOTREF(__pyx_t_9);
31114 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
31115 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
31116 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
31117 __pyx_t_13 = __Pyx_PyList_Append(__pyx_v_output, __pyx_t_9); if (unlikely(__pyx_t_13 == ((int)-1))) __PYX_ERR(0, 910, __pyx_L1_error)
31118 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
31119
31120 /* "pysam/libcvcf.pyx":909
31121 * data['format'], self._format, value=False)]
31122 *
31123 * for s in self._samples: # <<<<<<<<<<<<<<
31124 * output.append(self.format_formatdata(
31125 * data[s], self._format, key=False))
31126 */
31127 }
31128 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
31129
31130 /* "pysam/libcvcf.pyx":913
31131 * data[s], self._format, key=False))
31132 *
31133 * stream.write( "\t".join(output) + "\n" ) # <<<<<<<<<<<<<<
31134 *
31135 * def _parse_header(self, stream):
31136 */
31137 __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_stream, __pyx_n_s_write); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 913, __pyx_L1_error)
31138 __Pyx_GOTREF(__pyx_t_9);
31139 __pyx_t_7 = PyUnicode_Join(__pyx_kp_u__25, __pyx_v_output); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 913, __pyx_L1_error)
31140 __Pyx_GOTREF(__pyx_t_7);
31141 __pyx_t_1 = __Pyx_PyUnicode_ConcatInPlace(__pyx_t_7, __pyx_kp_u__14); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 913, __pyx_L1_error)
31142 __Pyx_GOTREF(__pyx_t_1);
31143 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
31144 __pyx_t_7 = NULL;
31145 __pyx_t_14 = 0;
31146 #if CYTHON_UNPACK_METHODS
31147 if (likely(PyMethod_Check(__pyx_t_9))) {
31148 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_9);
31149 if (likely(__pyx_t_7)) {
31150 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_9);
31151 __Pyx_INCREF(__pyx_t_7);
31152 __Pyx_INCREF(function);
31153 __Pyx_DECREF_SET(__pyx_t_9, function);
31154 __pyx_t_14 = 1;
31155 }
31156 }
31157 #endif
31158 {
31159 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_1};
31160 __pyx_t_11 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_14, 1+__pyx_t_14);
31161 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
31162 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
31163 if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 913, __pyx_L1_error)
31164 __Pyx_GOTREF(__pyx_t_11);
31165 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
31166 }
31167 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
31168
31169 /* "pysam/libcvcf.pyx":883
31170 *
31171 *
31172 * def write_data(self, stream, data): # <<<<<<<<<<<<<<
31173 * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
31174 * for k in required:
31175 */
31176
31177 /* function exit code */
31178 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
31179 goto __pyx_L0;
31180 __pyx_L1_error:;
31181 __Pyx_XDECREF(__pyx_t_1);
31182 __Pyx_XDECREF(__pyx_t_2);
31183 __Pyx_XDECREF(__pyx_t_3);
31184 __Pyx_XDECREF(__pyx_t_7);
31185 __Pyx_XDECREF(__pyx_t_8);
31186 __Pyx_XDECREF(__pyx_t_9);
31187 __Pyx_XDECREF(__pyx_t_10);
31188 __Pyx_XDECREF(__pyx_t_11);
31189 __Pyx_XDECREF(__pyx_t_12);
31190 __Pyx_AddTraceback("pysam.libcvcf.VCF.write_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
31191 __pyx_r = NULL;
31192 __pyx_L0:;
31193 __Pyx_XDECREF(__pyx_v_required);
31194 __Pyx_XDECREF(__pyx_v_k);
31195 __Pyx_XDECREF(__pyx_v_alt);
31196 __Pyx_XDECREF(__pyx_v_filter);
31197 __Pyx_XDECREF(__pyx_v_qual);
31198 __Pyx_XDECREF(__pyx_v_output);
31199 __Pyx_XDECREF(__pyx_v_s);
31200 __Pyx_XGIVEREF(__pyx_r);
31201 __Pyx_RefNannyFinishContext();
31202 return __pyx_r;
31203 }
31204
31205 /* "pysam/libcvcf.pyx":915
31206 * stream.write( "\t".join(output) + "\n" )
31207 *
31208 * def _parse_header(self, stream): # <<<<<<<<<<<<<<
31209 * self._lineno = 0
31210 * for line in stream:
31211 */
31212
31213 /* Python wrapper */
31214 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_37_parse_header(PyObject *__pyx_self,
31215 #if CYTHON_METH_FASTCALL
31216 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
31217 #else
31218 PyObject *__pyx_args, PyObject *__pyx_kwds
31219 #endif
31220 ); /*proto*/
31221 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_36_parse_header, "VCF._parse_header(self, stream)");
31222 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_37_parse_header = {"_parse_header", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_37_parse_header, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_36_parse_header};
31223 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_37_parse_header(PyObject *__pyx_self,
31224 #if CYTHON_METH_FASTCALL
31225 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
31226 #else
31227 PyObject *__pyx_args, PyObject *__pyx_kwds
31228 #endif
31229 ) {
31230 PyObject *__pyx_v_self = 0;
31231 PyObject *__pyx_v_stream = 0;
31232 #if !CYTHON_METH_FASTCALL
31233 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
31234 #endif
31235 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
31236 PyObject* values[2] = {0,0};
31237 int __pyx_lineno = 0;
31238 const char *__pyx_filename = NULL;
31239 int __pyx_clineno = 0;
31240 PyObject *__pyx_r = 0;
31241 __Pyx_RefNannyDeclarations
31242 __Pyx_RefNannySetupContext("_parse_header (wrapper)", 0);
31243 #if !CYTHON_METH_FASTCALL
31244 #if CYTHON_ASSUME_SAFE_MACROS
31245 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
31246 #else
31247 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
31248 #endif
31249 #endif
31250 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
31251 {
31252 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_stream,0};
31253 if (__pyx_kwds) {
31254 Py_ssize_t kw_args;
31255 switch (__pyx_nargs) {
31256 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
31257 CYTHON_FALLTHROUGH;
31258 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
31259 CYTHON_FALLTHROUGH;
31260 case 0: break;
31261 default: goto __pyx_L5_argtuple_error;
31262 }
31263 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
31264 switch (__pyx_nargs) {
31265 case 0:
31266 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
31267 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
31268 kw_args--;
31269 }
31270 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 915, __pyx_L3_error)
31271 else goto __pyx_L5_argtuple_error;
31272 CYTHON_FALLTHROUGH;
31273 case 1:
31274 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_stream)) != 0)) {
31275 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
31276 kw_args--;
31277 }
31278 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 915, __pyx_L3_error)
31279 else {
31280 __Pyx_RaiseArgtupleInvalid("_parse_header", 1, 2, 2, 1); __PYX_ERR(0, 915, __pyx_L3_error)
31281 }
31282 }
31283 if (unlikely(kw_args > 0)) {
31284 const Py_ssize_t kwd_pos_args = __pyx_nargs;
31285 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "_parse_header") < 0)) __PYX_ERR(0, 915, __pyx_L3_error)
31286 }
31287 } else if (unlikely(__pyx_nargs != 2)) {
31288 goto __pyx_L5_argtuple_error;
31289 } else {
31290 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
31291 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
31292 }
31293 __pyx_v_self = values[0];
31294 __pyx_v_stream = values[1];
31295 }
31296 goto __pyx_L6_skip;
31297 __pyx_L5_argtuple_error:;
31298 __Pyx_RaiseArgtupleInvalid("_parse_header", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 915, __pyx_L3_error)
31299 __pyx_L6_skip:;
31300 goto __pyx_L4_argument_unpacking_done;
31301 __pyx_L3_error:;
31302 {
31303 Py_ssize_t __pyx_temp;
31304 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
31305 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
31306 }
31307 }
31308 __Pyx_AddTraceback("pysam.libcvcf.VCF._parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename);
31309 __Pyx_RefNannyFinishContext();
31310 return NULL;
31311 __pyx_L4_argument_unpacking_done:;
31312 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_36_parse_header(__pyx_self, __pyx_v_self, __pyx_v_stream);
31313
31314 /* function exit code */
31315 {
31316 Py_ssize_t __pyx_temp;
31317 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
31318 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
31319 }
31320 }
31321 __Pyx_RefNannyFinishContext();
31322 return __pyx_r;
31323 }
31324
31325 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) {
31326 PyObject *__pyx_v_line = NULL;
31327 PyObject *__pyx_r = NULL;
31328 __Pyx_RefNannyDeclarations
31329 PyObject *__pyx_t_1 = NULL;
31330 Py_ssize_t __pyx_t_2;
31331 PyObject *(*__pyx_t_3)(PyObject *);
31332 PyObject *__pyx_t_4 = NULL;
31333 PyObject *__pyx_t_5 = NULL;
31334 struct __pyx_opt_args_5pysam_9libcutils_force_str __pyx_t_6;
31335 PyObject *__pyx_t_7 = NULL;
31336 unsigned int __pyx_t_8;
31337 int __pyx_t_9;
31338 PyObject *__pyx_t_10 = NULL;
31339 PyObject *__pyx_t_11 = NULL;
31340 int __pyx_lineno = 0;
31341 const char *__pyx_filename = NULL;
31342 int __pyx_clineno = 0;
31343 __Pyx_RefNannySetupContext("_parse_header", 1);
31344
31345 /* "pysam/libcvcf.pyx":916
31346 *
31347 * def _parse_header(self, stream):
31348 * self._lineno = 0 # <<<<<<<<<<<<<<
31349 * for line in stream:
31350 * line = force_str(line, self.encoding)
31351 */
31352 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_lineno, __pyx_int_0) < 0) __PYX_ERR(0, 916, __pyx_L1_error)
31353
31354 /* "pysam/libcvcf.pyx":917
31355 * def _parse_header(self, stream):
31356 * self._lineno = 0
31357 * for line in stream: # <<<<<<<<<<<<<<
31358 * line = force_str(line, self.encoding)
31359 * self._lineno += 1
31360 */
31361 if (likely(PyList_CheckExact(__pyx_v_stream)) || PyTuple_CheckExact(__pyx_v_stream)) {
31362 __pyx_t_1 = __pyx_v_stream; __Pyx_INCREF(__pyx_t_1);
31363 __pyx_t_2 = 0;
31364 __pyx_t_3 = NULL;
31365 } else {
31366 __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_stream); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 917, __pyx_L1_error)
31367 __Pyx_GOTREF(__pyx_t_1);
31368 __pyx_t_3 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 917, __pyx_L1_error)
31369 }
31370 for (;;) {
31371 if (likely(!__pyx_t_3)) {
31372 if (likely(PyList_CheckExact(__pyx_t_1))) {
31373 {
31374 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1);
31375 #if !CYTHON_ASSUME_SAFE_MACROS
31376 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 917, __pyx_L1_error)
31377 #endif
31378 if (__pyx_t_2 >= __pyx_temp) break;
31379 }
31380 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
31381 __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely((0 < 0))) __PYX_ERR(0, 917, __pyx_L1_error)
31382 #else
31383 __pyx_t_4 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 917, __pyx_L1_error)
31384 __Pyx_GOTREF(__pyx_t_4);
31385 #endif
31386 } else {
31387 {
31388 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1);
31389 #if !CYTHON_ASSUME_SAFE_MACROS
31390 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 917, __pyx_L1_error)
31391 #endif
31392 if (__pyx_t_2 >= __pyx_temp) break;
31393 }
31394 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
31395 __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely((0 < 0))) __PYX_ERR(0, 917, __pyx_L1_error)
31396 #else
31397 __pyx_t_4 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 917, __pyx_L1_error)
31398 __Pyx_GOTREF(__pyx_t_4);
31399 #endif
31400 }
31401 } else {
31402 __pyx_t_4 = __pyx_t_3(__pyx_t_1);
31403 if (unlikely(!__pyx_t_4)) {
31404 PyObject* exc_type = PyErr_Occurred();
31405 if (exc_type) {
31406 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
31407 else __PYX_ERR(0, 917, __pyx_L1_error)
31408 }
31409 break;
31410 }
31411 __Pyx_GOTREF(__pyx_t_4);
31412 }
31413 __Pyx_XDECREF_SET(__pyx_v_line, __pyx_t_4);
31414 __pyx_t_4 = 0;
31415
31416 /* "pysam/libcvcf.pyx":918
31417 * self._lineno = 0
31418 * for line in stream:
31419 * line = force_str(line, self.encoding) # <<<<<<<<<<<<<<
31420 * self._lineno += 1
31421 * if line.startswith('##'):
31422 */
31423 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_encoding); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 918, __pyx_L1_error)
31424 __Pyx_GOTREF(__pyx_t_4);
31425 __pyx_t_6.__pyx_n = 1;
31426 __pyx_t_6.encoding = __pyx_t_4;
31427 __pyx_t_5 = __pyx_f_5pysam_9libcutils_force_str(__pyx_v_line, &__pyx_t_6); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 918, __pyx_L1_error)
31428 __Pyx_GOTREF(__pyx_t_5);
31429 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
31430 __Pyx_DECREF_SET(__pyx_v_line, __pyx_t_5);
31431 __pyx_t_5 = 0;
31432
31433 /* "pysam/libcvcf.pyx":919
31434 * for line in stream:
31435 * line = force_str(line, self.encoding)
31436 * self._lineno += 1 # <<<<<<<<<<<<<<
31437 * if line.startswith('##'):
31438 * self.parse_header(line.strip())
31439 */
31440 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_lineno); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 919, __pyx_L1_error)
31441 __Pyx_GOTREF(__pyx_t_5);
31442 __pyx_t_4 = __Pyx_PyInt_AddObjC(__pyx_t_5, __pyx_int_1, 1, 1, 0); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 919, __pyx_L1_error)
31443 __Pyx_GOTREF(__pyx_t_4);
31444 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
31445 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_lineno, __pyx_t_4) < 0) __PYX_ERR(0, 919, __pyx_L1_error)
31446 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
31447
31448 /* "pysam/libcvcf.pyx":920
31449 * line = force_str(line, self.encoding)
31450 * self._lineno += 1
31451 * if line.startswith('##'): # <<<<<<<<<<<<<<
31452 * self.parse_header(line.strip())
31453 * elif line.startswith('#'):
31454 */
31455 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_startswith); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 920, __pyx_L1_error)
31456 __Pyx_GOTREF(__pyx_t_5);
31457 __pyx_t_7 = NULL;
31458 __pyx_t_8 = 0;
31459 #if CYTHON_UNPACK_METHODS
31460 if (likely(PyMethod_Check(__pyx_t_5))) {
31461 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_5);
31462 if (likely(__pyx_t_7)) {
31463 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
31464 __Pyx_INCREF(__pyx_t_7);
31465 __Pyx_INCREF(function);
31466 __Pyx_DECREF_SET(__pyx_t_5, function);
31467 __pyx_t_8 = 1;
31468 }
31469 }
31470 #endif
31471 {
31472 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_kp_u__23};
31473 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
31474 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
31475 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 920, __pyx_L1_error)
31476 __Pyx_GOTREF(__pyx_t_4);
31477 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
31478 }
31479 __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_9 < 0))) __PYX_ERR(0, 920, __pyx_L1_error)
31480 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
31481 if (__pyx_t_9) {
31482
31483 /* "pysam/libcvcf.pyx":921
31484 * self._lineno += 1
31485 * if line.startswith('##'):
31486 * self.parse_header(line.strip()) # <<<<<<<<<<<<<<
31487 * elif line.startswith('#'):
31488 * self.parse_heading(line.strip())
31489 */
31490 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parse_header); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 921, __pyx_L1_error)
31491 __Pyx_GOTREF(__pyx_t_5);
31492 __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_strip); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 921, __pyx_L1_error)
31493 __Pyx_GOTREF(__pyx_t_10);
31494 __pyx_t_11 = NULL;
31495 __pyx_t_8 = 0;
31496 #if CYTHON_UNPACK_METHODS
31497 if (likely(PyMethod_Check(__pyx_t_10))) {
31498 __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_10);
31499 if (likely(__pyx_t_11)) {
31500 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_10);
31501 __Pyx_INCREF(__pyx_t_11);
31502 __Pyx_INCREF(function);
31503 __Pyx_DECREF_SET(__pyx_t_10, function);
31504 __pyx_t_8 = 1;
31505 }
31506 }
31507 #endif
31508 {
31509 PyObject *__pyx_callargs[2] = {__pyx_t_11, NULL};
31510 __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_10, __pyx_callargs+1-__pyx_t_8, 0+__pyx_t_8);
31511 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
31512 if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 921, __pyx_L1_error)
31513 __Pyx_GOTREF(__pyx_t_7);
31514 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
31515 }
31516 __pyx_t_10 = NULL;
31517 __pyx_t_8 = 0;
31518 #if CYTHON_UNPACK_METHODS
31519 if (likely(PyMethod_Check(__pyx_t_5))) {
31520 __pyx_t_10 = PyMethod_GET_SELF(__pyx_t_5);
31521 if (likely(__pyx_t_10)) {
31522 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
31523 __Pyx_INCREF(__pyx_t_10);
31524 __Pyx_INCREF(function);
31525 __Pyx_DECREF_SET(__pyx_t_5, function);
31526 __pyx_t_8 = 1;
31527 }
31528 }
31529 #endif
31530 {
31531 PyObject *__pyx_callargs[2] = {__pyx_t_10, __pyx_t_7};
31532 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
31533 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
31534 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
31535 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 921, __pyx_L1_error)
31536 __Pyx_GOTREF(__pyx_t_4);
31537 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
31538 }
31539 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
31540
31541 /* "pysam/libcvcf.pyx":920
31542 * line = force_str(line, self.encoding)
31543 * self._lineno += 1
31544 * if line.startswith('##'): # <<<<<<<<<<<<<<
31545 * self.parse_header(line.strip())
31546 * elif line.startswith('#'):
31547 */
31548 goto __pyx_L5;
31549 }
31550
31551 /* "pysam/libcvcf.pyx":922
31552 * if line.startswith('##'):
31553 * self.parse_header(line.strip())
31554 * elif line.startswith('#'): # <<<<<<<<<<<<<<
31555 * self.parse_heading(line.strip())
31556 * self.enter_default_format()
31557 */
31558 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_startswith); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 922, __pyx_L1_error)
31559 __Pyx_GOTREF(__pyx_t_5);
31560 __pyx_t_7 = NULL;
31561 __pyx_t_8 = 0;
31562 #if CYTHON_UNPACK_METHODS
31563 if (likely(PyMethod_Check(__pyx_t_5))) {
31564 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_5);
31565 if (likely(__pyx_t_7)) {
31566 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
31567 __Pyx_INCREF(__pyx_t_7);
31568 __Pyx_INCREF(function);
31569 __Pyx_DECREF_SET(__pyx_t_5, function);
31570 __pyx_t_8 = 1;
31571 }
31572 }
31573 #endif
31574 {
31575 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_kp_u__24};
31576 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
31577 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
31578 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 922, __pyx_L1_error)
31579 __Pyx_GOTREF(__pyx_t_4);
31580 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
31581 }
31582 __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_9 < 0))) __PYX_ERR(0, 922, __pyx_L1_error)
31583 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
31584 if (__pyx_t_9) {
31585
31586 /* "pysam/libcvcf.pyx":923
31587 * self.parse_header(line.strip())
31588 * elif line.startswith('#'):
31589 * self.parse_heading(line.strip()) # <<<<<<<<<<<<<<
31590 * self.enter_default_format()
31591 * else:
31592 */
31593 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parse_heading); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 923, __pyx_L1_error)
31594 __Pyx_GOTREF(__pyx_t_5);
31595 __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_strip); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 923, __pyx_L1_error)
31596 __Pyx_GOTREF(__pyx_t_10);
31597 __pyx_t_11 = NULL;
31598 __pyx_t_8 = 0;
31599 #if CYTHON_UNPACK_METHODS
31600 if (likely(PyMethod_Check(__pyx_t_10))) {
31601 __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_10);
31602 if (likely(__pyx_t_11)) {
31603 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_10);
31604 __Pyx_INCREF(__pyx_t_11);
31605 __Pyx_INCREF(function);
31606 __Pyx_DECREF_SET(__pyx_t_10, function);
31607 __pyx_t_8 = 1;
31608 }
31609 }
31610 #endif
31611 {
31612 PyObject *__pyx_callargs[2] = {__pyx_t_11, NULL};
31613 __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_10, __pyx_callargs+1-__pyx_t_8, 0+__pyx_t_8);
31614 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
31615 if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 923, __pyx_L1_error)
31616 __Pyx_GOTREF(__pyx_t_7);
31617 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
31618 }
31619 __pyx_t_10 = NULL;
31620 __pyx_t_8 = 0;
31621 #if CYTHON_UNPACK_METHODS
31622 if (likely(PyMethod_Check(__pyx_t_5))) {
31623 __pyx_t_10 = PyMethod_GET_SELF(__pyx_t_5);
31624 if (likely(__pyx_t_10)) {
31625 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
31626 __Pyx_INCREF(__pyx_t_10);
31627 __Pyx_INCREF(function);
31628 __Pyx_DECREF_SET(__pyx_t_5, function);
31629 __pyx_t_8 = 1;
31630 }
31631 }
31632 #endif
31633 {
31634 PyObject *__pyx_callargs[2] = {__pyx_t_10, __pyx_t_7};
31635 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
31636 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
31637 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
31638 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 923, __pyx_L1_error)
31639 __Pyx_GOTREF(__pyx_t_4);
31640 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
31641 }
31642 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
31643
31644 /* "pysam/libcvcf.pyx":924
31645 * elif line.startswith('#'):
31646 * self.parse_heading(line.strip())
31647 * self.enter_default_format() # <<<<<<<<<<<<<<
31648 * else:
31649 * break
31650 */
31651 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_enter_default_format); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 924, __pyx_L1_error)
31652 __Pyx_GOTREF(__pyx_t_5);
31653 __pyx_t_7 = NULL;
31654 __pyx_t_8 = 0;
31655 #if CYTHON_UNPACK_METHODS
31656 if (likely(PyMethod_Check(__pyx_t_5))) {
31657 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_5);
31658 if (likely(__pyx_t_7)) {
31659 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
31660 __Pyx_INCREF(__pyx_t_7);
31661 __Pyx_INCREF(function);
31662 __Pyx_DECREF_SET(__pyx_t_5, function);
31663 __pyx_t_8 = 1;
31664 }
31665 }
31666 #endif
31667 {
31668 PyObject *__pyx_callargs[2] = {__pyx_t_7, NULL};
31669 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_8, 0+__pyx_t_8);
31670 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
31671 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 924, __pyx_L1_error)
31672 __Pyx_GOTREF(__pyx_t_4);
31673 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
31674 }
31675 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
31676
31677 /* "pysam/libcvcf.pyx":922
31678 * if line.startswith('##'):
31679 * self.parse_header(line.strip())
31680 * elif line.startswith('#'): # <<<<<<<<<<<<<<
31681 * self.parse_heading(line.strip())
31682 * self.enter_default_format()
31683 */
31684 goto __pyx_L5;
31685 }
31686
31687 /* "pysam/libcvcf.pyx":926
31688 * self.enter_default_format()
31689 * else:
31690 * break # <<<<<<<<<<<<<<
31691 * return line
31692 *
31693 */
31694 /*else*/ {
31695 goto __pyx_L4_break;
31696 }
31697 __pyx_L5:;
31698
31699 /* "pysam/libcvcf.pyx":917
31700 * def _parse_header(self, stream):
31701 * self._lineno = 0
31702 * for line in stream: # <<<<<<<<<<<<<<
31703 * line = force_str(line, self.encoding)
31704 * self._lineno += 1
31705 */
31706 }
31707 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
31708 goto __pyx_L6_for_end;
31709 __pyx_L4_break:;
31710 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
31711 goto __pyx_L6_for_end;
31712 __pyx_L6_for_end:;
31713
31714 /* "pysam/libcvcf.pyx":927
31715 * else:
31716 * break
31717 * return line # <<<<<<<<<<<<<<
31718 *
31719 * def _parse(self, line, stream):
31720 */
31721 __Pyx_XDECREF(__pyx_r);
31722 if (unlikely(!__pyx_v_line)) { __Pyx_RaiseUnboundLocalError("line"); __PYX_ERR(0, 927, __pyx_L1_error) }
31723 __Pyx_INCREF(__pyx_v_line);
31724 __pyx_r = __pyx_v_line;
31725 goto __pyx_L0;
31726
31727 /* "pysam/libcvcf.pyx":915
31728 * stream.write( "\t".join(output) + "\n" )
31729 *
31730 * def _parse_header(self, stream): # <<<<<<<<<<<<<<
31731 * self._lineno = 0
31732 * for line in stream:
31733 */
31734
31735 /* function exit code */
31736 __pyx_L1_error:;
31737 __Pyx_XDECREF(__pyx_t_1);
31738 __Pyx_XDECREF(__pyx_t_4);
31739 __Pyx_XDECREF(__pyx_t_5);
31740 __Pyx_XDECREF(__pyx_t_7);
31741 __Pyx_XDECREF(__pyx_t_10);
31742 __Pyx_XDECREF(__pyx_t_11);
31743 __Pyx_AddTraceback("pysam.libcvcf.VCF._parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename);
31744 __pyx_r = NULL;
31745 __pyx_L0:;
31746 __Pyx_XDECREF(__pyx_v_line);
31747 __Pyx_XGIVEREF(__pyx_r);
31748 __Pyx_RefNannyFinishContext();
31749 return __pyx_r;
31750 }
31751 static PyObject *__pyx_gb_5pysam_7libcvcf_3VCF_40generator(__pyx_CoroutineObject *__pyx_generator, CYTHON_UNUSED PyThreadState *__pyx_tstate, PyObject *__pyx_sent_value); /* proto */
31752
31753 /* "pysam/libcvcf.pyx":929
31754 * return line
31755 *
31756 * def _parse(self, line, stream): # <<<<<<<<<<<<<<
31757 * # deal with files with header only
31758 * if line.startswith("##"): return
31759 */
31760
31761 /* Python wrapper */
31762 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_39_parse(PyObject *__pyx_self,
31763 #if CYTHON_METH_FASTCALL
31764 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
31765 #else
31766 PyObject *__pyx_args, PyObject *__pyx_kwds
31767 #endif
31768 ); /*proto*/
31769 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_38_parse, "VCF._parse(self, line, stream)");
31770 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_39_parse = {"_parse", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_39_parse, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_38_parse};
31771 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_39_parse(PyObject *__pyx_self,
31772 #if CYTHON_METH_FASTCALL
31773 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
31774 #else
31775 PyObject *__pyx_args, PyObject *__pyx_kwds
31776 #endif
31777 ) {
31778 PyObject *__pyx_v_self = 0;
31779 PyObject *__pyx_v_line = 0;
31780 PyObject *__pyx_v_stream = 0;
31781 #if !CYTHON_METH_FASTCALL
31782 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
31783 #endif
31784 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
31785 PyObject* values[3] = {0,0,0};
31786 int __pyx_lineno = 0;
31787 const char *__pyx_filename = NULL;
31788 int __pyx_clineno = 0;
31789 PyObject *__pyx_r = 0;
31790 __Pyx_RefNannyDeclarations
31791 __Pyx_RefNannySetupContext("_parse (wrapper)", 0);
31792 #if !CYTHON_METH_FASTCALL
31793 #if CYTHON_ASSUME_SAFE_MACROS
31794 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
31795 #else
31796 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
31797 #endif
31798 #endif
31799 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
31800 {
31801 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_line,&__pyx_n_s_stream,0};
31802 if (__pyx_kwds) {
31803 Py_ssize_t kw_args;
31804 switch (__pyx_nargs) {
31805 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
31806 CYTHON_FALLTHROUGH;
31807 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
31808 CYTHON_FALLTHROUGH;
31809 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
31810 CYTHON_FALLTHROUGH;
31811 case 0: break;
31812 default: goto __pyx_L5_argtuple_error;
31813 }
31814 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
31815 switch (__pyx_nargs) {
31816 case 0:
31817 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
31818 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
31819 kw_args--;
31820 }
31821 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 929, __pyx_L3_error)
31822 else goto __pyx_L5_argtuple_error;
31823 CYTHON_FALLTHROUGH;
31824 case 1:
31825 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_line)) != 0)) {
31826 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
31827 kw_args--;
31828 }
31829 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 929, __pyx_L3_error)
31830 else {
31831 __Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, 1); __PYX_ERR(0, 929, __pyx_L3_error)
31832 }
31833 CYTHON_FALLTHROUGH;
31834 case 2:
31835 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_stream)) != 0)) {
31836 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
31837 kw_args--;
31838 }
31839 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 929, __pyx_L3_error)
31840 else {
31841 __Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, 2); __PYX_ERR(0, 929, __pyx_L3_error)
31842 }
31843 }
31844 if (unlikely(kw_args > 0)) {
31845 const Py_ssize_t kwd_pos_args = __pyx_nargs;
31846 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "_parse") < 0)) __PYX_ERR(0, 929, __pyx_L3_error)
31847 }
31848 } else if (unlikely(__pyx_nargs != 3)) {
31849 goto __pyx_L5_argtuple_error;
31850 } else {
31851 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
31852 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
31853 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
31854 }
31855 __pyx_v_self = values[0];
31856 __pyx_v_line = values[1];
31857 __pyx_v_stream = values[2];
31858 }
31859 goto __pyx_L6_skip;
31860 __pyx_L5_argtuple_error:;
31861 __Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 929, __pyx_L3_error)
31862 __pyx_L6_skip:;
31863 goto __pyx_L4_argument_unpacking_done;
31864 __pyx_L3_error:;
31865 {
31866 Py_ssize_t __pyx_temp;
31867 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
31868 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
31869 }
31870 }
31871 __Pyx_AddTraceback("pysam.libcvcf.VCF._parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
31872 __Pyx_RefNannyFinishContext();
31873 return NULL;
31874 __pyx_L4_argument_unpacking_done:;
31875 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_38_parse(__pyx_self, __pyx_v_self, __pyx_v_line, __pyx_v_stream);
31876
31877 /* function exit code */
31878 {
31879 Py_ssize_t __pyx_temp;
31880 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
31881 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
31882 }
31883 }
31884 __Pyx_RefNannyFinishContext();
31885 return __pyx_r;
31886 }
31887
31888 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_stream) {
31889 struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse *__pyx_cur_scope;
31890 PyObject *__pyx_r = NULL;
31891 __Pyx_RefNannyDeclarations
31892 int __pyx_lineno = 0;
31893 const char *__pyx_filename = NULL;
31894 int __pyx_clineno = 0;
31895 __Pyx_RefNannySetupContext("_parse", 0);
31896 __pyx_cur_scope = (struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse *)__pyx_tp_new_5pysam_7libcvcf___pyx_scope_struct___parse(__pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse, __pyx_empty_tuple, NULL);
31897 if (unlikely(!__pyx_cur_scope)) {
31898 __pyx_cur_scope = ((struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse *)Py_None);
31899 __Pyx_INCREF(Py_None);
31900 __PYX_ERR(0, 929, __pyx_L1_error)
31901 } else {
31902 __Pyx_GOTREF((PyObject *)__pyx_cur_scope);
31903 }
31904 __pyx_cur_scope->__pyx_v_self = __pyx_v_self;
31905 __Pyx_INCREF(__pyx_cur_scope->__pyx_v_self);
31906 __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_self);
31907 __pyx_cur_scope->__pyx_v_line = __pyx_v_line;
31908 __Pyx_INCREF(__pyx_cur_scope->__pyx_v_line);
31909 __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_line);
31910 __pyx_cur_scope->__pyx_v_stream = __pyx_v_stream;
31911 __Pyx_INCREF(__pyx_cur_scope->__pyx_v_stream);
31912 __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_stream);
31913 {
31914 __pyx_CoroutineObject *gen = __Pyx_Generator_New((__pyx_coroutine_body_t) __pyx_gb_5pysam_7libcvcf_3VCF_40generator, __pyx_codeobj__29, (PyObject *) __pyx_cur_scope, __pyx_n_s_parse, __pyx_n_s_VCF__parse, __pyx_n_s_pysam_libcvcf); if (unlikely(!gen)) __PYX_ERR(0, 929, __pyx_L1_error)
31915 __Pyx_DECREF(__pyx_cur_scope);
31916 __Pyx_RefNannyFinishContext();
31917 return (PyObject *) gen;
31918 }
31919
31920 /* function exit code */
31921 __pyx_L1_error:;
31922 __Pyx_AddTraceback("pysam.libcvcf.VCF._parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
31923 __pyx_r = NULL;
31924 __Pyx_DECREF((PyObject *)__pyx_cur_scope);
31925 __Pyx_XGIVEREF(__pyx_r);
31926 __Pyx_RefNannyFinishContext();
31927 return __pyx_r;
31928 }
31929
31930 static PyObject *__pyx_gb_5pysam_7libcvcf_3VCF_40generator(__pyx_CoroutineObject *__pyx_generator, CYTHON_UNUSED PyThreadState *__pyx_tstate, PyObject *__pyx_sent_value) /* generator body */
31931 {
31932 struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse *__pyx_cur_scope = ((struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse *)__pyx_generator->closure);
31933 PyObject *__pyx_r = NULL;
31934 PyObject *__pyx_t_1 = NULL;
31935 PyObject *__pyx_t_2 = NULL;
31936 PyObject *__pyx_t_3 = NULL;
31937 unsigned int __pyx_t_4;
31938 int __pyx_t_5;
31939 Py_ssize_t __pyx_t_6;
31940 PyObject *__pyx_t_7 = NULL;
31941 PyObject *__pyx_t_8 = NULL;
31942 PyObject *(*__pyx_t_9)(PyObject *);
31943 int __pyx_t_10;
31944 PyObject *__pyx_t_11 = NULL;
31945 int __pyx_lineno = 0;
31946 const char *__pyx_filename = NULL;
31947 int __pyx_clineno = 0;
31948 __Pyx_RefNannyDeclarations
31949 __Pyx_RefNannySetupContext("_parse", 0);
31950 switch (__pyx_generator->resume_label) {
31951 case 0: goto __pyx_L3_first_run;
31952 case 1: goto __pyx_L7_resume_from_yield;
31953 case 2: goto __pyx_L14_resume_from_yield;
31954 default: /* CPython raises the right error here */
31955 __Pyx_RefNannyFinishContext();
31956 return NULL;
31957 }
31958 __pyx_L3_first_run:;
31959 if (unlikely(!__pyx_sent_value)) __PYX_ERR(0, 929, __pyx_L1_error)
31960
31961 /* "pysam/libcvcf.pyx":931
31962 * def _parse(self, line, stream):
31963 * # deal with files with header only
31964 * if line.startswith("##"): return # <<<<<<<<<<<<<<
31965 * if len(line.strip()) > 0:
31966 * d = self.parse_data( line.strip() )
31967 */
31968 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_cur_scope->__pyx_v_line, __pyx_n_s_startswith); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 931, __pyx_L1_error)
31969 __Pyx_GOTREF(__pyx_t_2);
31970 __pyx_t_3 = NULL;
31971 __pyx_t_4 = 0;
31972 #if CYTHON_UNPACK_METHODS
31973 if (likely(PyMethod_Check(__pyx_t_2))) {
31974 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
31975 if (likely(__pyx_t_3)) {
31976 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
31977 __Pyx_INCREF(__pyx_t_3);
31978 __Pyx_INCREF(function);
31979 __Pyx_DECREF_SET(__pyx_t_2, function);
31980 __pyx_t_4 = 1;
31981 }
31982 }
31983 #endif
31984 {
31985 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_kp_u__23};
31986 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
31987 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
31988 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 931, __pyx_L1_error)
31989 __Pyx_GOTREF(__pyx_t_1);
31990 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
31991 }
31992 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 931, __pyx_L1_error)
31993 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
31994 if (__pyx_t_5) {
31995 __Pyx_XDECREF(__pyx_r);
31996 __pyx_r = NULL;
31997 goto __pyx_L0;
31998 }
31999
32000 /* "pysam/libcvcf.pyx":932
32001 * # deal with files with header only
32002 * if line.startswith("##"): return
32003 * if len(line.strip()) > 0: # <<<<<<<<<<<<<<
32004 * d = self.parse_data( line.strip() )
32005 * if d: yield d
32006 */
32007 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_cur_scope->__pyx_v_line, __pyx_n_s_strip); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 932, __pyx_L1_error)
32008 __Pyx_GOTREF(__pyx_t_2);
32009 __pyx_t_3 = NULL;
32010 __pyx_t_4 = 0;
32011 #if CYTHON_UNPACK_METHODS
32012 if (likely(PyMethod_Check(__pyx_t_2))) {
32013 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
32014 if (likely(__pyx_t_3)) {
32015 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
32016 __Pyx_INCREF(__pyx_t_3);
32017 __Pyx_INCREF(function);
32018 __Pyx_DECREF_SET(__pyx_t_2, function);
32019 __pyx_t_4 = 1;
32020 }
32021 }
32022 #endif
32023 {
32024 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
32025 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
32026 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
32027 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 932, __pyx_L1_error)
32028 __Pyx_GOTREF(__pyx_t_1);
32029 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
32030 }
32031 __pyx_t_6 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_6 == ((Py_ssize_t)-1))) __PYX_ERR(0, 932, __pyx_L1_error)
32032 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
32033 __pyx_t_5 = (__pyx_t_6 > 0);
32034 if (__pyx_t_5) {
32035
32036 /* "pysam/libcvcf.pyx":933
32037 * if line.startswith("##"): return
32038 * if len(line.strip()) > 0:
32039 * d = self.parse_data( line.strip() ) # <<<<<<<<<<<<<<
32040 * if d: yield d
32041 * for line in stream:
32042 */
32043 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s_parse_data); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 933, __pyx_L1_error)
32044 __Pyx_GOTREF(__pyx_t_2);
32045 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_cur_scope->__pyx_v_line, __pyx_n_s_strip); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 933, __pyx_L1_error)
32046 __Pyx_GOTREF(__pyx_t_7);
32047 __pyx_t_8 = NULL;
32048 __pyx_t_4 = 0;
32049 #if CYTHON_UNPACK_METHODS
32050 if (likely(PyMethod_Check(__pyx_t_7))) {
32051 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_7);
32052 if (likely(__pyx_t_8)) {
32053 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7);
32054 __Pyx_INCREF(__pyx_t_8);
32055 __Pyx_INCREF(function);
32056 __Pyx_DECREF_SET(__pyx_t_7, function);
32057 __pyx_t_4 = 1;
32058 }
32059 }
32060 #endif
32061 {
32062 PyObject *__pyx_callargs[2] = {__pyx_t_8, NULL};
32063 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_7, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
32064 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
32065 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 933, __pyx_L1_error)
32066 __Pyx_GOTREF(__pyx_t_3);
32067 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
32068 }
32069 __pyx_t_7 = NULL;
32070 __pyx_t_4 = 0;
32071 #if CYTHON_UNPACK_METHODS
32072 if (likely(PyMethod_Check(__pyx_t_2))) {
32073 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_2);
32074 if (likely(__pyx_t_7)) {
32075 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
32076 __Pyx_INCREF(__pyx_t_7);
32077 __Pyx_INCREF(function);
32078 __Pyx_DECREF_SET(__pyx_t_2, function);
32079 __pyx_t_4 = 1;
32080 }
32081 }
32082 #endif
32083 {
32084 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_3};
32085 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
32086 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
32087 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
32088 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 933, __pyx_L1_error)
32089 __Pyx_GOTREF(__pyx_t_1);
32090 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
32091 }
32092 __Pyx_GIVEREF(__pyx_t_1);
32093 __pyx_cur_scope->__pyx_v_d = __pyx_t_1;
32094 __pyx_t_1 = 0;
32095
32096 /* "pysam/libcvcf.pyx":934
32097 * if len(line.strip()) > 0:
32098 * d = self.parse_data( line.strip() )
32099 * if d: yield d # <<<<<<<<<<<<<<
32100 * for line in stream:
32101 * self._lineno += 1
32102 */
32103 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_cur_scope->__pyx_v_d); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 934, __pyx_L1_error)
32104 if (__pyx_t_5) {
32105 __Pyx_INCREF(__pyx_cur_scope->__pyx_v_d);
32106 __pyx_r = __pyx_cur_scope->__pyx_v_d;
32107 __Pyx_XGIVEREF(__pyx_r);
32108 __Pyx_RefNannyFinishContext();
32109 __Pyx_Coroutine_ResetAndClearException(__pyx_generator);
32110 /* return from generator, yielding value */
32111 __pyx_generator->resume_label = 1;
32112 return __pyx_r;
32113 __pyx_L7_resume_from_yield:;
32114 if (unlikely(!__pyx_sent_value)) __PYX_ERR(0, 934, __pyx_L1_error)
32115 }
32116
32117 /* "pysam/libcvcf.pyx":932
32118 * # deal with files with header only
32119 * if line.startswith("##"): return
32120 * if len(line.strip()) > 0: # <<<<<<<<<<<<<<
32121 * d = self.parse_data( line.strip() )
32122 * if d: yield d
32123 */
32124 }
32125
32126 /* "pysam/libcvcf.pyx":935
32127 * d = self.parse_data( line.strip() )
32128 * if d: yield d
32129 * for line in stream: # <<<<<<<<<<<<<<
32130 * self._lineno += 1
32131 * if self._lines and self._lineno > self._lines: raise StopIteration
32132 */
32133 if (likely(PyList_CheckExact(__pyx_cur_scope->__pyx_v_stream)) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_stream)) {
32134 __pyx_t_1 = __pyx_cur_scope->__pyx_v_stream; __Pyx_INCREF(__pyx_t_1);
32135 __pyx_t_6 = 0;
32136 __pyx_t_9 = NULL;
32137 } else {
32138 __pyx_t_6 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_stream); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 935, __pyx_L1_error)
32139 __Pyx_GOTREF(__pyx_t_1);
32140 __pyx_t_9 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 935, __pyx_L1_error)
32141 }
32142 for (;;) {
32143 if (likely(!__pyx_t_9)) {
32144 if (likely(PyList_CheckExact(__pyx_t_1))) {
32145 {
32146 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1);
32147 #if !CYTHON_ASSUME_SAFE_MACROS
32148 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 935, __pyx_L1_error)
32149 #endif
32150 if (__pyx_t_6 >= __pyx_temp) break;
32151 }
32152 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
32153 __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_6); __Pyx_INCREF(__pyx_t_2); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 935, __pyx_L1_error)
32154 #else
32155 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 935, __pyx_L1_error)
32156 __Pyx_GOTREF(__pyx_t_2);
32157 #endif
32158 } else {
32159 {
32160 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1);
32161 #if !CYTHON_ASSUME_SAFE_MACROS
32162 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 935, __pyx_L1_error)
32163 #endif
32164 if (__pyx_t_6 >= __pyx_temp) break;
32165 }
32166 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
32167 __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_6); __Pyx_INCREF(__pyx_t_2); __pyx_t_6++; if (unlikely((0 < 0))) __PYX_ERR(0, 935, __pyx_L1_error)
32168 #else
32169 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 935, __pyx_L1_error)
32170 __Pyx_GOTREF(__pyx_t_2);
32171 #endif
32172 }
32173 } else {
32174 __pyx_t_2 = __pyx_t_9(__pyx_t_1);
32175 if (unlikely(!__pyx_t_2)) {
32176 PyObject* exc_type = PyErr_Occurred();
32177 if (exc_type) {
32178 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
32179 else __PYX_ERR(0, 935, __pyx_L1_error)
32180 }
32181 break;
32182 }
32183 __Pyx_GOTREF(__pyx_t_2);
32184 }
32185 __Pyx_GOTREF(__pyx_cur_scope->__pyx_v_line);
32186 __Pyx_DECREF_SET(__pyx_cur_scope->__pyx_v_line, __pyx_t_2);
32187 __Pyx_GIVEREF(__pyx_t_2);
32188 __pyx_t_2 = 0;
32189
32190 /* "pysam/libcvcf.pyx":936
32191 * if d: yield d
32192 * for line in stream:
32193 * self._lineno += 1 # <<<<<<<<<<<<<<
32194 * if self._lines and self._lineno > self._lines: raise StopIteration
32195 * d = self.parse_data( line.strip() )
32196 */
32197 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s_lineno); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 936, __pyx_L1_error)
32198 __Pyx_GOTREF(__pyx_t_2);
32199 __pyx_t_3 = __Pyx_PyInt_AddObjC(__pyx_t_2, __pyx_int_1, 1, 1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 936, __pyx_L1_error)
32200 __Pyx_GOTREF(__pyx_t_3);
32201 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
32202 if (__Pyx_PyObject_SetAttrStr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s_lineno, __pyx_t_3) < 0) __PYX_ERR(0, 936, __pyx_L1_error)
32203 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
32204
32205 /* "pysam/libcvcf.pyx":937
32206 * for line in stream:
32207 * self._lineno += 1
32208 * if self._lines and self._lineno > self._lines: raise StopIteration # <<<<<<<<<<<<<<
32209 * d = self.parse_data( line.strip() )
32210 * if d: yield d
32211 */
32212 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s_lines_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 937, __pyx_L1_error)
32213 __Pyx_GOTREF(__pyx_t_3);
32214 __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 937, __pyx_L1_error)
32215 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
32216 if (__pyx_t_10) {
32217 } else {
32218 __pyx_t_5 = __pyx_t_10;
32219 goto __pyx_L11_bool_binop_done;
32220 }
32221 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s_lineno); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 937, __pyx_L1_error)
32222 __Pyx_GOTREF(__pyx_t_3);
32223 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s_lines_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 937, __pyx_L1_error)
32224 __Pyx_GOTREF(__pyx_t_2);
32225 __pyx_t_7 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_GT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 937, __pyx_L1_error)
32226 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
32227 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
32228 __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 937, __pyx_L1_error)
32229 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
32230 __pyx_t_5 = __pyx_t_10;
32231 __pyx_L11_bool_binop_done:;
32232 if (unlikely(__pyx_t_5)) {
32233 __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
32234 __PYX_ERR(0, 937, __pyx_L1_error)
32235 }
32236
32237 /* "pysam/libcvcf.pyx":938
32238 * self._lineno += 1
32239 * if self._lines and self._lineno > self._lines: raise StopIteration
32240 * d = self.parse_data( line.strip() ) # <<<<<<<<<<<<<<
32241 * if d: yield d
32242 *
32243 */
32244 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s_parse_data); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 938, __pyx_L1_error)
32245 __Pyx_GOTREF(__pyx_t_2);
32246 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_cur_scope->__pyx_v_line, __pyx_n_s_strip); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 938, __pyx_L1_error)
32247 __Pyx_GOTREF(__pyx_t_8);
32248 __pyx_t_11 = NULL;
32249 __pyx_t_4 = 0;
32250 #if CYTHON_UNPACK_METHODS
32251 if (likely(PyMethod_Check(__pyx_t_8))) {
32252 __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_8);
32253 if (likely(__pyx_t_11)) {
32254 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_8);
32255 __Pyx_INCREF(__pyx_t_11);
32256 __Pyx_INCREF(function);
32257 __Pyx_DECREF_SET(__pyx_t_8, function);
32258 __pyx_t_4 = 1;
32259 }
32260 }
32261 #endif
32262 {
32263 PyObject *__pyx_callargs[2] = {__pyx_t_11, NULL};
32264 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
32265 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
32266 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 938, __pyx_L1_error)
32267 __Pyx_GOTREF(__pyx_t_3);
32268 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
32269 }
32270 __pyx_t_8 = NULL;
32271 __pyx_t_4 = 0;
32272 #if CYTHON_UNPACK_METHODS
32273 if (likely(PyMethod_Check(__pyx_t_2))) {
32274 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_2);
32275 if (likely(__pyx_t_8)) {
32276 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
32277 __Pyx_INCREF(__pyx_t_8);
32278 __Pyx_INCREF(function);
32279 __Pyx_DECREF_SET(__pyx_t_2, function);
32280 __pyx_t_4 = 1;
32281 }
32282 }
32283 #endif
32284 {
32285 PyObject *__pyx_callargs[2] = {__pyx_t_8, __pyx_t_3};
32286 __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
32287 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
32288 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
32289 if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 938, __pyx_L1_error)
32290 __Pyx_GOTREF(__pyx_t_7);
32291 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
32292 }
32293 __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_d);
32294 __Pyx_XDECREF_SET(__pyx_cur_scope->__pyx_v_d, __pyx_t_7);
32295 __Pyx_GIVEREF(__pyx_t_7);
32296 __pyx_t_7 = 0;
32297
32298 /* "pysam/libcvcf.pyx":939
32299 * if self._lines and self._lineno > self._lines: raise StopIteration
32300 * d = self.parse_data( line.strip() )
32301 * if d: yield d # <<<<<<<<<<<<<<
32302 *
32303 * ######################################################################################################
32304 */
32305 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_cur_scope->__pyx_v_d); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 939, __pyx_L1_error)
32306 if (__pyx_t_5) {
32307 __Pyx_INCREF(__pyx_cur_scope->__pyx_v_d);
32308 __pyx_r = __pyx_cur_scope->__pyx_v_d;
32309 __Pyx_XGIVEREF(__pyx_t_1);
32310 __pyx_cur_scope->__pyx_t_0 = __pyx_t_1;
32311 __pyx_cur_scope->__pyx_t_1 = __pyx_t_6;
32312 __pyx_cur_scope->__pyx_t_2 = __pyx_t_9;
32313 __Pyx_XGIVEREF(__pyx_r);
32314 __Pyx_RefNannyFinishContext();
32315 __Pyx_Coroutine_ResetAndClearException(__pyx_generator);
32316 /* return from generator, yielding value */
32317 __pyx_generator->resume_label = 2;
32318 return __pyx_r;
32319 __pyx_L14_resume_from_yield:;
32320 __pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
32321 __pyx_cur_scope->__pyx_t_0 = 0;
32322 __Pyx_XGOTREF(__pyx_t_1);
32323 __pyx_t_6 = __pyx_cur_scope->__pyx_t_1;
32324 __pyx_t_9 = __pyx_cur_scope->__pyx_t_2;
32325 if (unlikely(!__pyx_sent_value)) __PYX_ERR(0, 939, __pyx_L1_error)
32326 }
32327
32328 /* "pysam/libcvcf.pyx":935
32329 * d = self.parse_data( line.strip() )
32330 * if d: yield d
32331 * for line in stream: # <<<<<<<<<<<<<<
32332 * self._lineno += 1
32333 * if self._lines and self._lineno > self._lines: raise StopIteration
32334 */
32335 }
32336 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
32337 CYTHON_MAYBE_UNUSED_VAR(__pyx_cur_scope);
32338
32339 /* "pysam/libcvcf.pyx":929
32340 * return line
32341 *
32342 * def _parse(self, line, stream): # <<<<<<<<<<<<<<
32343 * # deal with files with header only
32344 * if line.startswith("##"): return
32345 */
32346
32347 /* function exit code */
32348 PyErr_SetNone(PyExc_StopIteration);
32349 goto __pyx_L0;
32350 __pyx_L1_error:;
32351 __Pyx_Generator_Replace_StopIteration(0);
32352 __Pyx_XDECREF(__pyx_t_1);
32353 __Pyx_XDECREF(__pyx_t_2);
32354 __Pyx_XDECREF(__pyx_t_3);
32355 __Pyx_XDECREF(__pyx_t_7);
32356 __Pyx_XDECREF(__pyx_t_8);
32357 __Pyx_XDECREF(__pyx_t_11);
32358 __Pyx_AddTraceback("_parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
32359 __pyx_L0:;
32360 __Pyx_XDECREF(__pyx_r); __pyx_r = 0;
32361 #if !CYTHON_USE_EXC_INFO_STACK
32362 __Pyx_Coroutine_ResetAndClearException(__pyx_generator);
32363 #endif
32364 __pyx_generator->resume_label = -1;
32365 __Pyx_Coroutine_clear((PyObject*)__pyx_generator);
32366 __Pyx_RefNannyFinishContext();
32367 return __pyx_r;
32368 }
32369
32370 /* "pysam/libcvcf.pyx":947
32371 * ######################################################################################################
32372 *
32373 * def getsamples(self): # <<<<<<<<<<<<<<
32374 * """ List of samples in VCF file """
32375 * return self._samples
32376 */
32377
32378 /* Python wrapper */
32379 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_42getsamples(PyObject *__pyx_self,
32380 #if CYTHON_METH_FASTCALL
32381 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
32382 #else
32383 PyObject *__pyx_args, PyObject *__pyx_kwds
32384 #endif
32385 ); /*proto*/
32386 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_41getsamples, "VCF.getsamples(self)\n List of samples in VCF file ");
32387 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_42getsamples = {"getsamples", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_42getsamples, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_41getsamples};
32388 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_42getsamples(PyObject *__pyx_self,
32389 #if CYTHON_METH_FASTCALL
32390 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
32391 #else
32392 PyObject *__pyx_args, PyObject *__pyx_kwds
32393 #endif
32394 ) {
32395 PyObject *__pyx_v_self = 0;
32396 #if !CYTHON_METH_FASTCALL
32397 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
32398 #endif
32399 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
32400 PyObject* values[1] = {0};
32401 int __pyx_lineno = 0;
32402 const char *__pyx_filename = NULL;
32403 int __pyx_clineno = 0;
32404 PyObject *__pyx_r = 0;
32405 __Pyx_RefNannyDeclarations
32406 __Pyx_RefNannySetupContext("getsamples (wrapper)", 0);
32407 #if !CYTHON_METH_FASTCALL
32408 #if CYTHON_ASSUME_SAFE_MACROS
32409 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
32410 #else
32411 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
32412 #endif
32413 #endif
32414 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
32415 {
32416 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0};
32417 if (__pyx_kwds) {
32418 Py_ssize_t kw_args;
32419 switch (__pyx_nargs) {
32420 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
32421 CYTHON_FALLTHROUGH;
32422 case 0: break;
32423 default: goto __pyx_L5_argtuple_error;
32424 }
32425 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
32426 switch (__pyx_nargs) {
32427 case 0:
32428 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
32429 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
32430 kw_args--;
32431 }
32432 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 947, __pyx_L3_error)
32433 else goto __pyx_L5_argtuple_error;
32434 }
32435 if (unlikely(kw_args > 0)) {
32436 const Py_ssize_t kwd_pos_args = __pyx_nargs;
32437 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "getsamples") < 0)) __PYX_ERR(0, 947, __pyx_L3_error)
32438 }
32439 } else if (unlikely(__pyx_nargs != 1)) {
32440 goto __pyx_L5_argtuple_error;
32441 } else {
32442 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
32443 }
32444 __pyx_v_self = values[0];
32445 }
32446 goto __pyx_L6_skip;
32447 __pyx_L5_argtuple_error:;
32448 __Pyx_RaiseArgtupleInvalid("getsamples", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 947, __pyx_L3_error)
32449 __pyx_L6_skip:;
32450 goto __pyx_L4_argument_unpacking_done;
32451 __pyx_L3_error:;
32452 {
32453 Py_ssize_t __pyx_temp;
32454 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
32455 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
32456 }
32457 }
32458 __Pyx_AddTraceback("pysam.libcvcf.VCF.getsamples", __pyx_clineno, __pyx_lineno, __pyx_filename);
32459 __Pyx_RefNannyFinishContext();
32460 return NULL;
32461 __pyx_L4_argument_unpacking_done:;
32462 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_41getsamples(__pyx_self, __pyx_v_self);
32463
32464 /* function exit code */
32465 {
32466 Py_ssize_t __pyx_temp;
32467 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
32468 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
32469 }
32470 }
32471 __Pyx_RefNannyFinishContext();
32472 return __pyx_r;
32473 }
32474
32475 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
32476 PyObject *__pyx_r = NULL;
32477 __Pyx_RefNannyDeclarations
32478 PyObject *__pyx_t_1 = NULL;
32479 int __pyx_lineno = 0;
32480 const char *__pyx_filename = NULL;
32481 int __pyx_clineno = 0;
32482 __Pyx_RefNannySetupContext("getsamples", 1);
32483
32484 /* "pysam/libcvcf.pyx":949
32485 * def getsamples(self):
32486 * """ List of samples in VCF file """
32487 * return self._samples # <<<<<<<<<<<<<<
32488 *
32489 * def setsamples(self,samples):
32490 */
32491 __Pyx_XDECREF(__pyx_r);
32492 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_samples); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 949, __pyx_L1_error)
32493 __Pyx_GOTREF(__pyx_t_1);
32494 __pyx_r = __pyx_t_1;
32495 __pyx_t_1 = 0;
32496 goto __pyx_L0;
32497
32498 /* "pysam/libcvcf.pyx":947
32499 * ######################################################################################################
32500 *
32501 * def getsamples(self): # <<<<<<<<<<<<<<
32502 * """ List of samples in VCF file """
32503 * return self._samples
32504 */
32505
32506 /* function exit code */
32507 __pyx_L1_error:;
32508 __Pyx_XDECREF(__pyx_t_1);
32509 __Pyx_AddTraceback("pysam.libcvcf.VCF.getsamples", __pyx_clineno, __pyx_lineno, __pyx_filename);
32510 __pyx_r = NULL;
32511 __pyx_L0:;
32512 __Pyx_XGIVEREF(__pyx_r);
32513 __Pyx_RefNannyFinishContext();
32514 return __pyx_r;
32515 }
32516
32517 /* "pysam/libcvcf.pyx":951
32518 * return self._samples
32519 *
32520 * def setsamples(self,samples): # <<<<<<<<<<<<<<
32521 * """ List of samples in VCF file """
32522 * self._samples = samples
32523 */
32524
32525 /* Python wrapper */
32526 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_44setsamples(PyObject *__pyx_self,
32527 #if CYTHON_METH_FASTCALL
32528 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
32529 #else
32530 PyObject *__pyx_args, PyObject *__pyx_kwds
32531 #endif
32532 ); /*proto*/
32533 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_43setsamples, "VCF.setsamples(self, samples)\n List of samples in VCF file ");
32534 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_44setsamples = {"setsamples", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_44setsamples, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_43setsamples};
32535 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_44setsamples(PyObject *__pyx_self,
32536 #if CYTHON_METH_FASTCALL
32537 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
32538 #else
32539 PyObject *__pyx_args, PyObject *__pyx_kwds
32540 #endif
32541 ) {
32542 PyObject *__pyx_v_self = 0;
32543 PyObject *__pyx_v_samples = 0;
32544 #if !CYTHON_METH_FASTCALL
32545 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
32546 #endif
32547 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
32548 PyObject* values[2] = {0,0};
32549 int __pyx_lineno = 0;
32550 const char *__pyx_filename = NULL;
32551 int __pyx_clineno = 0;
32552 PyObject *__pyx_r = 0;
32553 __Pyx_RefNannyDeclarations
32554 __Pyx_RefNannySetupContext("setsamples (wrapper)", 0);
32555 #if !CYTHON_METH_FASTCALL
32556 #if CYTHON_ASSUME_SAFE_MACROS
32557 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
32558 #else
32559 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
32560 #endif
32561 #endif
32562 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
32563 {
32564 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_samples_3,0};
32565 if (__pyx_kwds) {
32566 Py_ssize_t kw_args;
32567 switch (__pyx_nargs) {
32568 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
32569 CYTHON_FALLTHROUGH;
32570 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
32571 CYTHON_FALLTHROUGH;
32572 case 0: break;
32573 default: goto __pyx_L5_argtuple_error;
32574 }
32575 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
32576 switch (__pyx_nargs) {
32577 case 0:
32578 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
32579 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
32580 kw_args--;
32581 }
32582 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 951, __pyx_L3_error)
32583 else goto __pyx_L5_argtuple_error;
32584 CYTHON_FALLTHROUGH;
32585 case 1:
32586 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_samples_3)) != 0)) {
32587 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
32588 kw_args--;
32589 }
32590 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 951, __pyx_L3_error)
32591 else {
32592 __Pyx_RaiseArgtupleInvalid("setsamples", 1, 2, 2, 1); __PYX_ERR(0, 951, __pyx_L3_error)
32593 }
32594 }
32595 if (unlikely(kw_args > 0)) {
32596 const Py_ssize_t kwd_pos_args = __pyx_nargs;
32597 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "setsamples") < 0)) __PYX_ERR(0, 951, __pyx_L3_error)
32598 }
32599 } else if (unlikely(__pyx_nargs != 2)) {
32600 goto __pyx_L5_argtuple_error;
32601 } else {
32602 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
32603 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
32604 }
32605 __pyx_v_self = values[0];
32606 __pyx_v_samples = values[1];
32607 }
32608 goto __pyx_L6_skip;
32609 __pyx_L5_argtuple_error:;
32610 __Pyx_RaiseArgtupleInvalid("setsamples", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 951, __pyx_L3_error)
32611 __pyx_L6_skip:;
32612 goto __pyx_L4_argument_unpacking_done;
32613 __pyx_L3_error:;
32614 {
32615 Py_ssize_t __pyx_temp;
32616 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
32617 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
32618 }
32619 }
32620 __Pyx_AddTraceback("pysam.libcvcf.VCF.setsamples", __pyx_clineno, __pyx_lineno, __pyx_filename);
32621 __Pyx_RefNannyFinishContext();
32622 return NULL;
32623 __pyx_L4_argument_unpacking_done:;
32624 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_43setsamples(__pyx_self, __pyx_v_self, __pyx_v_samples);
32625
32626 /* function exit code */
32627 {
32628 Py_ssize_t __pyx_temp;
32629 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
32630 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
32631 }
32632 }
32633 __Pyx_RefNannyFinishContext();
32634 return __pyx_r;
32635 }
32636
32637 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_samples) {
32638 PyObject *__pyx_r = NULL;
32639 __Pyx_RefNannyDeclarations
32640 int __pyx_lineno = 0;
32641 const char *__pyx_filename = NULL;
32642 int __pyx_clineno = 0;
32643 __Pyx_RefNannySetupContext("setsamples", 1);
32644
32645 /* "pysam/libcvcf.pyx":953
32646 * def setsamples(self,samples):
32647 * """ List of samples in VCF file """
32648 * self._samples = samples # <<<<<<<<<<<<<<
32649 *
32650 * def getheader(self):
32651 */
32652 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_samples, __pyx_v_samples) < 0) __PYX_ERR(0, 953, __pyx_L1_error)
32653
32654 /* "pysam/libcvcf.pyx":951
32655 * return self._samples
32656 *
32657 * def setsamples(self,samples): # <<<<<<<<<<<<<<
32658 * """ List of samples in VCF file """
32659 * self._samples = samples
32660 */
32661
32662 /* function exit code */
32663 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
32664 goto __pyx_L0;
32665 __pyx_L1_error:;
32666 __Pyx_AddTraceback("pysam.libcvcf.VCF.setsamples", __pyx_clineno, __pyx_lineno, __pyx_filename);
32667 __pyx_r = NULL;
32668 __pyx_L0:;
32669 __Pyx_XGIVEREF(__pyx_r);
32670 __Pyx_RefNannyFinishContext();
32671 return __pyx_r;
32672 }
32673
32674 /* "pysam/libcvcf.pyx":955
32675 * self._samples = samples
32676 *
32677 * def getheader(self): # <<<<<<<<<<<<<<
32678 * """ List of header key-value pairs (strings) """
32679 * return self._header
32680 */
32681
32682 /* Python wrapper */
32683 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_46getheader(PyObject *__pyx_self,
32684 #if CYTHON_METH_FASTCALL
32685 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
32686 #else
32687 PyObject *__pyx_args, PyObject *__pyx_kwds
32688 #endif
32689 ); /*proto*/
32690 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_45getheader, "VCF.getheader(self)\n List of header key-value pairs (strings) ");
32691 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_46getheader = {"getheader", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_46getheader, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_45getheader};
32692 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_46getheader(PyObject *__pyx_self,
32693 #if CYTHON_METH_FASTCALL
32694 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
32695 #else
32696 PyObject *__pyx_args, PyObject *__pyx_kwds
32697 #endif
32698 ) {
32699 PyObject *__pyx_v_self = 0;
32700 #if !CYTHON_METH_FASTCALL
32701 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
32702 #endif
32703 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
32704 PyObject* values[1] = {0};
32705 int __pyx_lineno = 0;
32706 const char *__pyx_filename = NULL;
32707 int __pyx_clineno = 0;
32708 PyObject *__pyx_r = 0;
32709 __Pyx_RefNannyDeclarations
32710 __Pyx_RefNannySetupContext("getheader (wrapper)", 0);
32711 #if !CYTHON_METH_FASTCALL
32712 #if CYTHON_ASSUME_SAFE_MACROS
32713 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
32714 #else
32715 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
32716 #endif
32717 #endif
32718 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
32719 {
32720 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0};
32721 if (__pyx_kwds) {
32722 Py_ssize_t kw_args;
32723 switch (__pyx_nargs) {
32724 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
32725 CYTHON_FALLTHROUGH;
32726 case 0: break;
32727 default: goto __pyx_L5_argtuple_error;
32728 }
32729 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
32730 switch (__pyx_nargs) {
32731 case 0:
32732 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
32733 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
32734 kw_args--;
32735 }
32736 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 955, __pyx_L3_error)
32737 else goto __pyx_L5_argtuple_error;
32738 }
32739 if (unlikely(kw_args > 0)) {
32740 const Py_ssize_t kwd_pos_args = __pyx_nargs;
32741 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "getheader") < 0)) __PYX_ERR(0, 955, __pyx_L3_error)
32742 }
32743 } else if (unlikely(__pyx_nargs != 1)) {
32744 goto __pyx_L5_argtuple_error;
32745 } else {
32746 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
32747 }
32748 __pyx_v_self = values[0];
32749 }
32750 goto __pyx_L6_skip;
32751 __pyx_L5_argtuple_error:;
32752 __Pyx_RaiseArgtupleInvalid("getheader", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 955, __pyx_L3_error)
32753 __pyx_L6_skip:;
32754 goto __pyx_L4_argument_unpacking_done;
32755 __pyx_L3_error:;
32756 {
32757 Py_ssize_t __pyx_temp;
32758 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
32759 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
32760 }
32761 }
32762 __Pyx_AddTraceback("pysam.libcvcf.VCF.getheader", __pyx_clineno, __pyx_lineno, __pyx_filename);
32763 __Pyx_RefNannyFinishContext();
32764 return NULL;
32765 __pyx_L4_argument_unpacking_done:;
32766 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_45getheader(__pyx_self, __pyx_v_self);
32767
32768 /* function exit code */
32769 {
32770 Py_ssize_t __pyx_temp;
32771 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
32772 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
32773 }
32774 }
32775 __Pyx_RefNannyFinishContext();
32776 return __pyx_r;
32777 }
32778
32779 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
32780 PyObject *__pyx_r = NULL;
32781 __Pyx_RefNannyDeclarations
32782 PyObject *__pyx_t_1 = NULL;
32783 int __pyx_lineno = 0;
32784 const char *__pyx_filename = NULL;
32785 int __pyx_clineno = 0;
32786 __Pyx_RefNannySetupContext("getheader", 1);
32787
32788 /* "pysam/libcvcf.pyx":957
32789 * def getheader(self):
32790 * """ List of header key-value pairs (strings) """
32791 * return self._header # <<<<<<<<<<<<<<
32792 *
32793 * def setheader(self,header):
32794 */
32795 __Pyx_XDECREF(__pyx_r);
32796 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_header); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 957, __pyx_L1_error)
32797 __Pyx_GOTREF(__pyx_t_1);
32798 __pyx_r = __pyx_t_1;
32799 __pyx_t_1 = 0;
32800 goto __pyx_L0;
32801
32802 /* "pysam/libcvcf.pyx":955
32803 * self._samples = samples
32804 *
32805 * def getheader(self): # <<<<<<<<<<<<<<
32806 * """ List of header key-value pairs (strings) """
32807 * return self._header
32808 */
32809
32810 /* function exit code */
32811 __pyx_L1_error:;
32812 __Pyx_XDECREF(__pyx_t_1);
32813 __Pyx_AddTraceback("pysam.libcvcf.VCF.getheader", __pyx_clineno, __pyx_lineno, __pyx_filename);
32814 __pyx_r = NULL;
32815 __pyx_L0:;
32816 __Pyx_XGIVEREF(__pyx_r);
32817 __Pyx_RefNannyFinishContext();
32818 return __pyx_r;
32819 }
32820
32821 /* "pysam/libcvcf.pyx":959
32822 * return self._header
32823 *
32824 * def setheader(self,header): # <<<<<<<<<<<<<<
32825 * """ List of header key-value pairs (strings) """
32826 * self._header = header
32827 */
32828
32829 /* Python wrapper */
32830 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_48setheader(PyObject *__pyx_self,
32831 #if CYTHON_METH_FASTCALL
32832 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
32833 #else
32834 PyObject *__pyx_args, PyObject *__pyx_kwds
32835 #endif
32836 ); /*proto*/
32837 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_47setheader, "VCF.setheader(self, header)\n List of header key-value pairs (strings) ");
32838 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_48setheader = {"setheader", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_48setheader, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_47setheader};
32839 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_48setheader(PyObject *__pyx_self,
32840 #if CYTHON_METH_FASTCALL
32841 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
32842 #else
32843 PyObject *__pyx_args, PyObject *__pyx_kwds
32844 #endif
32845 ) {
32846 PyObject *__pyx_v_self = 0;
32847 PyObject *__pyx_v_header = 0;
32848 #if !CYTHON_METH_FASTCALL
32849 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
32850 #endif
32851 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
32852 PyObject* values[2] = {0,0};
32853 int __pyx_lineno = 0;
32854 const char *__pyx_filename = NULL;
32855 int __pyx_clineno = 0;
32856 PyObject *__pyx_r = 0;
32857 __Pyx_RefNannyDeclarations
32858 __Pyx_RefNannySetupContext("setheader (wrapper)", 0);
32859 #if !CYTHON_METH_FASTCALL
32860 #if CYTHON_ASSUME_SAFE_MACROS
32861 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
32862 #else
32863 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
32864 #endif
32865 #endif
32866 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
32867 {
32868 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_header_2,0};
32869 if (__pyx_kwds) {
32870 Py_ssize_t kw_args;
32871 switch (__pyx_nargs) {
32872 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
32873 CYTHON_FALLTHROUGH;
32874 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
32875 CYTHON_FALLTHROUGH;
32876 case 0: break;
32877 default: goto __pyx_L5_argtuple_error;
32878 }
32879 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
32880 switch (__pyx_nargs) {
32881 case 0:
32882 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
32883 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
32884 kw_args--;
32885 }
32886 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 959, __pyx_L3_error)
32887 else goto __pyx_L5_argtuple_error;
32888 CYTHON_FALLTHROUGH;
32889 case 1:
32890 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_header_2)) != 0)) {
32891 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
32892 kw_args--;
32893 }
32894 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 959, __pyx_L3_error)
32895 else {
32896 __Pyx_RaiseArgtupleInvalid("setheader", 1, 2, 2, 1); __PYX_ERR(0, 959, __pyx_L3_error)
32897 }
32898 }
32899 if (unlikely(kw_args > 0)) {
32900 const Py_ssize_t kwd_pos_args = __pyx_nargs;
32901 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "setheader") < 0)) __PYX_ERR(0, 959, __pyx_L3_error)
32902 }
32903 } else if (unlikely(__pyx_nargs != 2)) {
32904 goto __pyx_L5_argtuple_error;
32905 } else {
32906 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
32907 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
32908 }
32909 __pyx_v_self = values[0];
32910 __pyx_v_header = values[1];
32911 }
32912 goto __pyx_L6_skip;
32913 __pyx_L5_argtuple_error:;
32914 __Pyx_RaiseArgtupleInvalid("setheader", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 959, __pyx_L3_error)
32915 __pyx_L6_skip:;
32916 goto __pyx_L4_argument_unpacking_done;
32917 __pyx_L3_error:;
32918 {
32919 Py_ssize_t __pyx_temp;
32920 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
32921 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
32922 }
32923 }
32924 __Pyx_AddTraceback("pysam.libcvcf.VCF.setheader", __pyx_clineno, __pyx_lineno, __pyx_filename);
32925 __Pyx_RefNannyFinishContext();
32926 return NULL;
32927 __pyx_L4_argument_unpacking_done:;
32928 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_47setheader(__pyx_self, __pyx_v_self, __pyx_v_header);
32929
32930 /* function exit code */
32931 {
32932 Py_ssize_t __pyx_temp;
32933 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
32934 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
32935 }
32936 }
32937 __Pyx_RefNannyFinishContext();
32938 return __pyx_r;
32939 }
32940
32941 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_header) {
32942 PyObject *__pyx_r = NULL;
32943 __Pyx_RefNannyDeclarations
32944 int __pyx_lineno = 0;
32945 const char *__pyx_filename = NULL;
32946 int __pyx_clineno = 0;
32947 __Pyx_RefNannySetupContext("setheader", 1);
32948
32949 /* "pysam/libcvcf.pyx":961
32950 * def setheader(self,header):
32951 * """ List of header key-value pairs (strings) """
32952 * self._header = header # <<<<<<<<<<<<<<
32953 *
32954 * def getinfo(self):
32955 */
32956 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_header, __pyx_v_header) < 0) __PYX_ERR(0, 961, __pyx_L1_error)
32957
32958 /* "pysam/libcvcf.pyx":959
32959 * return self._header
32960 *
32961 * def setheader(self,header): # <<<<<<<<<<<<<<
32962 * """ List of header key-value pairs (strings) """
32963 * self._header = header
32964 */
32965
32966 /* function exit code */
32967 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
32968 goto __pyx_L0;
32969 __pyx_L1_error:;
32970 __Pyx_AddTraceback("pysam.libcvcf.VCF.setheader", __pyx_clineno, __pyx_lineno, __pyx_filename);
32971 __pyx_r = NULL;
32972 __pyx_L0:;
32973 __Pyx_XGIVEREF(__pyx_r);
32974 __Pyx_RefNannyFinishContext();
32975 return __pyx_r;
32976 }
32977
32978 /* "pysam/libcvcf.pyx":963
32979 * self._header = header
32980 *
32981 * def getinfo(self): # <<<<<<<<<<<<<<
32982 * """ Dictionary of ##INFO tags, as VCF.FORMAT values """
32983 * return self._info
32984 */
32985
32986 /* Python wrapper */
32987 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_50getinfo(PyObject *__pyx_self,
32988 #if CYTHON_METH_FASTCALL
32989 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
32990 #else
32991 PyObject *__pyx_args, PyObject *__pyx_kwds
32992 #endif
32993 ); /*proto*/
32994 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_49getinfo, "VCF.getinfo(self)\n Dictionary of ##INFO tags, as VCF.FORMAT values ");
32995 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_50getinfo = {"getinfo", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_50getinfo, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_49getinfo};
32996 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_50getinfo(PyObject *__pyx_self,
32997 #if CYTHON_METH_FASTCALL
32998 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
32999 #else
33000 PyObject *__pyx_args, PyObject *__pyx_kwds
33001 #endif
33002 ) {
33003 PyObject *__pyx_v_self = 0;
33004 #if !CYTHON_METH_FASTCALL
33005 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
33006 #endif
33007 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
33008 PyObject* values[1] = {0};
33009 int __pyx_lineno = 0;
33010 const char *__pyx_filename = NULL;
33011 int __pyx_clineno = 0;
33012 PyObject *__pyx_r = 0;
33013 __Pyx_RefNannyDeclarations
33014 __Pyx_RefNannySetupContext("getinfo (wrapper)", 0);
33015 #if !CYTHON_METH_FASTCALL
33016 #if CYTHON_ASSUME_SAFE_MACROS
33017 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
33018 #else
33019 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
33020 #endif
33021 #endif
33022 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
33023 {
33024 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0};
33025 if (__pyx_kwds) {
33026 Py_ssize_t kw_args;
33027 switch (__pyx_nargs) {
33028 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33029 CYTHON_FALLTHROUGH;
33030 case 0: break;
33031 default: goto __pyx_L5_argtuple_error;
33032 }
33033 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
33034 switch (__pyx_nargs) {
33035 case 0:
33036 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
33037 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
33038 kw_args--;
33039 }
33040 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 963, __pyx_L3_error)
33041 else goto __pyx_L5_argtuple_error;
33042 }
33043 if (unlikely(kw_args > 0)) {
33044 const Py_ssize_t kwd_pos_args = __pyx_nargs;
33045 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "getinfo") < 0)) __PYX_ERR(0, 963, __pyx_L3_error)
33046 }
33047 } else if (unlikely(__pyx_nargs != 1)) {
33048 goto __pyx_L5_argtuple_error;
33049 } else {
33050 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33051 }
33052 __pyx_v_self = values[0];
33053 }
33054 goto __pyx_L6_skip;
33055 __pyx_L5_argtuple_error:;
33056 __Pyx_RaiseArgtupleInvalid("getinfo", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 963, __pyx_L3_error)
33057 __pyx_L6_skip:;
33058 goto __pyx_L4_argument_unpacking_done;
33059 __pyx_L3_error:;
33060 {
33061 Py_ssize_t __pyx_temp;
33062 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33063 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33064 }
33065 }
33066 __Pyx_AddTraceback("pysam.libcvcf.VCF.getinfo", __pyx_clineno, __pyx_lineno, __pyx_filename);
33067 __Pyx_RefNannyFinishContext();
33068 return NULL;
33069 __pyx_L4_argument_unpacking_done:;
33070 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_49getinfo(__pyx_self, __pyx_v_self);
33071
33072 /* function exit code */
33073 {
33074 Py_ssize_t __pyx_temp;
33075 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33076 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33077 }
33078 }
33079 __Pyx_RefNannyFinishContext();
33080 return __pyx_r;
33081 }
33082
33083 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
33084 PyObject *__pyx_r = NULL;
33085 __Pyx_RefNannyDeclarations
33086 PyObject *__pyx_t_1 = NULL;
33087 int __pyx_lineno = 0;
33088 const char *__pyx_filename = NULL;
33089 int __pyx_clineno = 0;
33090 __Pyx_RefNannySetupContext("getinfo", 1);
33091
33092 /* "pysam/libcvcf.pyx":965
33093 * def getinfo(self):
33094 * """ Dictionary of ##INFO tags, as VCF.FORMAT values """
33095 * return self._info # <<<<<<<<<<<<<<
33096 *
33097 * def setinfo(self,info):
33098 */
33099 __Pyx_XDECREF(__pyx_r);
33100 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_info); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 965, __pyx_L1_error)
33101 __Pyx_GOTREF(__pyx_t_1);
33102 __pyx_r = __pyx_t_1;
33103 __pyx_t_1 = 0;
33104 goto __pyx_L0;
33105
33106 /* "pysam/libcvcf.pyx":963
33107 * self._header = header
33108 *
33109 * def getinfo(self): # <<<<<<<<<<<<<<
33110 * """ Dictionary of ##INFO tags, as VCF.FORMAT values """
33111 * return self._info
33112 */
33113
33114 /* function exit code */
33115 __pyx_L1_error:;
33116 __Pyx_XDECREF(__pyx_t_1);
33117 __Pyx_AddTraceback("pysam.libcvcf.VCF.getinfo", __pyx_clineno, __pyx_lineno, __pyx_filename);
33118 __pyx_r = NULL;
33119 __pyx_L0:;
33120 __Pyx_XGIVEREF(__pyx_r);
33121 __Pyx_RefNannyFinishContext();
33122 return __pyx_r;
33123 }
33124
33125 /* "pysam/libcvcf.pyx":967
33126 * return self._info
33127 *
33128 * def setinfo(self,info): # <<<<<<<<<<<<<<
33129 * """ Dictionary of ##INFO tags, as VCF.FORMAT values """
33130 * self._info = info
33131 */
33132
33133 /* Python wrapper */
33134 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_52setinfo(PyObject *__pyx_self,
33135 #if CYTHON_METH_FASTCALL
33136 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
33137 #else
33138 PyObject *__pyx_args, PyObject *__pyx_kwds
33139 #endif
33140 ); /*proto*/
33141 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_51setinfo, "VCF.setinfo(self, info)\n Dictionary of ##INFO tags, as VCF.FORMAT values ");
33142 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_52setinfo = {"setinfo", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_52setinfo, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_51setinfo};
33143 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_52setinfo(PyObject *__pyx_self,
33144 #if CYTHON_METH_FASTCALL
33145 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
33146 #else
33147 PyObject *__pyx_args, PyObject *__pyx_kwds
33148 #endif
33149 ) {
33150 PyObject *__pyx_v_self = 0;
33151 PyObject *__pyx_v_info = 0;
33152 #if !CYTHON_METH_FASTCALL
33153 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
33154 #endif
33155 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
33156 PyObject* values[2] = {0,0};
33157 int __pyx_lineno = 0;
33158 const char *__pyx_filename = NULL;
33159 int __pyx_clineno = 0;
33160 PyObject *__pyx_r = 0;
33161 __Pyx_RefNannyDeclarations
33162 __Pyx_RefNannySetupContext("setinfo (wrapper)", 0);
33163 #if !CYTHON_METH_FASTCALL
33164 #if CYTHON_ASSUME_SAFE_MACROS
33165 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
33166 #else
33167 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
33168 #endif
33169 #endif
33170 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
33171 {
33172 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_info_2,0};
33173 if (__pyx_kwds) {
33174 Py_ssize_t kw_args;
33175 switch (__pyx_nargs) {
33176 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
33177 CYTHON_FALLTHROUGH;
33178 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33179 CYTHON_FALLTHROUGH;
33180 case 0: break;
33181 default: goto __pyx_L5_argtuple_error;
33182 }
33183 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
33184 switch (__pyx_nargs) {
33185 case 0:
33186 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
33187 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
33188 kw_args--;
33189 }
33190 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 967, __pyx_L3_error)
33191 else goto __pyx_L5_argtuple_error;
33192 CYTHON_FALLTHROUGH;
33193 case 1:
33194 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_info_2)) != 0)) {
33195 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
33196 kw_args--;
33197 }
33198 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 967, __pyx_L3_error)
33199 else {
33200 __Pyx_RaiseArgtupleInvalid("setinfo", 1, 2, 2, 1); __PYX_ERR(0, 967, __pyx_L3_error)
33201 }
33202 }
33203 if (unlikely(kw_args > 0)) {
33204 const Py_ssize_t kwd_pos_args = __pyx_nargs;
33205 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "setinfo") < 0)) __PYX_ERR(0, 967, __pyx_L3_error)
33206 }
33207 } else if (unlikely(__pyx_nargs != 2)) {
33208 goto __pyx_L5_argtuple_error;
33209 } else {
33210 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33211 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
33212 }
33213 __pyx_v_self = values[0];
33214 __pyx_v_info = values[1];
33215 }
33216 goto __pyx_L6_skip;
33217 __pyx_L5_argtuple_error:;
33218 __Pyx_RaiseArgtupleInvalid("setinfo", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 967, __pyx_L3_error)
33219 __pyx_L6_skip:;
33220 goto __pyx_L4_argument_unpacking_done;
33221 __pyx_L3_error:;
33222 {
33223 Py_ssize_t __pyx_temp;
33224 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33225 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33226 }
33227 }
33228 __Pyx_AddTraceback("pysam.libcvcf.VCF.setinfo", __pyx_clineno, __pyx_lineno, __pyx_filename);
33229 __Pyx_RefNannyFinishContext();
33230 return NULL;
33231 __pyx_L4_argument_unpacking_done:;
33232 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_51setinfo(__pyx_self, __pyx_v_self, __pyx_v_info);
33233
33234 /* function exit code */
33235 {
33236 Py_ssize_t __pyx_temp;
33237 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33238 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33239 }
33240 }
33241 __Pyx_RefNannyFinishContext();
33242 return __pyx_r;
33243 }
33244
33245 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_info) {
33246 PyObject *__pyx_r = NULL;
33247 __Pyx_RefNannyDeclarations
33248 int __pyx_lineno = 0;
33249 const char *__pyx_filename = NULL;
33250 int __pyx_clineno = 0;
33251 __Pyx_RefNannySetupContext("setinfo", 1);
33252
33253 /* "pysam/libcvcf.pyx":969
33254 * def setinfo(self,info):
33255 * """ Dictionary of ##INFO tags, as VCF.FORMAT values """
33256 * self._info = info # <<<<<<<<<<<<<<
33257 *
33258 * def getformat(self):
33259 */
33260 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_info, __pyx_v_info) < 0) __PYX_ERR(0, 969, __pyx_L1_error)
33261
33262 /* "pysam/libcvcf.pyx":967
33263 * return self._info
33264 *
33265 * def setinfo(self,info): # <<<<<<<<<<<<<<
33266 * """ Dictionary of ##INFO tags, as VCF.FORMAT values """
33267 * self._info = info
33268 */
33269
33270 /* function exit code */
33271 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
33272 goto __pyx_L0;
33273 __pyx_L1_error:;
33274 __Pyx_AddTraceback("pysam.libcvcf.VCF.setinfo", __pyx_clineno, __pyx_lineno, __pyx_filename);
33275 __pyx_r = NULL;
33276 __pyx_L0:;
33277 __Pyx_XGIVEREF(__pyx_r);
33278 __Pyx_RefNannyFinishContext();
33279 return __pyx_r;
33280 }
33281
33282 /* "pysam/libcvcf.pyx":971
33283 * self._info = info
33284 *
33285 * def getformat(self): # <<<<<<<<<<<<<<
33286 * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
33287 * return self._format
33288 */
33289
33290 /* Python wrapper */
33291 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_54getformat(PyObject *__pyx_self,
33292 #if CYTHON_METH_FASTCALL
33293 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
33294 #else
33295 PyObject *__pyx_args, PyObject *__pyx_kwds
33296 #endif
33297 ); /*proto*/
33298 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_53getformat, "VCF.getformat(self)\n Dictionary of ##FORMAT tags, as VCF.FORMAT values ");
33299 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_54getformat = {"getformat", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_54getformat, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_53getformat};
33300 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_54getformat(PyObject *__pyx_self,
33301 #if CYTHON_METH_FASTCALL
33302 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
33303 #else
33304 PyObject *__pyx_args, PyObject *__pyx_kwds
33305 #endif
33306 ) {
33307 PyObject *__pyx_v_self = 0;
33308 #if !CYTHON_METH_FASTCALL
33309 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
33310 #endif
33311 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
33312 PyObject* values[1] = {0};
33313 int __pyx_lineno = 0;
33314 const char *__pyx_filename = NULL;
33315 int __pyx_clineno = 0;
33316 PyObject *__pyx_r = 0;
33317 __Pyx_RefNannyDeclarations
33318 __Pyx_RefNannySetupContext("getformat (wrapper)", 0);
33319 #if !CYTHON_METH_FASTCALL
33320 #if CYTHON_ASSUME_SAFE_MACROS
33321 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
33322 #else
33323 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
33324 #endif
33325 #endif
33326 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
33327 {
33328 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0};
33329 if (__pyx_kwds) {
33330 Py_ssize_t kw_args;
33331 switch (__pyx_nargs) {
33332 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33333 CYTHON_FALLTHROUGH;
33334 case 0: break;
33335 default: goto __pyx_L5_argtuple_error;
33336 }
33337 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
33338 switch (__pyx_nargs) {
33339 case 0:
33340 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
33341 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
33342 kw_args--;
33343 }
33344 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 971, __pyx_L3_error)
33345 else goto __pyx_L5_argtuple_error;
33346 }
33347 if (unlikely(kw_args > 0)) {
33348 const Py_ssize_t kwd_pos_args = __pyx_nargs;
33349 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "getformat") < 0)) __PYX_ERR(0, 971, __pyx_L3_error)
33350 }
33351 } else if (unlikely(__pyx_nargs != 1)) {
33352 goto __pyx_L5_argtuple_error;
33353 } else {
33354 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33355 }
33356 __pyx_v_self = values[0];
33357 }
33358 goto __pyx_L6_skip;
33359 __pyx_L5_argtuple_error:;
33360 __Pyx_RaiseArgtupleInvalid("getformat", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 971, __pyx_L3_error)
33361 __pyx_L6_skip:;
33362 goto __pyx_L4_argument_unpacking_done;
33363 __pyx_L3_error:;
33364 {
33365 Py_ssize_t __pyx_temp;
33366 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33367 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33368 }
33369 }
33370 __Pyx_AddTraceback("pysam.libcvcf.VCF.getformat", __pyx_clineno, __pyx_lineno, __pyx_filename);
33371 __Pyx_RefNannyFinishContext();
33372 return NULL;
33373 __pyx_L4_argument_unpacking_done:;
33374 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_53getformat(__pyx_self, __pyx_v_self);
33375
33376 /* function exit code */
33377 {
33378 Py_ssize_t __pyx_temp;
33379 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33380 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33381 }
33382 }
33383 __Pyx_RefNannyFinishContext();
33384 return __pyx_r;
33385 }
33386
33387 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
33388 PyObject *__pyx_r = NULL;
33389 __Pyx_RefNannyDeclarations
33390 PyObject *__pyx_t_1 = NULL;
33391 int __pyx_lineno = 0;
33392 const char *__pyx_filename = NULL;
33393 int __pyx_clineno = 0;
33394 __Pyx_RefNannySetupContext("getformat", 1);
33395
33396 /* "pysam/libcvcf.pyx":973
33397 * def getformat(self):
33398 * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
33399 * return self._format # <<<<<<<<<<<<<<
33400 *
33401 * def setformat(self,format):
33402 */
33403 __Pyx_XDECREF(__pyx_r);
33404 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_format_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 973, __pyx_L1_error)
33405 __Pyx_GOTREF(__pyx_t_1);
33406 __pyx_r = __pyx_t_1;
33407 __pyx_t_1 = 0;
33408 goto __pyx_L0;
33409
33410 /* "pysam/libcvcf.pyx":971
33411 * self._info = info
33412 *
33413 * def getformat(self): # <<<<<<<<<<<<<<
33414 * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
33415 * return self._format
33416 */
33417
33418 /* function exit code */
33419 __pyx_L1_error:;
33420 __Pyx_XDECREF(__pyx_t_1);
33421 __Pyx_AddTraceback("pysam.libcvcf.VCF.getformat", __pyx_clineno, __pyx_lineno, __pyx_filename);
33422 __pyx_r = NULL;
33423 __pyx_L0:;
33424 __Pyx_XGIVEREF(__pyx_r);
33425 __Pyx_RefNannyFinishContext();
33426 return __pyx_r;
33427 }
33428
33429 /* "pysam/libcvcf.pyx":975
33430 * return self._format
33431 *
33432 * def setformat(self,format): # <<<<<<<<<<<<<<
33433 * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
33434 * self._format = format
33435 */
33436
33437 /* Python wrapper */
33438 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_56setformat(PyObject *__pyx_self,
33439 #if CYTHON_METH_FASTCALL
33440 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
33441 #else
33442 PyObject *__pyx_args, PyObject *__pyx_kwds
33443 #endif
33444 ); /*proto*/
33445 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_55setformat, "VCF.setformat(self, format)\n Dictionary of ##FORMAT tags, as VCF.FORMAT values ");
33446 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_56setformat = {"setformat", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_56setformat, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_55setformat};
33447 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_56setformat(PyObject *__pyx_self,
33448 #if CYTHON_METH_FASTCALL
33449 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
33450 #else
33451 PyObject *__pyx_args, PyObject *__pyx_kwds
33452 #endif
33453 ) {
33454 PyObject *__pyx_v_self = 0;
33455 PyObject *__pyx_v_format = 0;
33456 #if !CYTHON_METH_FASTCALL
33457 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
33458 #endif
33459 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
33460 PyObject* values[2] = {0,0};
33461 int __pyx_lineno = 0;
33462 const char *__pyx_filename = NULL;
33463 int __pyx_clineno = 0;
33464 PyObject *__pyx_r = 0;
33465 __Pyx_RefNannyDeclarations
33466 __Pyx_RefNannySetupContext("setformat (wrapper)", 0);
33467 #if !CYTHON_METH_FASTCALL
33468 #if CYTHON_ASSUME_SAFE_MACROS
33469 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
33470 #else
33471 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
33472 #endif
33473 #endif
33474 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
33475 {
33476 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_format,0};
33477 if (__pyx_kwds) {
33478 Py_ssize_t kw_args;
33479 switch (__pyx_nargs) {
33480 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
33481 CYTHON_FALLTHROUGH;
33482 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33483 CYTHON_FALLTHROUGH;
33484 case 0: break;
33485 default: goto __pyx_L5_argtuple_error;
33486 }
33487 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
33488 switch (__pyx_nargs) {
33489 case 0:
33490 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
33491 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
33492 kw_args--;
33493 }
33494 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 975, __pyx_L3_error)
33495 else goto __pyx_L5_argtuple_error;
33496 CYTHON_FALLTHROUGH;
33497 case 1:
33498 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_format)) != 0)) {
33499 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
33500 kw_args--;
33501 }
33502 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 975, __pyx_L3_error)
33503 else {
33504 __Pyx_RaiseArgtupleInvalid("setformat", 1, 2, 2, 1); __PYX_ERR(0, 975, __pyx_L3_error)
33505 }
33506 }
33507 if (unlikely(kw_args > 0)) {
33508 const Py_ssize_t kwd_pos_args = __pyx_nargs;
33509 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "setformat") < 0)) __PYX_ERR(0, 975, __pyx_L3_error)
33510 }
33511 } else if (unlikely(__pyx_nargs != 2)) {
33512 goto __pyx_L5_argtuple_error;
33513 } else {
33514 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33515 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
33516 }
33517 __pyx_v_self = values[0];
33518 __pyx_v_format = values[1];
33519 }
33520 goto __pyx_L6_skip;
33521 __pyx_L5_argtuple_error:;
33522 __Pyx_RaiseArgtupleInvalid("setformat", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 975, __pyx_L3_error)
33523 __pyx_L6_skip:;
33524 goto __pyx_L4_argument_unpacking_done;
33525 __pyx_L3_error:;
33526 {
33527 Py_ssize_t __pyx_temp;
33528 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33529 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33530 }
33531 }
33532 __Pyx_AddTraceback("pysam.libcvcf.VCF.setformat", __pyx_clineno, __pyx_lineno, __pyx_filename);
33533 __Pyx_RefNannyFinishContext();
33534 return NULL;
33535 __pyx_L4_argument_unpacking_done:;
33536 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_55setformat(__pyx_self, __pyx_v_self, __pyx_v_format);
33537
33538 /* function exit code */
33539 {
33540 Py_ssize_t __pyx_temp;
33541 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33542 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33543 }
33544 }
33545 __Pyx_RefNannyFinishContext();
33546 return __pyx_r;
33547 }
33548
33549 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format) {
33550 PyObject *__pyx_r = NULL;
33551 __Pyx_RefNannyDeclarations
33552 int __pyx_lineno = 0;
33553 const char *__pyx_filename = NULL;
33554 int __pyx_clineno = 0;
33555 __Pyx_RefNannySetupContext("setformat", 1);
33556
33557 /* "pysam/libcvcf.pyx":977
33558 * def setformat(self,format):
33559 * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
33560 * self._format = format # <<<<<<<<<<<<<<
33561 *
33562 * def getfilter(self):
33563 */
33564 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_format_2, __pyx_v_format) < 0) __PYX_ERR(0, 977, __pyx_L1_error)
33565
33566 /* "pysam/libcvcf.pyx":975
33567 * return self._format
33568 *
33569 * def setformat(self,format): # <<<<<<<<<<<<<<
33570 * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
33571 * self._format = format
33572 */
33573
33574 /* function exit code */
33575 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
33576 goto __pyx_L0;
33577 __pyx_L1_error:;
33578 __Pyx_AddTraceback("pysam.libcvcf.VCF.setformat", __pyx_clineno, __pyx_lineno, __pyx_filename);
33579 __pyx_r = NULL;
33580 __pyx_L0:;
33581 __Pyx_XGIVEREF(__pyx_r);
33582 __Pyx_RefNannyFinishContext();
33583 return __pyx_r;
33584 }
33585
33586 /* "pysam/libcvcf.pyx":979
33587 * self._format = format
33588 *
33589 * def getfilter(self): # <<<<<<<<<<<<<<
33590 * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
33591 * return self._filter
33592 */
33593
33594 /* Python wrapper */
33595 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_58getfilter(PyObject *__pyx_self,
33596 #if CYTHON_METH_FASTCALL
33597 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
33598 #else
33599 PyObject *__pyx_args, PyObject *__pyx_kwds
33600 #endif
33601 ); /*proto*/
33602 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_57getfilter, "VCF.getfilter(self)\n Dictionary of ##FILTER tags, as VCF.FORMAT values ");
33603 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_58getfilter = {"getfilter", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_58getfilter, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_57getfilter};
33604 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_58getfilter(PyObject *__pyx_self,
33605 #if CYTHON_METH_FASTCALL
33606 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
33607 #else
33608 PyObject *__pyx_args, PyObject *__pyx_kwds
33609 #endif
33610 ) {
33611 PyObject *__pyx_v_self = 0;
33612 #if !CYTHON_METH_FASTCALL
33613 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
33614 #endif
33615 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
33616 PyObject* values[1] = {0};
33617 int __pyx_lineno = 0;
33618 const char *__pyx_filename = NULL;
33619 int __pyx_clineno = 0;
33620 PyObject *__pyx_r = 0;
33621 __Pyx_RefNannyDeclarations
33622 __Pyx_RefNannySetupContext("getfilter (wrapper)", 0);
33623 #if !CYTHON_METH_FASTCALL
33624 #if CYTHON_ASSUME_SAFE_MACROS
33625 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
33626 #else
33627 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
33628 #endif
33629 #endif
33630 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
33631 {
33632 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0};
33633 if (__pyx_kwds) {
33634 Py_ssize_t kw_args;
33635 switch (__pyx_nargs) {
33636 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33637 CYTHON_FALLTHROUGH;
33638 case 0: break;
33639 default: goto __pyx_L5_argtuple_error;
33640 }
33641 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
33642 switch (__pyx_nargs) {
33643 case 0:
33644 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
33645 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
33646 kw_args--;
33647 }
33648 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 979, __pyx_L3_error)
33649 else goto __pyx_L5_argtuple_error;
33650 }
33651 if (unlikely(kw_args > 0)) {
33652 const Py_ssize_t kwd_pos_args = __pyx_nargs;
33653 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "getfilter") < 0)) __PYX_ERR(0, 979, __pyx_L3_error)
33654 }
33655 } else if (unlikely(__pyx_nargs != 1)) {
33656 goto __pyx_L5_argtuple_error;
33657 } else {
33658 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33659 }
33660 __pyx_v_self = values[0];
33661 }
33662 goto __pyx_L6_skip;
33663 __pyx_L5_argtuple_error:;
33664 __Pyx_RaiseArgtupleInvalid("getfilter", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 979, __pyx_L3_error)
33665 __pyx_L6_skip:;
33666 goto __pyx_L4_argument_unpacking_done;
33667 __pyx_L3_error:;
33668 {
33669 Py_ssize_t __pyx_temp;
33670 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33671 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33672 }
33673 }
33674 __Pyx_AddTraceback("pysam.libcvcf.VCF.getfilter", __pyx_clineno, __pyx_lineno, __pyx_filename);
33675 __Pyx_RefNannyFinishContext();
33676 return NULL;
33677 __pyx_L4_argument_unpacking_done:;
33678 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_57getfilter(__pyx_self, __pyx_v_self);
33679
33680 /* function exit code */
33681 {
33682 Py_ssize_t __pyx_temp;
33683 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33684 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33685 }
33686 }
33687 __Pyx_RefNannyFinishContext();
33688 return __pyx_r;
33689 }
33690
33691 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
33692 PyObject *__pyx_r = NULL;
33693 __Pyx_RefNannyDeclarations
33694 PyObject *__pyx_t_1 = NULL;
33695 int __pyx_lineno = 0;
33696 const char *__pyx_filename = NULL;
33697 int __pyx_clineno = 0;
33698 __Pyx_RefNannySetupContext("getfilter", 1);
33699
33700 /* "pysam/libcvcf.pyx":981
33701 * def getfilter(self):
33702 * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
33703 * return self._filter # <<<<<<<<<<<<<<
33704 *
33705 * def setfilter(self,filter):
33706 */
33707 __Pyx_XDECREF(__pyx_r);
33708 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_filter); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 981, __pyx_L1_error)
33709 __Pyx_GOTREF(__pyx_t_1);
33710 __pyx_r = __pyx_t_1;
33711 __pyx_t_1 = 0;
33712 goto __pyx_L0;
33713
33714 /* "pysam/libcvcf.pyx":979
33715 * self._format = format
33716 *
33717 * def getfilter(self): # <<<<<<<<<<<<<<
33718 * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
33719 * return self._filter
33720 */
33721
33722 /* function exit code */
33723 __pyx_L1_error:;
33724 __Pyx_XDECREF(__pyx_t_1);
33725 __Pyx_AddTraceback("pysam.libcvcf.VCF.getfilter", __pyx_clineno, __pyx_lineno, __pyx_filename);
33726 __pyx_r = NULL;
33727 __pyx_L0:;
33728 __Pyx_XGIVEREF(__pyx_r);
33729 __Pyx_RefNannyFinishContext();
33730 return __pyx_r;
33731 }
33732
33733 /* "pysam/libcvcf.pyx":983
33734 * return self._filter
33735 *
33736 * def setfilter(self,filter): # <<<<<<<<<<<<<<
33737 * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
33738 * self._filter = filter
33739 */
33740
33741 /* Python wrapper */
33742 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_60setfilter(PyObject *__pyx_self,
33743 #if CYTHON_METH_FASTCALL
33744 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
33745 #else
33746 PyObject *__pyx_args, PyObject *__pyx_kwds
33747 #endif
33748 ); /*proto*/
33749 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_59setfilter, "VCF.setfilter(self, filter)\n Dictionary of ##FILTER tags, as VCF.FORMAT values ");
33750 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_60setfilter = {"setfilter", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_60setfilter, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_59setfilter};
33751 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_60setfilter(PyObject *__pyx_self,
33752 #if CYTHON_METH_FASTCALL
33753 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
33754 #else
33755 PyObject *__pyx_args, PyObject *__pyx_kwds
33756 #endif
33757 ) {
33758 PyObject *__pyx_v_self = 0;
33759 PyObject *__pyx_v_filter = 0;
33760 #if !CYTHON_METH_FASTCALL
33761 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
33762 #endif
33763 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
33764 PyObject* values[2] = {0,0};
33765 int __pyx_lineno = 0;
33766 const char *__pyx_filename = NULL;
33767 int __pyx_clineno = 0;
33768 PyObject *__pyx_r = 0;
33769 __Pyx_RefNannyDeclarations
33770 __Pyx_RefNannySetupContext("setfilter (wrapper)", 0);
33771 #if !CYTHON_METH_FASTCALL
33772 #if CYTHON_ASSUME_SAFE_MACROS
33773 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
33774 #else
33775 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
33776 #endif
33777 #endif
33778 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
33779 {
33780 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_filter_2,0};
33781 if (__pyx_kwds) {
33782 Py_ssize_t kw_args;
33783 switch (__pyx_nargs) {
33784 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
33785 CYTHON_FALLTHROUGH;
33786 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33787 CYTHON_FALLTHROUGH;
33788 case 0: break;
33789 default: goto __pyx_L5_argtuple_error;
33790 }
33791 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
33792 switch (__pyx_nargs) {
33793 case 0:
33794 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
33795 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
33796 kw_args--;
33797 }
33798 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 983, __pyx_L3_error)
33799 else goto __pyx_L5_argtuple_error;
33800 CYTHON_FALLTHROUGH;
33801 case 1:
33802 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filter_2)) != 0)) {
33803 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
33804 kw_args--;
33805 }
33806 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 983, __pyx_L3_error)
33807 else {
33808 __Pyx_RaiseArgtupleInvalid("setfilter", 1, 2, 2, 1); __PYX_ERR(0, 983, __pyx_L3_error)
33809 }
33810 }
33811 if (unlikely(kw_args > 0)) {
33812 const Py_ssize_t kwd_pos_args = __pyx_nargs;
33813 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "setfilter") < 0)) __PYX_ERR(0, 983, __pyx_L3_error)
33814 }
33815 } else if (unlikely(__pyx_nargs != 2)) {
33816 goto __pyx_L5_argtuple_error;
33817 } else {
33818 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33819 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
33820 }
33821 __pyx_v_self = values[0];
33822 __pyx_v_filter = values[1];
33823 }
33824 goto __pyx_L6_skip;
33825 __pyx_L5_argtuple_error:;
33826 __Pyx_RaiseArgtupleInvalid("setfilter", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 983, __pyx_L3_error)
33827 __pyx_L6_skip:;
33828 goto __pyx_L4_argument_unpacking_done;
33829 __pyx_L3_error:;
33830 {
33831 Py_ssize_t __pyx_temp;
33832 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33833 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33834 }
33835 }
33836 __Pyx_AddTraceback("pysam.libcvcf.VCF.setfilter", __pyx_clineno, __pyx_lineno, __pyx_filename);
33837 __Pyx_RefNannyFinishContext();
33838 return NULL;
33839 __pyx_L4_argument_unpacking_done:;
33840 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_59setfilter(__pyx_self, __pyx_v_self, __pyx_v_filter);
33841
33842 /* function exit code */
33843 {
33844 Py_ssize_t __pyx_temp;
33845 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33846 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33847 }
33848 }
33849 __Pyx_RefNannyFinishContext();
33850 return __pyx_r;
33851 }
33852
33853 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filter) {
33854 PyObject *__pyx_r = NULL;
33855 __Pyx_RefNannyDeclarations
33856 int __pyx_lineno = 0;
33857 const char *__pyx_filename = NULL;
33858 int __pyx_clineno = 0;
33859 __Pyx_RefNannySetupContext("setfilter", 1);
33860
33861 /* "pysam/libcvcf.pyx":985
33862 * def setfilter(self,filter):
33863 * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
33864 * self._filter = filter # <<<<<<<<<<<<<<
33865 *
33866 * def setversion(self, version):
33867 */
33868 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_filter, __pyx_v_filter) < 0) __PYX_ERR(0, 985, __pyx_L1_error)
33869
33870 /* "pysam/libcvcf.pyx":983
33871 * return self._filter
33872 *
33873 * def setfilter(self,filter): # <<<<<<<<<<<<<<
33874 * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
33875 * self._filter = filter
33876 */
33877
33878 /* function exit code */
33879 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
33880 goto __pyx_L0;
33881 __pyx_L1_error:;
33882 __Pyx_AddTraceback("pysam.libcvcf.VCF.setfilter", __pyx_clineno, __pyx_lineno, __pyx_filename);
33883 __pyx_r = NULL;
33884 __pyx_L0:;
33885 __Pyx_XGIVEREF(__pyx_r);
33886 __Pyx_RefNannyFinishContext();
33887 return __pyx_r;
33888 }
33889
33890 /* "pysam/libcvcf.pyx":987
33891 * self._filter = filter
33892 *
33893 * def setversion(self, version): # <<<<<<<<<<<<<<
33894 * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")
33895 * self._version = version
33896 */
33897
33898 /* Python wrapper */
33899 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_62setversion(PyObject *__pyx_self,
33900 #if CYTHON_METH_FASTCALL
33901 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
33902 #else
33903 PyObject *__pyx_args, PyObject *__pyx_kwds
33904 #endif
33905 ); /*proto*/
33906 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_61setversion, "VCF.setversion(self, version)");
33907 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_62setversion = {"setversion", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_62setversion, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_61setversion};
33908 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_62setversion(PyObject *__pyx_self,
33909 #if CYTHON_METH_FASTCALL
33910 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
33911 #else
33912 PyObject *__pyx_args, PyObject *__pyx_kwds
33913 #endif
33914 ) {
33915 PyObject *__pyx_v_self = 0;
33916 PyObject *__pyx_v_version = 0;
33917 #if !CYTHON_METH_FASTCALL
33918 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
33919 #endif
33920 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
33921 PyObject* values[2] = {0,0};
33922 int __pyx_lineno = 0;
33923 const char *__pyx_filename = NULL;
33924 int __pyx_clineno = 0;
33925 PyObject *__pyx_r = 0;
33926 __Pyx_RefNannyDeclarations
33927 __Pyx_RefNannySetupContext("setversion (wrapper)", 0);
33928 #if !CYTHON_METH_FASTCALL
33929 #if CYTHON_ASSUME_SAFE_MACROS
33930 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
33931 #else
33932 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
33933 #endif
33934 #endif
33935 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
33936 {
33937 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_version_2,0};
33938 if (__pyx_kwds) {
33939 Py_ssize_t kw_args;
33940 switch (__pyx_nargs) {
33941 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
33942 CYTHON_FALLTHROUGH;
33943 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33944 CYTHON_FALLTHROUGH;
33945 case 0: break;
33946 default: goto __pyx_L5_argtuple_error;
33947 }
33948 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
33949 switch (__pyx_nargs) {
33950 case 0:
33951 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
33952 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
33953 kw_args--;
33954 }
33955 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 987, __pyx_L3_error)
33956 else goto __pyx_L5_argtuple_error;
33957 CYTHON_FALLTHROUGH;
33958 case 1:
33959 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_version_2)) != 0)) {
33960 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
33961 kw_args--;
33962 }
33963 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 987, __pyx_L3_error)
33964 else {
33965 __Pyx_RaiseArgtupleInvalid("setversion", 1, 2, 2, 1); __PYX_ERR(0, 987, __pyx_L3_error)
33966 }
33967 }
33968 if (unlikely(kw_args > 0)) {
33969 const Py_ssize_t kwd_pos_args = __pyx_nargs;
33970 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "setversion") < 0)) __PYX_ERR(0, 987, __pyx_L3_error)
33971 }
33972 } else if (unlikely(__pyx_nargs != 2)) {
33973 goto __pyx_L5_argtuple_error;
33974 } else {
33975 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
33976 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
33977 }
33978 __pyx_v_self = values[0];
33979 __pyx_v_version = values[1];
33980 }
33981 goto __pyx_L6_skip;
33982 __pyx_L5_argtuple_error:;
33983 __Pyx_RaiseArgtupleInvalid("setversion", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 987, __pyx_L3_error)
33984 __pyx_L6_skip:;
33985 goto __pyx_L4_argument_unpacking_done;
33986 __pyx_L3_error:;
33987 {
33988 Py_ssize_t __pyx_temp;
33989 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
33990 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
33991 }
33992 }
33993 __Pyx_AddTraceback("pysam.libcvcf.VCF.setversion", __pyx_clineno, __pyx_lineno, __pyx_filename);
33994 __Pyx_RefNannyFinishContext();
33995 return NULL;
33996 __pyx_L4_argument_unpacking_done:;
33997 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_61setversion(__pyx_self, __pyx_v_self, __pyx_v_version);
33998
33999 /* function exit code */
34000 {
34001 Py_ssize_t __pyx_temp;
34002 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
34003 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
34004 }
34005 }
34006 __Pyx_RefNannyFinishContext();
34007 return __pyx_r;
34008 }
34009
34010 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_version) {
34011 PyObject *__pyx_r = NULL;
34012 __Pyx_RefNannyDeclarations
34013 int __pyx_t_1;
34014 int __pyx_t_2;
34015 PyObject *__pyx_t_3 = NULL;
34016 int __pyx_lineno = 0;
34017 const char *__pyx_filename = NULL;
34018 int __pyx_clineno = 0;
34019 __Pyx_RefNannySetupContext("setversion", 1);
34020
34021 /* "pysam/libcvcf.pyx":988
34022 *
34023 * def setversion(self, version):
34024 * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") # <<<<<<<<<<<<<<
34025 * self._version = version
34026 *
34027 */
34028 __pyx_t_2 = (__Pyx_PyInt_BoolNeObjC(__pyx_v_version, __pyx_int_33, 33, 0)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 988, __pyx_L1_error)
34029 if (__pyx_t_2) {
34030 } else {
34031 __pyx_t_1 = __pyx_t_2;
34032 goto __pyx_L4_bool_binop_done;
34033 }
34034 __pyx_t_2 = (__Pyx_PyInt_BoolNeObjC(__pyx_v_version, __pyx_int_40, 40, 0)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 988, __pyx_L1_error)
34035 __pyx_t_1 = __pyx_t_2;
34036 __pyx_L4_bool_binop_done:;
34037 if (unlikely(__pyx_t_1)) {
34038 __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__30, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 988, __pyx_L1_error)
34039 __Pyx_GOTREF(__pyx_t_3);
34040 __Pyx_Raise(__pyx_t_3, 0, 0, 0);
34041 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
34042 __PYX_ERR(0, 988, __pyx_L1_error)
34043 }
34044
34045 /* "pysam/libcvcf.pyx":989
34046 * def setversion(self, version):
34047 * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")
34048 * self._version = version # <<<<<<<<<<<<<<
34049 *
34050 * def setregions(self, regions):
34051 */
34052 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_version, __pyx_v_version) < 0) __PYX_ERR(0, 989, __pyx_L1_error)
34053
34054 /* "pysam/libcvcf.pyx":987
34055 * self._filter = filter
34056 *
34057 * def setversion(self, version): # <<<<<<<<<<<<<<
34058 * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")
34059 * self._version = version
34060 */
34061
34062 /* function exit code */
34063 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
34064 goto __pyx_L0;
34065 __pyx_L1_error:;
34066 __Pyx_XDECREF(__pyx_t_3);
34067 __Pyx_AddTraceback("pysam.libcvcf.VCF.setversion", __pyx_clineno, __pyx_lineno, __pyx_filename);
34068 __pyx_r = NULL;
34069 __pyx_L0:;
34070 __Pyx_XGIVEREF(__pyx_r);
34071 __Pyx_RefNannyFinishContext();
34072 return __pyx_r;
34073 }
34074
34075 /* "pysam/libcvcf.pyx":991
34076 * self._version = version
34077 *
34078 * def setregions(self, regions): # <<<<<<<<<<<<<<
34079 * self._regions = regions
34080 *
34081 */
34082
34083 /* Python wrapper */
34084 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_64setregions(PyObject *__pyx_self,
34085 #if CYTHON_METH_FASTCALL
34086 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
34087 #else
34088 PyObject *__pyx_args, PyObject *__pyx_kwds
34089 #endif
34090 ); /*proto*/
34091 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_63setregions, "VCF.setregions(self, regions)");
34092 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_64setregions = {"setregions", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_64setregions, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_63setregions};
34093 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_64setregions(PyObject *__pyx_self,
34094 #if CYTHON_METH_FASTCALL
34095 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
34096 #else
34097 PyObject *__pyx_args, PyObject *__pyx_kwds
34098 #endif
34099 ) {
34100 PyObject *__pyx_v_self = 0;
34101 PyObject *__pyx_v_regions = 0;
34102 #if !CYTHON_METH_FASTCALL
34103 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
34104 #endif
34105 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
34106 PyObject* values[2] = {0,0};
34107 int __pyx_lineno = 0;
34108 const char *__pyx_filename = NULL;
34109 int __pyx_clineno = 0;
34110 PyObject *__pyx_r = 0;
34111 __Pyx_RefNannyDeclarations
34112 __Pyx_RefNannySetupContext("setregions (wrapper)", 0);
34113 #if !CYTHON_METH_FASTCALL
34114 #if CYTHON_ASSUME_SAFE_MACROS
34115 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
34116 #else
34117 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
34118 #endif
34119 #endif
34120 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
34121 {
34122 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_regions,0};
34123 if (__pyx_kwds) {
34124 Py_ssize_t kw_args;
34125 switch (__pyx_nargs) {
34126 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
34127 CYTHON_FALLTHROUGH;
34128 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
34129 CYTHON_FALLTHROUGH;
34130 case 0: break;
34131 default: goto __pyx_L5_argtuple_error;
34132 }
34133 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
34134 switch (__pyx_nargs) {
34135 case 0:
34136 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
34137 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
34138 kw_args--;
34139 }
34140 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L3_error)
34141 else goto __pyx_L5_argtuple_error;
34142 CYTHON_FALLTHROUGH;
34143 case 1:
34144 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_regions)) != 0)) {
34145 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
34146 kw_args--;
34147 }
34148 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L3_error)
34149 else {
34150 __Pyx_RaiseArgtupleInvalid("setregions", 1, 2, 2, 1); __PYX_ERR(0, 991, __pyx_L3_error)
34151 }
34152 }
34153 if (unlikely(kw_args > 0)) {
34154 const Py_ssize_t kwd_pos_args = __pyx_nargs;
34155 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "setregions") < 0)) __PYX_ERR(0, 991, __pyx_L3_error)
34156 }
34157 } else if (unlikely(__pyx_nargs != 2)) {
34158 goto __pyx_L5_argtuple_error;
34159 } else {
34160 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
34161 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
34162 }
34163 __pyx_v_self = values[0];
34164 __pyx_v_regions = values[1];
34165 }
34166 goto __pyx_L6_skip;
34167 __pyx_L5_argtuple_error:;
34168 __Pyx_RaiseArgtupleInvalid("setregions", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 991, __pyx_L3_error)
34169 __pyx_L6_skip:;
34170 goto __pyx_L4_argument_unpacking_done;
34171 __pyx_L3_error:;
34172 {
34173 Py_ssize_t __pyx_temp;
34174 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
34175 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
34176 }
34177 }
34178 __Pyx_AddTraceback("pysam.libcvcf.VCF.setregions", __pyx_clineno, __pyx_lineno, __pyx_filename);
34179 __Pyx_RefNannyFinishContext();
34180 return NULL;
34181 __pyx_L4_argument_unpacking_done:;
34182 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_63setregions(__pyx_self, __pyx_v_self, __pyx_v_regions);
34183
34184 /* function exit code */
34185 {
34186 Py_ssize_t __pyx_temp;
34187 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
34188 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
34189 }
34190 }
34191 __Pyx_RefNannyFinishContext();
34192 return __pyx_r;
34193 }
34194
34195 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_regions) {
34196 PyObject *__pyx_r = NULL;
34197 __Pyx_RefNannyDeclarations
34198 int __pyx_lineno = 0;
34199 const char *__pyx_filename = NULL;
34200 int __pyx_clineno = 0;
34201 __Pyx_RefNannySetupContext("setregions", 1);
34202
34203 /* "pysam/libcvcf.pyx":992
34204 *
34205 * def setregions(self, regions):
34206 * self._regions = regions # <<<<<<<<<<<<<<
34207 *
34208 * def setreference(self, ref):
34209 */
34210 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_regions_2, __pyx_v_regions) < 0) __PYX_ERR(0, 992, __pyx_L1_error)
34211
34212 /* "pysam/libcvcf.pyx":991
34213 * self._version = version
34214 *
34215 * def setregions(self, regions): # <<<<<<<<<<<<<<
34216 * self._regions = regions
34217 *
34218 */
34219
34220 /* function exit code */
34221 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
34222 goto __pyx_L0;
34223 __pyx_L1_error:;
34224 __Pyx_AddTraceback("pysam.libcvcf.VCF.setregions", __pyx_clineno, __pyx_lineno, __pyx_filename);
34225 __pyx_r = NULL;
34226 __pyx_L0:;
34227 __Pyx_XGIVEREF(__pyx_r);
34228 __Pyx_RefNannyFinishContext();
34229 return __pyx_r;
34230 }
34231
34232 /* "pysam/libcvcf.pyx":994
34233 * self._regions = regions
34234 *
34235 * def setreference(self, ref): # <<<<<<<<<<<<<<
34236 * """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
34237 * self._reference = ref
34238 */
34239
34240 /* Python wrapper */
34241 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_66setreference(PyObject *__pyx_self,
34242 #if CYTHON_METH_FASTCALL
34243 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
34244 #else
34245 PyObject *__pyx_args, PyObject *__pyx_kwds
34246 #endif
34247 ); /*proto*/
34248 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_65setreference, "VCF.setreference(self, ref)\n Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile ");
34249 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_66setreference = {"setreference", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_66setreference, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_65setreference};
34250 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_66setreference(PyObject *__pyx_self,
34251 #if CYTHON_METH_FASTCALL
34252 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
34253 #else
34254 PyObject *__pyx_args, PyObject *__pyx_kwds
34255 #endif
34256 ) {
34257 PyObject *__pyx_v_self = 0;
34258 PyObject *__pyx_v_ref = 0;
34259 #if !CYTHON_METH_FASTCALL
34260 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
34261 #endif
34262 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
34263 PyObject* values[2] = {0,0};
34264 int __pyx_lineno = 0;
34265 const char *__pyx_filename = NULL;
34266 int __pyx_clineno = 0;
34267 PyObject *__pyx_r = 0;
34268 __Pyx_RefNannyDeclarations
34269 __Pyx_RefNannySetupContext("setreference (wrapper)", 0);
34270 #if !CYTHON_METH_FASTCALL
34271 #if CYTHON_ASSUME_SAFE_MACROS
34272 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
34273 #else
34274 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
34275 #endif
34276 #endif
34277 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
34278 {
34279 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_ref,0};
34280 if (__pyx_kwds) {
34281 Py_ssize_t kw_args;
34282 switch (__pyx_nargs) {
34283 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
34284 CYTHON_FALLTHROUGH;
34285 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
34286 CYTHON_FALLTHROUGH;
34287 case 0: break;
34288 default: goto __pyx_L5_argtuple_error;
34289 }
34290 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
34291 switch (__pyx_nargs) {
34292 case 0:
34293 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
34294 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
34295 kw_args--;
34296 }
34297 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 994, __pyx_L3_error)
34298 else goto __pyx_L5_argtuple_error;
34299 CYTHON_FALLTHROUGH;
34300 case 1:
34301 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_ref)) != 0)) {
34302 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
34303 kw_args--;
34304 }
34305 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 994, __pyx_L3_error)
34306 else {
34307 __Pyx_RaiseArgtupleInvalid("setreference", 1, 2, 2, 1); __PYX_ERR(0, 994, __pyx_L3_error)
34308 }
34309 }
34310 if (unlikely(kw_args > 0)) {
34311 const Py_ssize_t kwd_pos_args = __pyx_nargs;
34312 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "setreference") < 0)) __PYX_ERR(0, 994, __pyx_L3_error)
34313 }
34314 } else if (unlikely(__pyx_nargs != 2)) {
34315 goto __pyx_L5_argtuple_error;
34316 } else {
34317 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
34318 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
34319 }
34320 __pyx_v_self = values[0];
34321 __pyx_v_ref = values[1];
34322 }
34323 goto __pyx_L6_skip;
34324 __pyx_L5_argtuple_error:;
34325 __Pyx_RaiseArgtupleInvalid("setreference", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 994, __pyx_L3_error)
34326 __pyx_L6_skip:;
34327 goto __pyx_L4_argument_unpacking_done;
34328 __pyx_L3_error:;
34329 {
34330 Py_ssize_t __pyx_temp;
34331 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
34332 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
34333 }
34334 }
34335 __Pyx_AddTraceback("pysam.libcvcf.VCF.setreference", __pyx_clineno, __pyx_lineno, __pyx_filename);
34336 __Pyx_RefNannyFinishContext();
34337 return NULL;
34338 __pyx_L4_argument_unpacking_done:;
34339 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_65setreference(__pyx_self, __pyx_v_self, __pyx_v_ref);
34340
34341 /* function exit code */
34342 {
34343 Py_ssize_t __pyx_temp;
34344 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
34345 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
34346 }
34347 }
34348 __Pyx_RefNannyFinishContext();
34349 return __pyx_r;
34350 }
34351
34352 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_ref) {
34353 PyObject *__pyx_r = NULL;
34354 __Pyx_RefNannyDeclarations
34355 int __pyx_lineno = 0;
34356 const char *__pyx_filename = NULL;
34357 int __pyx_clineno = 0;
34358 __Pyx_RefNannySetupContext("setreference", 1);
34359
34360 /* "pysam/libcvcf.pyx":996
34361 * def setreference(self, ref):
34362 * """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
34363 * self._reference = ref # <<<<<<<<<<<<<<
34364 *
34365 * def ignoreerror(self, errorstring):
34366 */
34367 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_reference_2, __pyx_v_ref) < 0) __PYX_ERR(0, 996, __pyx_L1_error)
34368
34369 /* "pysam/libcvcf.pyx":994
34370 * self._regions = regions
34371 *
34372 * def setreference(self, ref): # <<<<<<<<<<<<<<
34373 * """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
34374 * self._reference = ref
34375 */
34376
34377 /* function exit code */
34378 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
34379 goto __pyx_L0;
34380 __pyx_L1_error:;
34381 __Pyx_AddTraceback("pysam.libcvcf.VCF.setreference", __pyx_clineno, __pyx_lineno, __pyx_filename);
34382 __pyx_r = NULL;
34383 __pyx_L0:;
34384 __Pyx_XGIVEREF(__pyx_r);
34385 __Pyx_RefNannyFinishContext();
34386 return __pyx_r;
34387 }
34388
34389 /* "pysam/libcvcf.pyx":998
34390 * self._reference = ref
34391 *
34392 * def ignoreerror(self, errorstring): # <<<<<<<<<<<<<<
34393 * try: self._ignored_errors.add(self.__dict__[errorstring])
34394 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
34395 */
34396
34397 /* Python wrapper */
34398 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_68ignoreerror(PyObject *__pyx_self,
34399 #if CYTHON_METH_FASTCALL
34400 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
34401 #else
34402 PyObject *__pyx_args, PyObject *__pyx_kwds
34403 #endif
34404 ); /*proto*/
34405 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_67ignoreerror, "VCF.ignoreerror(self, errorstring)");
34406 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_68ignoreerror = {"ignoreerror", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_68ignoreerror, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_67ignoreerror};
34407 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_68ignoreerror(PyObject *__pyx_self,
34408 #if CYTHON_METH_FASTCALL
34409 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
34410 #else
34411 PyObject *__pyx_args, PyObject *__pyx_kwds
34412 #endif
34413 ) {
34414 PyObject *__pyx_v_self = 0;
34415 PyObject *__pyx_v_errorstring = 0;
34416 #if !CYTHON_METH_FASTCALL
34417 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
34418 #endif
34419 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
34420 PyObject* values[2] = {0,0};
34421 int __pyx_lineno = 0;
34422 const char *__pyx_filename = NULL;
34423 int __pyx_clineno = 0;
34424 PyObject *__pyx_r = 0;
34425 __Pyx_RefNannyDeclarations
34426 __Pyx_RefNannySetupContext("ignoreerror (wrapper)", 0);
34427 #if !CYTHON_METH_FASTCALL
34428 #if CYTHON_ASSUME_SAFE_MACROS
34429 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
34430 #else
34431 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
34432 #endif
34433 #endif
34434 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
34435 {
34436 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_errorstring,0};
34437 if (__pyx_kwds) {
34438 Py_ssize_t kw_args;
34439 switch (__pyx_nargs) {
34440 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
34441 CYTHON_FALLTHROUGH;
34442 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
34443 CYTHON_FALLTHROUGH;
34444 case 0: break;
34445 default: goto __pyx_L5_argtuple_error;
34446 }
34447 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
34448 switch (__pyx_nargs) {
34449 case 0:
34450 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
34451 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
34452 kw_args--;
34453 }
34454 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 998, __pyx_L3_error)
34455 else goto __pyx_L5_argtuple_error;
34456 CYTHON_FALLTHROUGH;
34457 case 1:
34458 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_errorstring)) != 0)) {
34459 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
34460 kw_args--;
34461 }
34462 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 998, __pyx_L3_error)
34463 else {
34464 __Pyx_RaiseArgtupleInvalid("ignoreerror", 1, 2, 2, 1); __PYX_ERR(0, 998, __pyx_L3_error)
34465 }
34466 }
34467 if (unlikely(kw_args > 0)) {
34468 const Py_ssize_t kwd_pos_args = __pyx_nargs;
34469 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "ignoreerror") < 0)) __PYX_ERR(0, 998, __pyx_L3_error)
34470 }
34471 } else if (unlikely(__pyx_nargs != 2)) {
34472 goto __pyx_L5_argtuple_error;
34473 } else {
34474 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
34475 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
34476 }
34477 __pyx_v_self = values[0];
34478 __pyx_v_errorstring = values[1];
34479 }
34480 goto __pyx_L6_skip;
34481 __pyx_L5_argtuple_error:;
34482 __Pyx_RaiseArgtupleInvalid("ignoreerror", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 998, __pyx_L3_error)
34483 __pyx_L6_skip:;
34484 goto __pyx_L4_argument_unpacking_done;
34485 __pyx_L3_error:;
34486 {
34487 Py_ssize_t __pyx_temp;
34488 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
34489 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
34490 }
34491 }
34492 __Pyx_AddTraceback("pysam.libcvcf.VCF.ignoreerror", __pyx_clineno, __pyx_lineno, __pyx_filename);
34493 __Pyx_RefNannyFinishContext();
34494 return NULL;
34495 __pyx_L4_argument_unpacking_done:;
34496 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_67ignoreerror(__pyx_self, __pyx_v_self, __pyx_v_errorstring);
34497
34498 /* function exit code */
34499 {
34500 Py_ssize_t __pyx_temp;
34501 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
34502 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
34503 }
34504 }
34505 __Pyx_RefNannyFinishContext();
34506 return __pyx_r;
34507 }
34508
34509 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring) {
34510 PyObject *__pyx_r = NULL;
34511 __Pyx_RefNannyDeclarations
34512 PyObject *__pyx_t_1 = NULL;
34513 PyObject *__pyx_t_2 = NULL;
34514 PyObject *__pyx_t_3 = NULL;
34515 PyObject *__pyx_t_4 = NULL;
34516 PyObject *__pyx_t_5 = NULL;
34517 PyObject *__pyx_t_6 = NULL;
34518 PyObject *__pyx_t_7 = NULL;
34519 unsigned int __pyx_t_8;
34520 int __pyx_t_9;
34521 PyObject *__pyx_t_10 = NULL;
34522 int __pyx_lineno = 0;
34523 const char *__pyx_filename = NULL;
34524 int __pyx_clineno = 0;
34525 __Pyx_RefNannySetupContext("ignoreerror", 1);
34526
34527 /* "pysam/libcvcf.pyx":999
34528 *
34529 * def ignoreerror(self, errorstring):
34530 * try: self._ignored_errors.add(self.__dict__[errorstring]) # <<<<<<<<<<<<<<
34531 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
34532 *
34533 */
34534 {
34535 __Pyx_PyThreadState_declare
34536 __Pyx_PyThreadState_assign
34537 __Pyx_ExceptionSave(&__pyx_t_1, &__pyx_t_2, &__pyx_t_3);
34538 __Pyx_XGOTREF(__pyx_t_1);
34539 __Pyx_XGOTREF(__pyx_t_2);
34540 __Pyx_XGOTREF(__pyx_t_3);
34541 /*try:*/ {
34542 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_ignored_errors); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 999, __pyx_L3_error)
34543 __Pyx_GOTREF(__pyx_t_5);
34544 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_add); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 999, __pyx_L3_error)
34545 __Pyx_GOTREF(__pyx_t_6);
34546 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
34547 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 999, __pyx_L3_error)
34548 __Pyx_GOTREF(__pyx_t_5);
34549 __pyx_t_7 = __Pyx_PyObject_GetItem(__pyx_t_5, __pyx_v_errorstring); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 999, __pyx_L3_error)
34550 __Pyx_GOTREF(__pyx_t_7);
34551 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
34552 __pyx_t_5 = NULL;
34553 __pyx_t_8 = 0;
34554 #if CYTHON_UNPACK_METHODS
34555 if (likely(PyMethod_Check(__pyx_t_6))) {
34556 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_6);
34557 if (likely(__pyx_t_5)) {
34558 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
34559 __Pyx_INCREF(__pyx_t_5);
34560 __Pyx_INCREF(function);
34561 __Pyx_DECREF_SET(__pyx_t_6, function);
34562 __pyx_t_8 = 1;
34563 }
34564 }
34565 #endif
34566 {
34567 PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_t_7};
34568 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
34569 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
34570 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
34571 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 999, __pyx_L3_error)
34572 __Pyx_GOTREF(__pyx_t_4);
34573 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
34574 }
34575 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
34576 }
34577 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
34578 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
34579 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
34580 goto __pyx_L8_try_end;
34581 __pyx_L3_error:;
34582 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
34583 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
34584 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
34585 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
34586
34587 /* "pysam/libcvcf.pyx":1000
34588 * def ignoreerror(self, errorstring):
34589 * try: self._ignored_errors.add(self.__dict__[errorstring])
34590 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) # <<<<<<<<<<<<<<
34591 *
34592 * def warnerror(self, errorstring):
34593 */
34594 __pyx_t_9 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_KeyError);
34595 if (__pyx_t_9) {
34596 __Pyx_AddTraceback("pysam.libcvcf.VCF.ignoreerror", __pyx_clineno, __pyx_lineno, __pyx_filename);
34597 if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(0, 1000, __pyx_L5_except_error)
34598 __Pyx_XGOTREF(__pyx_t_4);
34599 __Pyx_XGOTREF(__pyx_t_6);
34600 __Pyx_XGOTREF(__pyx_t_7);
34601 __pyx_t_5 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_Invalid_error_string_s, __pyx_v_errorstring); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1000, __pyx_L5_except_error)
34602 __Pyx_GOTREF(__pyx_t_5);
34603 __pyx_t_10 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_5); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 1000, __pyx_L5_except_error)
34604 __Pyx_GOTREF(__pyx_t_10);
34605 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
34606 __Pyx_Raise(__pyx_t_10, 0, 0, 0);
34607 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
34608 __PYX_ERR(0, 1000, __pyx_L5_except_error)
34609 }
34610 goto __pyx_L5_except_error;
34611
34612 /* "pysam/libcvcf.pyx":999
34613 *
34614 * def ignoreerror(self, errorstring):
34615 * try: self._ignored_errors.add(self.__dict__[errorstring]) # <<<<<<<<<<<<<<
34616 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
34617 *
34618 */
34619 __pyx_L5_except_error:;
34620 __Pyx_XGIVEREF(__pyx_t_1);
34621 __Pyx_XGIVEREF(__pyx_t_2);
34622 __Pyx_XGIVEREF(__pyx_t_3);
34623 __Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3);
34624 goto __pyx_L1_error;
34625 __pyx_L8_try_end:;
34626 }
34627
34628 /* "pysam/libcvcf.pyx":998
34629 * self._reference = ref
34630 *
34631 * def ignoreerror(self, errorstring): # <<<<<<<<<<<<<<
34632 * try: self._ignored_errors.add(self.__dict__[errorstring])
34633 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
34634 */
34635
34636 /* function exit code */
34637 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
34638 goto __pyx_L0;
34639 __pyx_L1_error:;
34640 __Pyx_XDECREF(__pyx_t_4);
34641 __Pyx_XDECREF(__pyx_t_5);
34642 __Pyx_XDECREF(__pyx_t_6);
34643 __Pyx_XDECREF(__pyx_t_7);
34644 __Pyx_XDECREF(__pyx_t_10);
34645 __Pyx_AddTraceback("pysam.libcvcf.VCF.ignoreerror", __pyx_clineno, __pyx_lineno, __pyx_filename);
34646 __pyx_r = NULL;
34647 __pyx_L0:;
34648 __Pyx_XGIVEREF(__pyx_r);
34649 __Pyx_RefNannyFinishContext();
34650 return __pyx_r;
34651 }
34652
34653 /* "pysam/libcvcf.pyx":1002
34654 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
34655 *
34656 * def warnerror(self, errorstring): # <<<<<<<<<<<<<<
34657 * try: self._warn_errors.add(self.__dict__[errorstring])
34658 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
34659 */
34660
34661 /* Python wrapper */
34662 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_70warnerror(PyObject *__pyx_self,
34663 #if CYTHON_METH_FASTCALL
34664 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
34665 #else
34666 PyObject *__pyx_args, PyObject *__pyx_kwds
34667 #endif
34668 ); /*proto*/
34669 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_69warnerror, "VCF.warnerror(self, errorstring)");
34670 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_70warnerror = {"warnerror", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_70warnerror, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_69warnerror};
34671 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_70warnerror(PyObject *__pyx_self,
34672 #if CYTHON_METH_FASTCALL
34673 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
34674 #else
34675 PyObject *__pyx_args, PyObject *__pyx_kwds
34676 #endif
34677 ) {
34678 PyObject *__pyx_v_self = 0;
34679 PyObject *__pyx_v_errorstring = 0;
34680 #if !CYTHON_METH_FASTCALL
34681 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
34682 #endif
34683 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
34684 PyObject* values[2] = {0,0};
34685 int __pyx_lineno = 0;
34686 const char *__pyx_filename = NULL;
34687 int __pyx_clineno = 0;
34688 PyObject *__pyx_r = 0;
34689 __Pyx_RefNannyDeclarations
34690 __Pyx_RefNannySetupContext("warnerror (wrapper)", 0);
34691 #if !CYTHON_METH_FASTCALL
34692 #if CYTHON_ASSUME_SAFE_MACROS
34693 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
34694 #else
34695 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
34696 #endif
34697 #endif
34698 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
34699 {
34700 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_errorstring,0};
34701 if (__pyx_kwds) {
34702 Py_ssize_t kw_args;
34703 switch (__pyx_nargs) {
34704 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
34705 CYTHON_FALLTHROUGH;
34706 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
34707 CYTHON_FALLTHROUGH;
34708 case 0: break;
34709 default: goto __pyx_L5_argtuple_error;
34710 }
34711 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
34712 switch (__pyx_nargs) {
34713 case 0:
34714 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
34715 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
34716 kw_args--;
34717 }
34718 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1002, __pyx_L3_error)
34719 else goto __pyx_L5_argtuple_error;
34720 CYTHON_FALLTHROUGH;
34721 case 1:
34722 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_errorstring)) != 0)) {
34723 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
34724 kw_args--;
34725 }
34726 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1002, __pyx_L3_error)
34727 else {
34728 __Pyx_RaiseArgtupleInvalid("warnerror", 1, 2, 2, 1); __PYX_ERR(0, 1002, __pyx_L3_error)
34729 }
34730 }
34731 if (unlikely(kw_args > 0)) {
34732 const Py_ssize_t kwd_pos_args = __pyx_nargs;
34733 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "warnerror") < 0)) __PYX_ERR(0, 1002, __pyx_L3_error)
34734 }
34735 } else if (unlikely(__pyx_nargs != 2)) {
34736 goto __pyx_L5_argtuple_error;
34737 } else {
34738 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
34739 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
34740 }
34741 __pyx_v_self = values[0];
34742 __pyx_v_errorstring = values[1];
34743 }
34744 goto __pyx_L6_skip;
34745 __pyx_L5_argtuple_error:;
34746 __Pyx_RaiseArgtupleInvalid("warnerror", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 1002, __pyx_L3_error)
34747 __pyx_L6_skip:;
34748 goto __pyx_L4_argument_unpacking_done;
34749 __pyx_L3_error:;
34750 {
34751 Py_ssize_t __pyx_temp;
34752 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
34753 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
34754 }
34755 }
34756 __Pyx_AddTraceback("pysam.libcvcf.VCF.warnerror", __pyx_clineno, __pyx_lineno, __pyx_filename);
34757 __Pyx_RefNannyFinishContext();
34758 return NULL;
34759 __pyx_L4_argument_unpacking_done:;
34760 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_69warnerror(__pyx_self, __pyx_v_self, __pyx_v_errorstring);
34761
34762 /* function exit code */
34763 {
34764 Py_ssize_t __pyx_temp;
34765 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
34766 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
34767 }
34768 }
34769 __Pyx_RefNannyFinishContext();
34770 return __pyx_r;
34771 }
34772
34773 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring) {
34774 PyObject *__pyx_r = NULL;
34775 __Pyx_RefNannyDeclarations
34776 PyObject *__pyx_t_1 = NULL;
34777 PyObject *__pyx_t_2 = NULL;
34778 PyObject *__pyx_t_3 = NULL;
34779 PyObject *__pyx_t_4 = NULL;
34780 PyObject *__pyx_t_5 = NULL;
34781 PyObject *__pyx_t_6 = NULL;
34782 PyObject *__pyx_t_7 = NULL;
34783 unsigned int __pyx_t_8;
34784 int __pyx_t_9;
34785 PyObject *__pyx_t_10 = NULL;
34786 int __pyx_lineno = 0;
34787 const char *__pyx_filename = NULL;
34788 int __pyx_clineno = 0;
34789 __Pyx_RefNannySetupContext("warnerror", 1);
34790
34791 /* "pysam/libcvcf.pyx":1003
34792 *
34793 * def warnerror(self, errorstring):
34794 * try: self._warn_errors.add(self.__dict__[errorstring]) # <<<<<<<<<<<<<<
34795 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
34796 *
34797 */
34798 {
34799 __Pyx_PyThreadState_declare
34800 __Pyx_PyThreadState_assign
34801 __Pyx_ExceptionSave(&__pyx_t_1, &__pyx_t_2, &__pyx_t_3);
34802 __Pyx_XGOTREF(__pyx_t_1);
34803 __Pyx_XGOTREF(__pyx_t_2);
34804 __Pyx_XGOTREF(__pyx_t_3);
34805 /*try:*/ {
34806 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_warn_errors); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1003, __pyx_L3_error)
34807 __Pyx_GOTREF(__pyx_t_5);
34808 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_add); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1003, __pyx_L3_error)
34809 __Pyx_GOTREF(__pyx_t_6);
34810 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
34811 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1003, __pyx_L3_error)
34812 __Pyx_GOTREF(__pyx_t_5);
34813 __pyx_t_7 = __Pyx_PyObject_GetItem(__pyx_t_5, __pyx_v_errorstring); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1003, __pyx_L3_error)
34814 __Pyx_GOTREF(__pyx_t_7);
34815 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
34816 __pyx_t_5 = NULL;
34817 __pyx_t_8 = 0;
34818 #if CYTHON_UNPACK_METHODS
34819 if (likely(PyMethod_Check(__pyx_t_6))) {
34820 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_6);
34821 if (likely(__pyx_t_5)) {
34822 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
34823 __Pyx_INCREF(__pyx_t_5);
34824 __Pyx_INCREF(function);
34825 __Pyx_DECREF_SET(__pyx_t_6, function);
34826 __pyx_t_8 = 1;
34827 }
34828 }
34829 #endif
34830 {
34831 PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_t_7};
34832 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
34833 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
34834 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
34835 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1003, __pyx_L3_error)
34836 __Pyx_GOTREF(__pyx_t_4);
34837 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
34838 }
34839 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
34840 }
34841 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
34842 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
34843 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
34844 goto __pyx_L8_try_end;
34845 __pyx_L3_error:;
34846 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
34847 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
34848 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
34849 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
34850
34851 /* "pysam/libcvcf.pyx":1004
34852 * def warnerror(self, errorstring):
34853 * try: self._warn_errors.add(self.__dict__[errorstring])
34854 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) # <<<<<<<<<<<<<<
34855 *
34856 * def parse(self, stream):
34857 */
34858 __pyx_t_9 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_KeyError);
34859 if (__pyx_t_9) {
34860 __Pyx_AddTraceback("pysam.libcvcf.VCF.warnerror", __pyx_clineno, __pyx_lineno, __pyx_filename);
34861 if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(0, 1004, __pyx_L5_except_error)
34862 __Pyx_XGOTREF(__pyx_t_4);
34863 __Pyx_XGOTREF(__pyx_t_6);
34864 __Pyx_XGOTREF(__pyx_t_7);
34865 __pyx_t_5 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_Invalid_error_string_s, __pyx_v_errorstring); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1004, __pyx_L5_except_error)
34866 __Pyx_GOTREF(__pyx_t_5);
34867 __pyx_t_10 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_5); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 1004, __pyx_L5_except_error)
34868 __Pyx_GOTREF(__pyx_t_10);
34869 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
34870 __Pyx_Raise(__pyx_t_10, 0, 0, 0);
34871 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
34872 __PYX_ERR(0, 1004, __pyx_L5_except_error)
34873 }
34874 goto __pyx_L5_except_error;
34875
34876 /* "pysam/libcvcf.pyx":1003
34877 *
34878 * def warnerror(self, errorstring):
34879 * try: self._warn_errors.add(self.__dict__[errorstring]) # <<<<<<<<<<<<<<
34880 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
34881 *
34882 */
34883 __pyx_L5_except_error:;
34884 __Pyx_XGIVEREF(__pyx_t_1);
34885 __Pyx_XGIVEREF(__pyx_t_2);
34886 __Pyx_XGIVEREF(__pyx_t_3);
34887 __Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3);
34888 goto __pyx_L1_error;
34889 __pyx_L8_try_end:;
34890 }
34891
34892 /* "pysam/libcvcf.pyx":1002
34893 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
34894 *
34895 * def warnerror(self, errorstring): # <<<<<<<<<<<<<<
34896 * try: self._warn_errors.add(self.__dict__[errorstring])
34897 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
34898 */
34899
34900 /* function exit code */
34901 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
34902 goto __pyx_L0;
34903 __pyx_L1_error:;
34904 __Pyx_XDECREF(__pyx_t_4);
34905 __Pyx_XDECREF(__pyx_t_5);
34906 __Pyx_XDECREF(__pyx_t_6);
34907 __Pyx_XDECREF(__pyx_t_7);
34908 __Pyx_XDECREF(__pyx_t_10);
34909 __Pyx_AddTraceback("pysam.libcvcf.VCF.warnerror", __pyx_clineno, __pyx_lineno, __pyx_filename);
34910 __pyx_r = NULL;
34911 __pyx_L0:;
34912 __Pyx_XGIVEREF(__pyx_r);
34913 __Pyx_RefNannyFinishContext();
34914 return __pyx_r;
34915 }
34916
34917 /* "pysam/libcvcf.pyx":1006
34918 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
34919 *
34920 * def parse(self, stream): # <<<<<<<<<<<<<<
34921 * """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
34922 * last_line = self._parse_header(stream)
34923 */
34924
34925 /* Python wrapper */
34926 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_72parse(PyObject *__pyx_self,
34927 #if CYTHON_METH_FASTCALL
34928 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
34929 #else
34930 PyObject *__pyx_args, PyObject *__pyx_kwds
34931 #endif
34932 ); /*proto*/
34933 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_71parse, "VCF.parse(self, stream)\n Parse a stream of VCF-formatted lines. Initializes class instance and return generator ");
34934 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_72parse = {"parse", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_72parse, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_71parse};
34935 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_72parse(PyObject *__pyx_self,
34936 #if CYTHON_METH_FASTCALL
34937 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
34938 #else
34939 PyObject *__pyx_args, PyObject *__pyx_kwds
34940 #endif
34941 ) {
34942 PyObject *__pyx_v_self = 0;
34943 PyObject *__pyx_v_stream = 0;
34944 #if !CYTHON_METH_FASTCALL
34945 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
34946 #endif
34947 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
34948 PyObject* values[2] = {0,0};
34949 int __pyx_lineno = 0;
34950 const char *__pyx_filename = NULL;
34951 int __pyx_clineno = 0;
34952 PyObject *__pyx_r = 0;
34953 __Pyx_RefNannyDeclarations
34954 __Pyx_RefNannySetupContext("parse (wrapper)", 0);
34955 #if !CYTHON_METH_FASTCALL
34956 #if CYTHON_ASSUME_SAFE_MACROS
34957 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
34958 #else
34959 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
34960 #endif
34961 #endif
34962 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
34963 {
34964 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_stream,0};
34965 if (__pyx_kwds) {
34966 Py_ssize_t kw_args;
34967 switch (__pyx_nargs) {
34968 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
34969 CYTHON_FALLTHROUGH;
34970 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
34971 CYTHON_FALLTHROUGH;
34972 case 0: break;
34973 default: goto __pyx_L5_argtuple_error;
34974 }
34975 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
34976 switch (__pyx_nargs) {
34977 case 0:
34978 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
34979 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
34980 kw_args--;
34981 }
34982 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1006, __pyx_L3_error)
34983 else goto __pyx_L5_argtuple_error;
34984 CYTHON_FALLTHROUGH;
34985 case 1:
34986 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_stream)) != 0)) {
34987 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
34988 kw_args--;
34989 }
34990 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1006, __pyx_L3_error)
34991 else {
34992 __Pyx_RaiseArgtupleInvalid("parse", 1, 2, 2, 1); __PYX_ERR(0, 1006, __pyx_L3_error)
34993 }
34994 }
34995 if (unlikely(kw_args > 0)) {
34996 const Py_ssize_t kwd_pos_args = __pyx_nargs;
34997 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "parse") < 0)) __PYX_ERR(0, 1006, __pyx_L3_error)
34998 }
34999 } else if (unlikely(__pyx_nargs != 2)) {
35000 goto __pyx_L5_argtuple_error;
35001 } else {
35002 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
35003 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
35004 }
35005 __pyx_v_self = values[0];
35006 __pyx_v_stream = values[1];
35007 }
35008 goto __pyx_L6_skip;
35009 __pyx_L5_argtuple_error:;
35010 __Pyx_RaiseArgtupleInvalid("parse", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 1006, __pyx_L3_error)
35011 __pyx_L6_skip:;
35012 goto __pyx_L4_argument_unpacking_done;
35013 __pyx_L3_error:;
35014 {
35015 Py_ssize_t __pyx_temp;
35016 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
35017 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
35018 }
35019 }
35020 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
35021 __Pyx_RefNannyFinishContext();
35022 return NULL;
35023 __pyx_L4_argument_unpacking_done:;
35024 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_71parse(__pyx_self, __pyx_v_self, __pyx_v_stream);
35025
35026 /* function exit code */
35027 {
35028 Py_ssize_t __pyx_temp;
35029 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
35030 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
35031 }
35032 }
35033 __Pyx_RefNannyFinishContext();
35034 return __pyx_r;
35035 }
35036
35037 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) {
35038 PyObject *__pyx_v_last_line = NULL;
35039 PyObject *__pyx_r = NULL;
35040 __Pyx_RefNannyDeclarations
35041 PyObject *__pyx_t_1 = NULL;
35042 PyObject *__pyx_t_2 = NULL;
35043 PyObject *__pyx_t_3 = NULL;
35044 unsigned int __pyx_t_4;
35045 int __pyx_lineno = 0;
35046 const char *__pyx_filename = NULL;
35047 int __pyx_clineno = 0;
35048 __Pyx_RefNannySetupContext("parse", 1);
35049
35050 /* "pysam/libcvcf.pyx":1008
35051 * def parse(self, stream):
35052 * """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
35053 * last_line = self._parse_header(stream) # <<<<<<<<<<<<<<
35054 * # now return a generator that does the actual work. In this way the pre-processing is done
35055 * # before the first piece of data is yielded
35056 */
35057 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parse_header_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1008, __pyx_L1_error)
35058 __Pyx_GOTREF(__pyx_t_2);
35059 __pyx_t_3 = NULL;
35060 __pyx_t_4 = 0;
35061 #if CYTHON_UNPACK_METHODS
35062 if (likely(PyMethod_Check(__pyx_t_2))) {
35063 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
35064 if (likely(__pyx_t_3)) {
35065 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
35066 __Pyx_INCREF(__pyx_t_3);
35067 __Pyx_INCREF(function);
35068 __Pyx_DECREF_SET(__pyx_t_2, function);
35069 __pyx_t_4 = 1;
35070 }
35071 }
35072 #endif
35073 {
35074 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_v_stream};
35075 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
35076 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
35077 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1008, __pyx_L1_error)
35078 __Pyx_GOTREF(__pyx_t_1);
35079 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
35080 }
35081 __pyx_v_last_line = __pyx_t_1;
35082 __pyx_t_1 = 0;
35083
35084 /* "pysam/libcvcf.pyx":1011
35085 * # now return a generator that does the actual work. In this way the pre-processing is done
35086 * # before the first piece of data is yielded
35087 * return self._parse(last_line, stream) # <<<<<<<<<<<<<<
35088 *
35089 * def write(self, stream, datagenerator):
35090 */
35091 __Pyx_XDECREF(__pyx_r);
35092 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parse); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1011, __pyx_L1_error)
35093 __Pyx_GOTREF(__pyx_t_2);
35094 __pyx_t_3 = NULL;
35095 __pyx_t_4 = 0;
35096 #if CYTHON_UNPACK_METHODS
35097 if (likely(PyMethod_Check(__pyx_t_2))) {
35098 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
35099 if (likely(__pyx_t_3)) {
35100 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
35101 __Pyx_INCREF(__pyx_t_3);
35102 __Pyx_INCREF(function);
35103 __Pyx_DECREF_SET(__pyx_t_2, function);
35104 __pyx_t_4 = 1;
35105 }
35106 }
35107 #endif
35108 {
35109 PyObject *__pyx_callargs[3] = {__pyx_t_3, __pyx_v_last_line, __pyx_v_stream};
35110 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
35111 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
35112 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1011, __pyx_L1_error)
35113 __Pyx_GOTREF(__pyx_t_1);
35114 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
35115 }
35116 __pyx_r = __pyx_t_1;
35117 __pyx_t_1 = 0;
35118 goto __pyx_L0;
35119
35120 /* "pysam/libcvcf.pyx":1006
35121 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
35122 *
35123 * def parse(self, stream): # <<<<<<<<<<<<<<
35124 * """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
35125 * last_line = self._parse_header(stream)
35126 */
35127
35128 /* function exit code */
35129 __pyx_L1_error:;
35130 __Pyx_XDECREF(__pyx_t_1);
35131 __Pyx_XDECREF(__pyx_t_2);
35132 __Pyx_XDECREF(__pyx_t_3);
35133 __Pyx_AddTraceback("pysam.libcvcf.VCF.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
35134 __pyx_r = NULL;
35135 __pyx_L0:;
35136 __Pyx_XDECREF(__pyx_v_last_line);
35137 __Pyx_XGIVEREF(__pyx_r);
35138 __Pyx_RefNannyFinishContext();
35139 return __pyx_r;
35140 }
35141
35142 /* "pysam/libcvcf.pyx":1013
35143 * return self._parse(last_line, stream)
35144 *
35145 * def write(self, stream, datagenerator): # <<<<<<<<<<<<<<
35146 * """ Writes a VCF file to a stream, using a data generator (or list) """
35147 * self.write_header(stream)
35148 */
35149
35150 /* Python wrapper */
35151 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_74write(PyObject *__pyx_self,
35152 #if CYTHON_METH_FASTCALL
35153 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
35154 #else
35155 PyObject *__pyx_args, PyObject *__pyx_kwds
35156 #endif
35157 ); /*proto*/
35158 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_73write, "VCF.write(self, stream, datagenerator)\n Writes a VCF file to a stream, using a data generator (or list) ");
35159 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_74write = {"write", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_74write, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_73write};
35160 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_74write(PyObject *__pyx_self,
35161 #if CYTHON_METH_FASTCALL
35162 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
35163 #else
35164 PyObject *__pyx_args, PyObject *__pyx_kwds
35165 #endif
35166 ) {
35167 PyObject *__pyx_v_self = 0;
35168 PyObject *__pyx_v_stream = 0;
35169 PyObject *__pyx_v_datagenerator = 0;
35170 #if !CYTHON_METH_FASTCALL
35171 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
35172 #endif
35173 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
35174 PyObject* values[3] = {0,0,0};
35175 int __pyx_lineno = 0;
35176 const char *__pyx_filename = NULL;
35177 int __pyx_clineno = 0;
35178 PyObject *__pyx_r = 0;
35179 __Pyx_RefNannyDeclarations
35180 __Pyx_RefNannySetupContext("write (wrapper)", 0);
35181 #if !CYTHON_METH_FASTCALL
35182 #if CYTHON_ASSUME_SAFE_MACROS
35183 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
35184 #else
35185 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
35186 #endif
35187 #endif
35188 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
35189 {
35190 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_stream,&__pyx_n_s_datagenerator,0};
35191 if (__pyx_kwds) {
35192 Py_ssize_t kw_args;
35193 switch (__pyx_nargs) {
35194 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
35195 CYTHON_FALLTHROUGH;
35196 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
35197 CYTHON_FALLTHROUGH;
35198 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
35199 CYTHON_FALLTHROUGH;
35200 case 0: break;
35201 default: goto __pyx_L5_argtuple_error;
35202 }
35203 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
35204 switch (__pyx_nargs) {
35205 case 0:
35206 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
35207 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
35208 kw_args--;
35209 }
35210 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1013, __pyx_L3_error)
35211 else goto __pyx_L5_argtuple_error;
35212 CYTHON_FALLTHROUGH;
35213 case 1:
35214 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_stream)) != 0)) {
35215 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
35216 kw_args--;
35217 }
35218 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1013, __pyx_L3_error)
35219 else {
35220 __Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, 1); __PYX_ERR(0, 1013, __pyx_L3_error)
35221 }
35222 CYTHON_FALLTHROUGH;
35223 case 2:
35224 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_datagenerator)) != 0)) {
35225 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
35226 kw_args--;
35227 }
35228 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1013, __pyx_L3_error)
35229 else {
35230 __Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, 2); __PYX_ERR(0, 1013, __pyx_L3_error)
35231 }
35232 }
35233 if (unlikely(kw_args > 0)) {
35234 const Py_ssize_t kwd_pos_args = __pyx_nargs;
35235 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "write") < 0)) __PYX_ERR(0, 1013, __pyx_L3_error)
35236 }
35237 } else if (unlikely(__pyx_nargs != 3)) {
35238 goto __pyx_L5_argtuple_error;
35239 } else {
35240 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
35241 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
35242 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
35243 }
35244 __pyx_v_self = values[0];
35245 __pyx_v_stream = values[1];
35246 __pyx_v_datagenerator = values[2];
35247 }
35248 goto __pyx_L6_skip;
35249 __pyx_L5_argtuple_error:;
35250 __Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 1013, __pyx_L3_error)
35251 __pyx_L6_skip:;
35252 goto __pyx_L4_argument_unpacking_done;
35253 __pyx_L3_error:;
35254 {
35255 Py_ssize_t __pyx_temp;
35256 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
35257 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
35258 }
35259 }
35260 __Pyx_AddTraceback("pysam.libcvcf.VCF.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
35261 __Pyx_RefNannyFinishContext();
35262 return NULL;
35263 __pyx_L4_argument_unpacking_done:;
35264 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_73write(__pyx_self, __pyx_v_self, __pyx_v_stream, __pyx_v_datagenerator);
35265
35266 /* function exit code */
35267 {
35268 Py_ssize_t __pyx_temp;
35269 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
35270 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
35271 }
35272 }
35273 __Pyx_RefNannyFinishContext();
35274 return __pyx_r;
35275 }
35276
35277 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_datagenerator) {
35278 PyObject *__pyx_v_data = NULL;
35279 PyObject *__pyx_r = NULL;
35280 __Pyx_RefNannyDeclarations
35281 PyObject *__pyx_t_1 = NULL;
35282 PyObject *__pyx_t_2 = NULL;
35283 PyObject *__pyx_t_3 = NULL;
35284 unsigned int __pyx_t_4;
35285 Py_ssize_t __pyx_t_5;
35286 PyObject *(*__pyx_t_6)(PyObject *);
35287 PyObject *__pyx_t_7 = NULL;
35288 int __pyx_lineno = 0;
35289 const char *__pyx_filename = NULL;
35290 int __pyx_clineno = 0;
35291 __Pyx_RefNannySetupContext("write", 1);
35292
35293 /* "pysam/libcvcf.pyx":1015
35294 * def write(self, stream, datagenerator):
35295 * """ Writes a VCF file to a stream, using a data generator (or list) """
35296 * self.write_header(stream) # <<<<<<<<<<<<<<
35297 * self.write_heading(stream)
35298 * for data in datagenerator: self.write_data(stream,data)
35299 */
35300 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_write_header); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1015, __pyx_L1_error)
35301 __Pyx_GOTREF(__pyx_t_2);
35302 __pyx_t_3 = NULL;
35303 __pyx_t_4 = 0;
35304 #if CYTHON_UNPACK_METHODS
35305 if (likely(PyMethod_Check(__pyx_t_2))) {
35306 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
35307 if (likely(__pyx_t_3)) {
35308 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
35309 __Pyx_INCREF(__pyx_t_3);
35310 __Pyx_INCREF(function);
35311 __Pyx_DECREF_SET(__pyx_t_2, function);
35312 __pyx_t_4 = 1;
35313 }
35314 }
35315 #endif
35316 {
35317 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_v_stream};
35318 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
35319 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
35320 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1015, __pyx_L1_error)
35321 __Pyx_GOTREF(__pyx_t_1);
35322 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
35323 }
35324 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
35325
35326 /* "pysam/libcvcf.pyx":1016
35327 * """ Writes a VCF file to a stream, using a data generator (or list) """
35328 * self.write_header(stream)
35329 * self.write_heading(stream) # <<<<<<<<<<<<<<
35330 * for data in datagenerator: self.write_data(stream,data)
35331 *
35332 */
35333 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_write_heading); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1016, __pyx_L1_error)
35334 __Pyx_GOTREF(__pyx_t_2);
35335 __pyx_t_3 = NULL;
35336 __pyx_t_4 = 0;
35337 #if CYTHON_UNPACK_METHODS
35338 if (likely(PyMethod_Check(__pyx_t_2))) {
35339 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
35340 if (likely(__pyx_t_3)) {
35341 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
35342 __Pyx_INCREF(__pyx_t_3);
35343 __Pyx_INCREF(function);
35344 __Pyx_DECREF_SET(__pyx_t_2, function);
35345 __pyx_t_4 = 1;
35346 }
35347 }
35348 #endif
35349 {
35350 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_v_stream};
35351 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
35352 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
35353 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1016, __pyx_L1_error)
35354 __Pyx_GOTREF(__pyx_t_1);
35355 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
35356 }
35357 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
35358
35359 /* "pysam/libcvcf.pyx":1017
35360 * self.write_header(stream)
35361 * self.write_heading(stream)
35362 * for data in datagenerator: self.write_data(stream,data) # <<<<<<<<<<<<<<
35363 *
35364 * def writeheader(self, stream):
35365 */
35366 if (likely(PyList_CheckExact(__pyx_v_datagenerator)) || PyTuple_CheckExact(__pyx_v_datagenerator)) {
35367 __pyx_t_1 = __pyx_v_datagenerator; __Pyx_INCREF(__pyx_t_1);
35368 __pyx_t_5 = 0;
35369 __pyx_t_6 = NULL;
35370 } else {
35371 __pyx_t_5 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_datagenerator); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1017, __pyx_L1_error)
35372 __Pyx_GOTREF(__pyx_t_1);
35373 __pyx_t_6 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1017, __pyx_L1_error)
35374 }
35375 for (;;) {
35376 if (likely(!__pyx_t_6)) {
35377 if (likely(PyList_CheckExact(__pyx_t_1))) {
35378 {
35379 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1);
35380 #if !CYTHON_ASSUME_SAFE_MACROS
35381 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 1017, __pyx_L1_error)
35382 #endif
35383 if (__pyx_t_5 >= __pyx_temp) break;
35384 }
35385 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
35386 __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely((0 < 0))) __PYX_ERR(0, 1017, __pyx_L1_error)
35387 #else
35388 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1017, __pyx_L1_error)
35389 __Pyx_GOTREF(__pyx_t_2);
35390 #endif
35391 } else {
35392 {
35393 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1);
35394 #if !CYTHON_ASSUME_SAFE_MACROS
35395 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 1017, __pyx_L1_error)
35396 #endif
35397 if (__pyx_t_5 >= __pyx_temp) break;
35398 }
35399 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
35400 __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely((0 < 0))) __PYX_ERR(0, 1017, __pyx_L1_error)
35401 #else
35402 __pyx_t_2 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1017, __pyx_L1_error)
35403 __Pyx_GOTREF(__pyx_t_2);
35404 #endif
35405 }
35406 } else {
35407 __pyx_t_2 = __pyx_t_6(__pyx_t_1);
35408 if (unlikely(!__pyx_t_2)) {
35409 PyObject* exc_type = PyErr_Occurred();
35410 if (exc_type) {
35411 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
35412 else __PYX_ERR(0, 1017, __pyx_L1_error)
35413 }
35414 break;
35415 }
35416 __Pyx_GOTREF(__pyx_t_2);
35417 }
35418 __Pyx_XDECREF_SET(__pyx_v_data, __pyx_t_2);
35419 __pyx_t_2 = 0;
35420 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_write_data); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1017, __pyx_L1_error)
35421 __Pyx_GOTREF(__pyx_t_3);
35422 __pyx_t_7 = NULL;
35423 __pyx_t_4 = 0;
35424 #if CYTHON_UNPACK_METHODS
35425 if (likely(PyMethod_Check(__pyx_t_3))) {
35426 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_3);
35427 if (likely(__pyx_t_7)) {
35428 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
35429 __Pyx_INCREF(__pyx_t_7);
35430 __Pyx_INCREF(function);
35431 __Pyx_DECREF_SET(__pyx_t_3, function);
35432 __pyx_t_4 = 1;
35433 }
35434 }
35435 #endif
35436 {
35437 PyObject *__pyx_callargs[3] = {__pyx_t_7, __pyx_v_stream, __pyx_v_data};
35438 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
35439 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
35440 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1017, __pyx_L1_error)
35441 __Pyx_GOTREF(__pyx_t_2);
35442 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
35443 }
35444 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
35445 }
35446 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
35447
35448 /* "pysam/libcvcf.pyx":1013
35449 * return self._parse(last_line, stream)
35450 *
35451 * def write(self, stream, datagenerator): # <<<<<<<<<<<<<<
35452 * """ Writes a VCF file to a stream, using a data generator (or list) """
35453 * self.write_header(stream)
35454 */
35455
35456 /* function exit code */
35457 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
35458 goto __pyx_L0;
35459 __pyx_L1_error:;
35460 __Pyx_XDECREF(__pyx_t_1);
35461 __Pyx_XDECREF(__pyx_t_2);
35462 __Pyx_XDECREF(__pyx_t_3);
35463 __Pyx_XDECREF(__pyx_t_7);
35464 __Pyx_AddTraceback("pysam.libcvcf.VCF.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
35465 __pyx_r = NULL;
35466 __pyx_L0:;
35467 __Pyx_XDECREF(__pyx_v_data);
35468 __Pyx_XGIVEREF(__pyx_r);
35469 __Pyx_RefNannyFinishContext();
35470 return __pyx_r;
35471 }
35472
35473 /* "pysam/libcvcf.pyx":1019
35474 * for data in datagenerator: self.write_data(stream,data)
35475 *
35476 * def writeheader(self, stream): # <<<<<<<<<<<<<<
35477 * """ Writes a VCF header """
35478 * self.write_header(stream)
35479 */
35480
35481 /* Python wrapper */
35482 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_76writeheader(PyObject *__pyx_self,
35483 #if CYTHON_METH_FASTCALL
35484 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
35485 #else
35486 PyObject *__pyx_args, PyObject *__pyx_kwds
35487 #endif
35488 ); /*proto*/
35489 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_75writeheader, "VCF.writeheader(self, stream)\n Writes a VCF header ");
35490 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_76writeheader = {"writeheader", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_76writeheader, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_75writeheader};
35491 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_76writeheader(PyObject *__pyx_self,
35492 #if CYTHON_METH_FASTCALL
35493 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
35494 #else
35495 PyObject *__pyx_args, PyObject *__pyx_kwds
35496 #endif
35497 ) {
35498 PyObject *__pyx_v_self = 0;
35499 PyObject *__pyx_v_stream = 0;
35500 #if !CYTHON_METH_FASTCALL
35501 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
35502 #endif
35503 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
35504 PyObject* values[2] = {0,0};
35505 int __pyx_lineno = 0;
35506 const char *__pyx_filename = NULL;
35507 int __pyx_clineno = 0;
35508 PyObject *__pyx_r = 0;
35509 __Pyx_RefNannyDeclarations
35510 __Pyx_RefNannySetupContext("writeheader (wrapper)", 0);
35511 #if !CYTHON_METH_FASTCALL
35512 #if CYTHON_ASSUME_SAFE_MACROS
35513 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
35514 #else
35515 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
35516 #endif
35517 #endif
35518 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
35519 {
35520 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_stream,0};
35521 if (__pyx_kwds) {
35522 Py_ssize_t kw_args;
35523 switch (__pyx_nargs) {
35524 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
35525 CYTHON_FALLTHROUGH;
35526 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
35527 CYTHON_FALLTHROUGH;
35528 case 0: break;
35529 default: goto __pyx_L5_argtuple_error;
35530 }
35531 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
35532 switch (__pyx_nargs) {
35533 case 0:
35534 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
35535 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
35536 kw_args--;
35537 }
35538 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1019, __pyx_L3_error)
35539 else goto __pyx_L5_argtuple_error;
35540 CYTHON_FALLTHROUGH;
35541 case 1:
35542 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_stream)) != 0)) {
35543 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
35544 kw_args--;
35545 }
35546 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1019, __pyx_L3_error)
35547 else {
35548 __Pyx_RaiseArgtupleInvalid("writeheader", 1, 2, 2, 1); __PYX_ERR(0, 1019, __pyx_L3_error)
35549 }
35550 }
35551 if (unlikely(kw_args > 0)) {
35552 const Py_ssize_t kwd_pos_args = __pyx_nargs;
35553 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "writeheader") < 0)) __PYX_ERR(0, 1019, __pyx_L3_error)
35554 }
35555 } else if (unlikely(__pyx_nargs != 2)) {
35556 goto __pyx_L5_argtuple_error;
35557 } else {
35558 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
35559 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
35560 }
35561 __pyx_v_self = values[0];
35562 __pyx_v_stream = values[1];
35563 }
35564 goto __pyx_L6_skip;
35565 __pyx_L5_argtuple_error:;
35566 __Pyx_RaiseArgtupleInvalid("writeheader", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 1019, __pyx_L3_error)
35567 __pyx_L6_skip:;
35568 goto __pyx_L4_argument_unpacking_done;
35569 __pyx_L3_error:;
35570 {
35571 Py_ssize_t __pyx_temp;
35572 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
35573 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
35574 }
35575 }
35576 __Pyx_AddTraceback("pysam.libcvcf.VCF.writeheader", __pyx_clineno, __pyx_lineno, __pyx_filename);
35577 __Pyx_RefNannyFinishContext();
35578 return NULL;
35579 __pyx_L4_argument_unpacking_done:;
35580 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_75writeheader(__pyx_self, __pyx_v_self, __pyx_v_stream);
35581
35582 /* function exit code */
35583 {
35584 Py_ssize_t __pyx_temp;
35585 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
35586 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
35587 }
35588 }
35589 __Pyx_RefNannyFinishContext();
35590 return __pyx_r;
35591 }
35592
35593 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) {
35594 PyObject *__pyx_r = NULL;
35595 __Pyx_RefNannyDeclarations
35596 PyObject *__pyx_t_1 = NULL;
35597 PyObject *__pyx_t_2 = NULL;
35598 PyObject *__pyx_t_3 = NULL;
35599 unsigned int __pyx_t_4;
35600 int __pyx_lineno = 0;
35601 const char *__pyx_filename = NULL;
35602 int __pyx_clineno = 0;
35603 __Pyx_RefNannySetupContext("writeheader", 1);
35604
35605 /* "pysam/libcvcf.pyx":1021
35606 * def writeheader(self, stream):
35607 * """ Writes a VCF header """
35608 * self.write_header(stream) # <<<<<<<<<<<<<<
35609 * self.write_heading(stream)
35610 *
35611 */
35612 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_write_header); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1021, __pyx_L1_error)
35613 __Pyx_GOTREF(__pyx_t_2);
35614 __pyx_t_3 = NULL;
35615 __pyx_t_4 = 0;
35616 #if CYTHON_UNPACK_METHODS
35617 if (likely(PyMethod_Check(__pyx_t_2))) {
35618 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
35619 if (likely(__pyx_t_3)) {
35620 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
35621 __Pyx_INCREF(__pyx_t_3);
35622 __Pyx_INCREF(function);
35623 __Pyx_DECREF_SET(__pyx_t_2, function);
35624 __pyx_t_4 = 1;
35625 }
35626 }
35627 #endif
35628 {
35629 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_v_stream};
35630 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
35631 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
35632 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1021, __pyx_L1_error)
35633 __Pyx_GOTREF(__pyx_t_1);
35634 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
35635 }
35636 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
35637
35638 /* "pysam/libcvcf.pyx":1022
35639 * """ Writes a VCF header """
35640 * self.write_header(stream)
35641 * self.write_heading(stream) # <<<<<<<<<<<<<<
35642 *
35643 * def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2):
35644 */
35645 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_write_heading); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1022, __pyx_L1_error)
35646 __Pyx_GOTREF(__pyx_t_2);
35647 __pyx_t_3 = NULL;
35648 __pyx_t_4 = 0;
35649 #if CYTHON_UNPACK_METHODS
35650 if (likely(PyMethod_Check(__pyx_t_2))) {
35651 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
35652 if (likely(__pyx_t_3)) {
35653 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
35654 __Pyx_INCREF(__pyx_t_3);
35655 __Pyx_INCREF(function);
35656 __Pyx_DECREF_SET(__pyx_t_2, function);
35657 __pyx_t_4 = 1;
35658 }
35659 }
35660 #endif
35661 {
35662 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_v_stream};
35663 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
35664 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
35665 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1022, __pyx_L1_error)
35666 __Pyx_GOTREF(__pyx_t_1);
35667 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
35668 }
35669 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
35670
35671 /* "pysam/libcvcf.pyx":1019
35672 * for data in datagenerator: self.write_data(stream,data)
35673 *
35674 * def writeheader(self, stream): # <<<<<<<<<<<<<<
35675 * """ Writes a VCF header """
35676 * self.write_header(stream)
35677 */
35678
35679 /* function exit code */
35680 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
35681 goto __pyx_L0;
35682 __pyx_L1_error:;
35683 __Pyx_XDECREF(__pyx_t_1);
35684 __Pyx_XDECREF(__pyx_t_2);
35685 __Pyx_XDECREF(__pyx_t_3);
35686 __Pyx_AddTraceback("pysam.libcvcf.VCF.writeheader", __pyx_clineno, __pyx_lineno, __pyx_filename);
35687 __pyx_r = NULL;
35688 __pyx_L0:;
35689 __Pyx_XGIVEREF(__pyx_r);
35690 __Pyx_RefNannyFinishContext();
35691 return __pyx_r;
35692 }
35693
35694 /* "pysam/libcvcf.pyx":1024
35695 * self.write_heading(stream)
35696 *
35697 * def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): # <<<<<<<<<<<<<<
35698 * """ Utility function: compares two calls for equality """
35699 * # a variant should always be assigned to a unique position, one base before
35700 */
35701
35702 /* Python wrapper */
35703 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_78compare_calls(PyObject *__pyx_self,
35704 #if CYTHON_METH_FASTCALL
35705 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
35706 #else
35707 PyObject *__pyx_args, PyObject *__pyx_kwds
35708 #endif
35709 ); /*proto*/
35710 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_77compare_calls, "VCF.compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2)\n Utility function: compares two calls for equality ");
35711 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_78compare_calls = {"compare_calls", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_78compare_calls, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_77compare_calls};
35712 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_78compare_calls(PyObject *__pyx_self,
35713 #if CYTHON_METH_FASTCALL
35714 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
35715 #else
35716 PyObject *__pyx_args, PyObject *__pyx_kwds
35717 #endif
35718 ) {
35719 CYTHON_UNUSED PyObject *__pyx_v_self = 0;
35720 PyObject *__pyx_v_pos1 = 0;
35721 PyObject *__pyx_v_ref1 = 0;
35722 PyObject *__pyx_v_alt1 = 0;
35723 PyObject *__pyx_v_pos2 = 0;
35724 PyObject *__pyx_v_ref2 = 0;
35725 PyObject *__pyx_v_alt2 = 0;
35726 #if !CYTHON_METH_FASTCALL
35727 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
35728 #endif
35729 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
35730 PyObject* values[7] = {0,0,0,0,0,0,0};
35731 int __pyx_lineno = 0;
35732 const char *__pyx_filename = NULL;
35733 int __pyx_clineno = 0;
35734 PyObject *__pyx_r = 0;
35735 __Pyx_RefNannyDeclarations
35736 __Pyx_RefNannySetupContext("compare_calls (wrapper)", 0);
35737 #if !CYTHON_METH_FASTCALL
35738 #if CYTHON_ASSUME_SAFE_MACROS
35739 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
35740 #else
35741 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
35742 #endif
35743 #endif
35744 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
35745 {
35746 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_pos1,&__pyx_n_s_ref1,&__pyx_n_s_alt1,&__pyx_n_s_pos2,&__pyx_n_s_ref2,&__pyx_n_s_alt2,0};
35747 if (__pyx_kwds) {
35748 Py_ssize_t kw_args;
35749 switch (__pyx_nargs) {
35750 case 7: values[6] = __Pyx_Arg_FASTCALL(__pyx_args, 6);
35751 CYTHON_FALLTHROUGH;
35752 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
35753 CYTHON_FALLTHROUGH;
35754 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
35755 CYTHON_FALLTHROUGH;
35756 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
35757 CYTHON_FALLTHROUGH;
35758 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
35759 CYTHON_FALLTHROUGH;
35760 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
35761 CYTHON_FALLTHROUGH;
35762 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
35763 CYTHON_FALLTHROUGH;
35764 case 0: break;
35765 default: goto __pyx_L5_argtuple_error;
35766 }
35767 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
35768 switch (__pyx_nargs) {
35769 case 0:
35770 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
35771 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
35772 kw_args--;
35773 }
35774 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1024, __pyx_L3_error)
35775 else goto __pyx_L5_argtuple_error;
35776 CYTHON_FALLTHROUGH;
35777 case 1:
35778 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pos1)) != 0)) {
35779 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
35780 kw_args--;
35781 }
35782 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1024, __pyx_L3_error)
35783 else {
35784 __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 1); __PYX_ERR(0, 1024, __pyx_L3_error)
35785 }
35786 CYTHON_FALLTHROUGH;
35787 case 2:
35788 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_ref1)) != 0)) {
35789 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
35790 kw_args--;
35791 }
35792 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1024, __pyx_L3_error)
35793 else {
35794 __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 2); __PYX_ERR(0, 1024, __pyx_L3_error)
35795 }
35796 CYTHON_FALLTHROUGH;
35797 case 3:
35798 if (likely((values[3] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_alt1)) != 0)) {
35799 (void)__Pyx_Arg_NewRef_FASTCALL(values[3]);
35800 kw_args--;
35801 }
35802 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1024, __pyx_L3_error)
35803 else {
35804 __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 3); __PYX_ERR(0, 1024, __pyx_L3_error)
35805 }
35806 CYTHON_FALLTHROUGH;
35807 case 4:
35808 if (likely((values[4] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pos2)) != 0)) {
35809 (void)__Pyx_Arg_NewRef_FASTCALL(values[4]);
35810 kw_args--;
35811 }
35812 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1024, __pyx_L3_error)
35813 else {
35814 __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 4); __PYX_ERR(0, 1024, __pyx_L3_error)
35815 }
35816 CYTHON_FALLTHROUGH;
35817 case 5:
35818 if (likely((values[5] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_ref2)) != 0)) {
35819 (void)__Pyx_Arg_NewRef_FASTCALL(values[5]);
35820 kw_args--;
35821 }
35822 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1024, __pyx_L3_error)
35823 else {
35824 __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 5); __PYX_ERR(0, 1024, __pyx_L3_error)
35825 }
35826 CYTHON_FALLTHROUGH;
35827 case 6:
35828 if (likely((values[6] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_alt2)) != 0)) {
35829 (void)__Pyx_Arg_NewRef_FASTCALL(values[6]);
35830 kw_args--;
35831 }
35832 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1024, __pyx_L3_error)
35833 else {
35834 __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 6); __PYX_ERR(0, 1024, __pyx_L3_error)
35835 }
35836 }
35837 if (unlikely(kw_args > 0)) {
35838 const Py_ssize_t kwd_pos_args = __pyx_nargs;
35839 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "compare_calls") < 0)) __PYX_ERR(0, 1024, __pyx_L3_error)
35840 }
35841 } else if (unlikely(__pyx_nargs != 7)) {
35842 goto __pyx_L5_argtuple_error;
35843 } else {
35844 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
35845 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
35846 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
35847 values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
35848 values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
35849 values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
35850 values[6] = __Pyx_Arg_FASTCALL(__pyx_args, 6);
35851 }
35852 __pyx_v_self = values[0];
35853 __pyx_v_pos1 = values[1];
35854 __pyx_v_ref1 = values[2];
35855 __pyx_v_alt1 = values[3];
35856 __pyx_v_pos2 = values[4];
35857 __pyx_v_ref2 = values[5];
35858 __pyx_v_alt2 = values[6];
35859 }
35860 goto __pyx_L6_skip;
35861 __pyx_L5_argtuple_error:;
35862 __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, __pyx_nargs); __PYX_ERR(0, 1024, __pyx_L3_error)
35863 __pyx_L6_skip:;
35864 goto __pyx_L4_argument_unpacking_done;
35865 __pyx_L3_error:;
35866 {
35867 Py_ssize_t __pyx_temp;
35868 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
35869 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
35870 }
35871 }
35872 __Pyx_AddTraceback("pysam.libcvcf.VCF.compare_calls", __pyx_clineno, __pyx_lineno, __pyx_filename);
35873 __Pyx_RefNannyFinishContext();
35874 return NULL;
35875 __pyx_L4_argument_unpacking_done:;
35876 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_77compare_calls(__pyx_self, __pyx_v_self, __pyx_v_pos1, __pyx_v_ref1, __pyx_v_alt1, __pyx_v_pos2, __pyx_v_ref2, __pyx_v_alt2);
35877
35878 /* function exit code */
35879 {
35880 Py_ssize_t __pyx_temp;
35881 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
35882 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
35883 }
35884 }
35885 __Pyx_RefNannyFinishContext();
35886 return __pyx_r;
35887 }
35888
35889 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_pos1, PyObject *__pyx_v_ref1, PyObject *__pyx_v_alt1, PyObject *__pyx_v_pos2, PyObject *__pyx_v_ref2, PyObject *__pyx_v_alt2) {
35890 PyObject *__pyx_r = NULL;
35891 __Pyx_RefNannyDeclarations
35892 PyObject *__pyx_t_1 = NULL;
35893 int __pyx_t_2;
35894 Py_ssize_t __pyx_t_3;
35895 int __pyx_t_4;
35896 PyObject *__pyx_t_5 = NULL;
35897 PyObject *__pyx_t_6 = NULL;
35898 int __pyx_lineno = 0;
35899 const char *__pyx_filename = NULL;
35900 int __pyx_clineno = 0;
35901 __Pyx_RefNannySetupContext("compare_calls", 0);
35902 __Pyx_INCREF(__pyx_v_ref1);
35903 __Pyx_INCREF(__pyx_v_alt1);
35904 __Pyx_INCREF(__pyx_v_ref2);
35905 __Pyx_INCREF(__pyx_v_alt2);
35906
35907 /* "pysam/libcvcf.pyx":1029
35908 * # the leftmost position of the alignment gap. If this rule is implemented
35909 * # correctly, the two positions must be equal for the calls to be identical.
35910 * if pos1 != pos2: return False # <<<<<<<<<<<<<<
35911 * # from both calls, trim rightmost bases when identical. Do this safely, i.e.
35912 * # only when the reference bases are not Ns
35913 */
35914 __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos1, __pyx_v_pos2, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1029, __pyx_L1_error)
35915 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 1029, __pyx_L1_error)
35916 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
35917 if (__pyx_t_2) {
35918 __Pyx_XDECREF(__pyx_r);
35919 __Pyx_INCREF(Py_False);
35920 __pyx_r = Py_False;
35921 goto __pyx_L0;
35922 }
35923
35924 /* "pysam/libcvcf.pyx":1032
35925 * # from both calls, trim rightmost bases when identical. Do this safely, i.e.
35926 * # only when the reference bases are not Ns
35927 * while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]: # <<<<<<<<<<<<<<
35928 * ref1 = ref1[:-1]
35929 * alt1 = alt1[:-1]
35930 */
35931 while (1) {
35932 __pyx_t_3 = PyObject_Length(__pyx_v_ref1); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 1032, __pyx_L1_error)
35933 __pyx_t_4 = (__pyx_t_3 > 0);
35934 if (__pyx_t_4) {
35935 } else {
35936 __pyx_t_2 = __pyx_t_4;
35937 goto __pyx_L6_bool_binop_done;
35938 }
35939 __pyx_t_3 = PyObject_Length(__pyx_v_alt1); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 1032, __pyx_L1_error)
35940 __pyx_t_4 = (__pyx_t_3 > 0);
35941 if (__pyx_t_4) {
35942 } else {
35943 __pyx_t_2 = __pyx_t_4;
35944 goto __pyx_L6_bool_binop_done;
35945 }
35946 __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_ref1, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1032, __pyx_L1_error)
35947 __Pyx_GOTREF(__pyx_t_1);
35948 __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_alt1, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1032, __pyx_L1_error)
35949 __Pyx_GOTREF(__pyx_t_5);
35950 __pyx_t_6 = PyObject_RichCompare(__pyx_t_1, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1032, __pyx_L1_error)
35951 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
35952 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
35953 __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(0, 1032, __pyx_L1_error)
35954 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
35955 __pyx_t_2 = __pyx_t_4;
35956 __pyx_L6_bool_binop_done:;
35957 if (!__pyx_t_2) break;
35958
35959 /* "pysam/libcvcf.pyx":1033
35960 * # only when the reference bases are not Ns
35961 * while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]:
35962 * ref1 = ref1[:-1] # <<<<<<<<<<<<<<
35963 * alt1 = alt1[:-1]
35964 * while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
35965 */
35966 __pyx_t_6 = __Pyx_PyObject_GetSlice(__pyx_v_ref1, 0, -1L, NULL, NULL, &__pyx_slice__28, 0, 1, 1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1033, __pyx_L1_error)
35967 __Pyx_GOTREF(__pyx_t_6);
35968 __Pyx_DECREF_SET(__pyx_v_ref1, __pyx_t_6);
35969 __pyx_t_6 = 0;
35970
35971 /* "pysam/libcvcf.pyx":1034
35972 * while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]:
35973 * ref1 = ref1[:-1]
35974 * alt1 = alt1[:-1] # <<<<<<<<<<<<<<
35975 * while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
35976 * ref2 = ref2[:-1]
35977 */
35978 __pyx_t_6 = __Pyx_PyObject_GetSlice(__pyx_v_alt1, 0, -1L, NULL, NULL, &__pyx_slice__28, 0, 1, 1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1034, __pyx_L1_error)
35979 __Pyx_GOTREF(__pyx_t_6);
35980 __Pyx_DECREF_SET(__pyx_v_alt1, __pyx_t_6);
35981 __pyx_t_6 = 0;
35982 }
35983
35984 /* "pysam/libcvcf.pyx":1035
35985 * ref1 = ref1[:-1]
35986 * alt1 = alt1[:-1]
35987 * while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]: # <<<<<<<<<<<<<<
35988 * ref2 = ref2[:-1]
35989 * alt2 = alt2[:-1]
35990 */
35991 while (1) {
35992 __pyx_t_3 = PyObject_Length(__pyx_v_ref2); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 1035, __pyx_L1_error)
35993 __pyx_t_4 = (__pyx_t_3 > 0);
35994 if (__pyx_t_4) {
35995 } else {
35996 __pyx_t_2 = __pyx_t_4;
35997 goto __pyx_L11_bool_binop_done;
35998 }
35999 __pyx_t_3 = PyObject_Length(__pyx_v_alt2); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 1035, __pyx_L1_error)
36000 __pyx_t_4 = (__pyx_t_3 > 0);
36001 if (__pyx_t_4) {
36002 } else {
36003 __pyx_t_2 = __pyx_t_4;
36004 goto __pyx_L11_bool_binop_done;
36005 }
36006 __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_ref2, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1035, __pyx_L1_error)
36007 __Pyx_GOTREF(__pyx_t_6);
36008 __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_alt2, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1035, __pyx_L1_error)
36009 __Pyx_GOTREF(__pyx_t_5);
36010 __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1035, __pyx_L1_error)
36011 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
36012 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
36013 __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(0, 1035, __pyx_L1_error)
36014 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
36015 __pyx_t_2 = __pyx_t_4;
36016 __pyx_L11_bool_binop_done:;
36017 if (!__pyx_t_2) break;
36018
36019 /* "pysam/libcvcf.pyx":1036
36020 * alt1 = alt1[:-1]
36021 * while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
36022 * ref2 = ref2[:-1] # <<<<<<<<<<<<<<
36023 * alt2 = alt2[:-1]
36024 * # now, the alternative alleles must be identical
36025 */
36026 __pyx_t_1 = __Pyx_PyObject_GetSlice(__pyx_v_ref2, 0, -1L, NULL, NULL, &__pyx_slice__28, 0, 1, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1036, __pyx_L1_error)
36027 __Pyx_GOTREF(__pyx_t_1);
36028 __Pyx_DECREF_SET(__pyx_v_ref2, __pyx_t_1);
36029 __pyx_t_1 = 0;
36030
36031 /* "pysam/libcvcf.pyx":1037
36032 * while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
36033 * ref2 = ref2[:-1]
36034 * alt2 = alt2[:-1] # <<<<<<<<<<<<<<
36035 * # now, the alternative alleles must be identical
36036 * return alt1 == alt2
36037 */
36038 __pyx_t_1 = __Pyx_PyObject_GetSlice(__pyx_v_alt2, 0, -1L, NULL, NULL, &__pyx_slice__28, 0, 1, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1037, __pyx_L1_error)
36039 __Pyx_GOTREF(__pyx_t_1);
36040 __Pyx_DECREF_SET(__pyx_v_alt2, __pyx_t_1);
36041 __pyx_t_1 = 0;
36042 }
36043
36044 /* "pysam/libcvcf.pyx":1039
36045 * alt2 = alt2[:-1]
36046 * # now, the alternative alleles must be identical
36047 * return alt1 == alt2 # <<<<<<<<<<<<<<
36048 *
36049 * ###########################################################################################################
36050 */
36051 __Pyx_XDECREF(__pyx_r);
36052 __pyx_t_1 = PyObject_RichCompare(__pyx_v_alt1, __pyx_v_alt2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1039, __pyx_L1_error)
36053 __pyx_r = __pyx_t_1;
36054 __pyx_t_1 = 0;
36055 goto __pyx_L0;
36056
36057 /* "pysam/libcvcf.pyx":1024
36058 * self.write_heading(stream)
36059 *
36060 * def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): # <<<<<<<<<<<<<<
36061 * """ Utility function: compares two calls for equality """
36062 * # a variant should always be assigned to a unique position, one base before
36063 */
36064
36065 /* function exit code */
36066 __pyx_L1_error:;
36067 __Pyx_XDECREF(__pyx_t_1);
36068 __Pyx_XDECREF(__pyx_t_5);
36069 __Pyx_XDECREF(__pyx_t_6);
36070 __Pyx_AddTraceback("pysam.libcvcf.VCF.compare_calls", __pyx_clineno, __pyx_lineno, __pyx_filename);
36071 __pyx_r = NULL;
36072 __pyx_L0:;
36073 __Pyx_XDECREF(__pyx_v_ref1);
36074 __Pyx_XDECREF(__pyx_v_alt1);
36075 __Pyx_XDECREF(__pyx_v_ref2);
36076 __Pyx_XDECREF(__pyx_v_alt2);
36077 __Pyx_XGIVEREF(__pyx_r);
36078 __Pyx_RefNannyFinishContext();
36079 return __pyx_r;
36080 }
36081
36082 /* "pysam/libcvcf.pyx":1046
36083 * ###########################################################################################################
36084 *
36085 * def connect(self, filename, encoding="ascii"): # <<<<<<<<<<<<<<
36086 * '''connect to tabix file.'''
36087 * self.encoding=encoding
36088 */
36089
36090 /* Python wrapper */
36091 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_80connect(PyObject *__pyx_self,
36092 #if CYTHON_METH_FASTCALL
36093 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
36094 #else
36095 PyObject *__pyx_args, PyObject *__pyx_kwds
36096 #endif
36097 ); /*proto*/
36098 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_79connect, "VCF.connect(self, filename, encoding=u'ascii')\nconnect to tabix file.");
36099 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_80connect = {"connect", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_80connect, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_79connect};
36100 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_80connect(PyObject *__pyx_self,
36101 #if CYTHON_METH_FASTCALL
36102 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
36103 #else
36104 PyObject *__pyx_args, PyObject *__pyx_kwds
36105 #endif
36106 ) {
36107 PyObject *__pyx_v_self = 0;
36108 PyObject *__pyx_v_filename = 0;
36109 PyObject *__pyx_v_encoding = 0;
36110 #if !CYTHON_METH_FASTCALL
36111 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
36112 #endif
36113 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
36114 PyObject* values[3] = {0,0,0};
36115 int __pyx_lineno = 0;
36116 const char *__pyx_filename = NULL;
36117 int __pyx_clineno = 0;
36118 PyObject *__pyx_r = 0;
36119 __Pyx_RefNannyDeclarations
36120 __Pyx_RefNannySetupContext("connect (wrapper)", 0);
36121 #if !CYTHON_METH_FASTCALL
36122 #if CYTHON_ASSUME_SAFE_MACROS
36123 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
36124 #else
36125 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
36126 #endif
36127 #endif
36128 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
36129 {
36130 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_filename,&__pyx_n_s_encoding,0};
36131 values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject*)__pyx_n_u_ascii)));
36132 if (__pyx_kwds) {
36133 Py_ssize_t kw_args;
36134 switch (__pyx_nargs) {
36135 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
36136 CYTHON_FALLTHROUGH;
36137 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
36138 CYTHON_FALLTHROUGH;
36139 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
36140 CYTHON_FALLTHROUGH;
36141 case 0: break;
36142 default: goto __pyx_L5_argtuple_error;
36143 }
36144 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
36145 switch (__pyx_nargs) {
36146 case 0:
36147 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
36148 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
36149 kw_args--;
36150 }
36151 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1046, __pyx_L3_error)
36152 else goto __pyx_L5_argtuple_error;
36153 CYTHON_FALLTHROUGH;
36154 case 1:
36155 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename)) != 0)) {
36156 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
36157 kw_args--;
36158 }
36159 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1046, __pyx_L3_error)
36160 else {
36161 __Pyx_RaiseArgtupleInvalid("connect", 0, 2, 3, 1); __PYX_ERR(0, 1046, __pyx_L3_error)
36162 }
36163 CYTHON_FALLTHROUGH;
36164 case 2:
36165 if (kw_args > 0) {
36166 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_encoding);
36167 if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
36168 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1046, __pyx_L3_error)
36169 }
36170 }
36171 if (unlikely(kw_args > 0)) {
36172 const Py_ssize_t kwd_pos_args = __pyx_nargs;
36173 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "connect") < 0)) __PYX_ERR(0, 1046, __pyx_L3_error)
36174 }
36175 } else {
36176 switch (__pyx_nargs) {
36177 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
36178 CYTHON_FALLTHROUGH;
36179 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
36180 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
36181 break;
36182 default: goto __pyx_L5_argtuple_error;
36183 }
36184 }
36185 __pyx_v_self = values[0];
36186 __pyx_v_filename = values[1];
36187 __pyx_v_encoding = values[2];
36188 }
36189 goto __pyx_L6_skip;
36190 __pyx_L5_argtuple_error:;
36191 __Pyx_RaiseArgtupleInvalid("connect", 0, 2, 3, __pyx_nargs); __PYX_ERR(0, 1046, __pyx_L3_error)
36192 __pyx_L6_skip:;
36193 goto __pyx_L4_argument_unpacking_done;
36194 __pyx_L3_error:;
36195 {
36196 Py_ssize_t __pyx_temp;
36197 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
36198 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
36199 }
36200 }
36201 __Pyx_AddTraceback("pysam.libcvcf.VCF.connect", __pyx_clineno, __pyx_lineno, __pyx_filename);
36202 __Pyx_RefNannyFinishContext();
36203 return NULL;
36204 __pyx_L4_argument_unpacking_done:;
36205 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_79connect(__pyx_self, __pyx_v_self, __pyx_v_filename, __pyx_v_encoding);
36206
36207 /* function exit code */
36208 {
36209 Py_ssize_t __pyx_temp;
36210 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
36211 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
36212 }
36213 }
36214 __Pyx_RefNannyFinishContext();
36215 return __pyx_r;
36216 }
36217
36218 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_encoding) {
36219 PyObject *__pyx_r = NULL;
36220 __Pyx_RefNannyDeclarations
36221 PyObject *__pyx_t_1 = NULL;
36222 PyObject *__pyx_t_2 = NULL;
36223 PyObject *__pyx_t_3 = NULL;
36224 PyObject *__pyx_t_4 = NULL;
36225 unsigned int __pyx_t_5;
36226 int __pyx_lineno = 0;
36227 const char *__pyx_filename = NULL;
36228 int __pyx_clineno = 0;
36229 __Pyx_RefNannySetupContext("connect", 1);
36230
36231 /* "pysam/libcvcf.pyx":1048
36232 * def connect(self, filename, encoding="ascii"):
36233 * '''connect to tabix file.'''
36234 * self.encoding=encoding # <<<<<<<<<<<<<<
36235 * self.tabixfile = pysam.Tabixfile(filename, encoding=encoding)
36236 * self._parse_header(self.tabixfile.header)
36237 */
36238 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_encoding, __pyx_v_encoding) < 0) __PYX_ERR(0, 1048, __pyx_L1_error)
36239
36240 /* "pysam/libcvcf.pyx":1049
36241 * '''connect to tabix file.'''
36242 * self.encoding=encoding
36243 * self.tabixfile = pysam.Tabixfile(filename, encoding=encoding) # <<<<<<<<<<<<<<
36244 * self._parse_header(self.tabixfile.header)
36245 *
36246 */
36247 __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_pysam); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1049, __pyx_L1_error)
36248 __Pyx_GOTREF(__pyx_t_1);
36249 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_Tabixfile); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1049, __pyx_L1_error)
36250 __Pyx_GOTREF(__pyx_t_2);
36251 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
36252 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1049, __pyx_L1_error)
36253 __Pyx_GOTREF(__pyx_t_1);
36254 __Pyx_INCREF(__pyx_v_filename);
36255 __Pyx_GIVEREF(__pyx_v_filename);
36256 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_filename)) __PYX_ERR(0, 1049, __pyx_L1_error);
36257 __pyx_t_3 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1049, __pyx_L1_error)
36258 __Pyx_GOTREF(__pyx_t_3);
36259 if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_encoding, __pyx_v_encoding) < 0) __PYX_ERR(0, 1049, __pyx_L1_error)
36260 __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_1, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1049, __pyx_L1_error)
36261 __Pyx_GOTREF(__pyx_t_4);
36262 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
36263 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
36264 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
36265 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_tabixfile, __pyx_t_4) < 0) __PYX_ERR(0, 1049, __pyx_L1_error)
36266 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
36267
36268 /* "pysam/libcvcf.pyx":1050
36269 * self.encoding=encoding
36270 * self.tabixfile = pysam.Tabixfile(filename, encoding=encoding)
36271 * self._parse_header(self.tabixfile.header) # <<<<<<<<<<<<<<
36272 *
36273 * def __del__(self):
36274 */
36275 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parse_header_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1050, __pyx_L1_error)
36276 __Pyx_GOTREF(__pyx_t_3);
36277 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_tabixfile); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1050, __pyx_L1_error)
36278 __Pyx_GOTREF(__pyx_t_1);
36279 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_header_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1050, __pyx_L1_error)
36280 __Pyx_GOTREF(__pyx_t_2);
36281 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
36282 __pyx_t_1 = NULL;
36283 __pyx_t_5 = 0;
36284 #if CYTHON_UNPACK_METHODS
36285 if (likely(PyMethod_Check(__pyx_t_3))) {
36286 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_3);
36287 if (likely(__pyx_t_1)) {
36288 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
36289 __Pyx_INCREF(__pyx_t_1);
36290 __Pyx_INCREF(function);
36291 __Pyx_DECREF_SET(__pyx_t_3, function);
36292 __pyx_t_5 = 1;
36293 }
36294 }
36295 #endif
36296 {
36297 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_t_2};
36298 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
36299 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
36300 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
36301 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1050, __pyx_L1_error)
36302 __Pyx_GOTREF(__pyx_t_4);
36303 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
36304 }
36305 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
36306
36307 /* "pysam/libcvcf.pyx":1046
36308 * ###########################################################################################################
36309 *
36310 * def connect(self, filename, encoding="ascii"): # <<<<<<<<<<<<<<
36311 * '''connect to tabix file.'''
36312 * self.encoding=encoding
36313 */
36314
36315 /* function exit code */
36316 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
36317 goto __pyx_L0;
36318 __pyx_L1_error:;
36319 __Pyx_XDECREF(__pyx_t_1);
36320 __Pyx_XDECREF(__pyx_t_2);
36321 __Pyx_XDECREF(__pyx_t_3);
36322 __Pyx_XDECREF(__pyx_t_4);
36323 __Pyx_AddTraceback("pysam.libcvcf.VCF.connect", __pyx_clineno, __pyx_lineno, __pyx_filename);
36324 __pyx_r = NULL;
36325 __pyx_L0:;
36326 __Pyx_XGIVEREF(__pyx_r);
36327 __Pyx_RefNannyFinishContext();
36328 return __pyx_r;
36329 }
36330
36331 /* "pysam/libcvcf.pyx":1052
36332 * self._parse_header(self.tabixfile.header)
36333 *
36334 * def __del__(self): # <<<<<<<<<<<<<<
36335 * self.close()
36336 * self.tabixfile = None
36337 */
36338
36339 /* Python wrapper */
36340 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_82__del__(PyObject *__pyx_self,
36341 #if CYTHON_METH_FASTCALL
36342 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
36343 #else
36344 PyObject *__pyx_args, PyObject *__pyx_kwds
36345 #endif
36346 ); /*proto*/
36347 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_81__del__, "VCF.__del__(self)");
36348 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_82__del__ = {"__del__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_82__del__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_81__del__};
36349 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_82__del__(PyObject *__pyx_self,
36350 #if CYTHON_METH_FASTCALL
36351 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
36352 #else
36353 PyObject *__pyx_args, PyObject *__pyx_kwds
36354 #endif
36355 ) {
36356 PyObject *__pyx_v_self = 0;
36357 #if !CYTHON_METH_FASTCALL
36358 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
36359 #endif
36360 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
36361 PyObject* values[1] = {0};
36362 int __pyx_lineno = 0;
36363 const char *__pyx_filename = NULL;
36364 int __pyx_clineno = 0;
36365 PyObject *__pyx_r = 0;
36366 __Pyx_RefNannyDeclarations
36367 __Pyx_RefNannySetupContext("__del__ (wrapper)", 0);
36368 #if !CYTHON_METH_FASTCALL
36369 #if CYTHON_ASSUME_SAFE_MACROS
36370 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
36371 #else
36372 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
36373 #endif
36374 #endif
36375 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
36376 {
36377 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0};
36378 if (__pyx_kwds) {
36379 Py_ssize_t kw_args;
36380 switch (__pyx_nargs) {
36381 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
36382 CYTHON_FALLTHROUGH;
36383 case 0: break;
36384 default: goto __pyx_L5_argtuple_error;
36385 }
36386 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
36387 switch (__pyx_nargs) {
36388 case 0:
36389 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
36390 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
36391 kw_args--;
36392 }
36393 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1052, __pyx_L3_error)
36394 else goto __pyx_L5_argtuple_error;
36395 }
36396 if (unlikely(kw_args > 0)) {
36397 const Py_ssize_t kwd_pos_args = __pyx_nargs;
36398 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__del__") < 0)) __PYX_ERR(0, 1052, __pyx_L3_error)
36399 }
36400 } else if (unlikely(__pyx_nargs != 1)) {
36401 goto __pyx_L5_argtuple_error;
36402 } else {
36403 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
36404 }
36405 __pyx_v_self = values[0];
36406 }
36407 goto __pyx_L6_skip;
36408 __pyx_L5_argtuple_error:;
36409 __Pyx_RaiseArgtupleInvalid("__del__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 1052, __pyx_L3_error)
36410 __pyx_L6_skip:;
36411 goto __pyx_L4_argument_unpacking_done;
36412 __pyx_L3_error:;
36413 {
36414 Py_ssize_t __pyx_temp;
36415 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
36416 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
36417 }
36418 }
36419 __Pyx_AddTraceback("pysam.libcvcf.VCF.__del__", __pyx_clineno, __pyx_lineno, __pyx_filename);
36420 __Pyx_RefNannyFinishContext();
36421 return NULL;
36422 __pyx_L4_argument_unpacking_done:;
36423 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_81__del__(__pyx_self, __pyx_v_self);
36424
36425 /* function exit code */
36426 {
36427 Py_ssize_t __pyx_temp;
36428 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
36429 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
36430 }
36431 }
36432 __Pyx_RefNannyFinishContext();
36433 return __pyx_r;
36434 }
36435
36436 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_81__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
36437 PyObject *__pyx_r = NULL;
36438 __Pyx_RefNannyDeclarations
36439 PyObject *__pyx_t_1 = NULL;
36440 PyObject *__pyx_t_2 = NULL;
36441 PyObject *__pyx_t_3 = NULL;
36442 unsigned int __pyx_t_4;
36443 int __pyx_lineno = 0;
36444 const char *__pyx_filename = NULL;
36445 int __pyx_clineno = 0;
36446 __Pyx_RefNannySetupContext("__del__", 1);
36447
36448 /* "pysam/libcvcf.pyx":1053
36449 *
36450 * def __del__(self):
36451 * self.close() # <<<<<<<<<<<<<<
36452 * self.tabixfile = None
36453 *
36454 */
36455 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_close); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1053, __pyx_L1_error)
36456 __Pyx_GOTREF(__pyx_t_2);
36457 __pyx_t_3 = NULL;
36458 __pyx_t_4 = 0;
36459 #if CYTHON_UNPACK_METHODS
36460 if (likely(PyMethod_Check(__pyx_t_2))) {
36461 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
36462 if (likely(__pyx_t_3)) {
36463 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
36464 __Pyx_INCREF(__pyx_t_3);
36465 __Pyx_INCREF(function);
36466 __Pyx_DECREF_SET(__pyx_t_2, function);
36467 __pyx_t_4 = 1;
36468 }
36469 }
36470 #endif
36471 {
36472 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
36473 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
36474 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
36475 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1053, __pyx_L1_error)
36476 __Pyx_GOTREF(__pyx_t_1);
36477 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
36478 }
36479 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
36480
36481 /* "pysam/libcvcf.pyx":1054
36482 * def __del__(self):
36483 * self.close()
36484 * self.tabixfile = None # <<<<<<<<<<<<<<
36485 *
36486 * def close(self):
36487 */
36488 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_tabixfile, Py_None) < 0) __PYX_ERR(0, 1054, __pyx_L1_error)
36489
36490 /* "pysam/libcvcf.pyx":1052
36491 * self._parse_header(self.tabixfile.header)
36492 *
36493 * def __del__(self): # <<<<<<<<<<<<<<
36494 * self.close()
36495 * self.tabixfile = None
36496 */
36497
36498 /* function exit code */
36499 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
36500 goto __pyx_L0;
36501 __pyx_L1_error:;
36502 __Pyx_XDECREF(__pyx_t_1);
36503 __Pyx_XDECREF(__pyx_t_2);
36504 __Pyx_XDECREF(__pyx_t_3);
36505 __Pyx_AddTraceback("pysam.libcvcf.VCF.__del__", __pyx_clineno, __pyx_lineno, __pyx_filename);
36506 __pyx_r = NULL;
36507 __pyx_L0:;
36508 __Pyx_XGIVEREF(__pyx_r);
36509 __Pyx_RefNannyFinishContext();
36510 return __pyx_r;
36511 }
36512
36513 /* "pysam/libcvcf.pyx":1056
36514 * self.tabixfile = None
36515 *
36516 * def close(self): # <<<<<<<<<<<<<<
36517 * if self.tabixfile:
36518 * self.tabixfile.close()
36519 */
36520
36521 /* Python wrapper */
36522 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_84close(PyObject *__pyx_self,
36523 #if CYTHON_METH_FASTCALL
36524 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
36525 #else
36526 PyObject *__pyx_args, PyObject *__pyx_kwds
36527 #endif
36528 ); /*proto*/
36529 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_83close, "VCF.close(self)");
36530 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_84close = {"close", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_84close, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_83close};
36531 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_84close(PyObject *__pyx_self,
36532 #if CYTHON_METH_FASTCALL
36533 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
36534 #else
36535 PyObject *__pyx_args, PyObject *__pyx_kwds
36536 #endif
36537 ) {
36538 PyObject *__pyx_v_self = 0;
36539 #if !CYTHON_METH_FASTCALL
36540 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
36541 #endif
36542 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
36543 PyObject* values[1] = {0};
36544 int __pyx_lineno = 0;
36545 const char *__pyx_filename = NULL;
36546 int __pyx_clineno = 0;
36547 PyObject *__pyx_r = 0;
36548 __Pyx_RefNannyDeclarations
36549 __Pyx_RefNannySetupContext("close (wrapper)", 0);
36550 #if !CYTHON_METH_FASTCALL
36551 #if CYTHON_ASSUME_SAFE_MACROS
36552 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
36553 #else
36554 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
36555 #endif
36556 #endif
36557 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
36558 {
36559 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0};
36560 if (__pyx_kwds) {
36561 Py_ssize_t kw_args;
36562 switch (__pyx_nargs) {
36563 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
36564 CYTHON_FALLTHROUGH;
36565 case 0: break;
36566 default: goto __pyx_L5_argtuple_error;
36567 }
36568 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
36569 switch (__pyx_nargs) {
36570 case 0:
36571 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
36572 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
36573 kw_args--;
36574 }
36575 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1056, __pyx_L3_error)
36576 else goto __pyx_L5_argtuple_error;
36577 }
36578 if (unlikely(kw_args > 0)) {
36579 const Py_ssize_t kwd_pos_args = __pyx_nargs;
36580 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "close") < 0)) __PYX_ERR(0, 1056, __pyx_L3_error)
36581 }
36582 } else if (unlikely(__pyx_nargs != 1)) {
36583 goto __pyx_L5_argtuple_error;
36584 } else {
36585 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
36586 }
36587 __pyx_v_self = values[0];
36588 }
36589 goto __pyx_L6_skip;
36590 __pyx_L5_argtuple_error:;
36591 __Pyx_RaiseArgtupleInvalid("close", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 1056, __pyx_L3_error)
36592 __pyx_L6_skip:;
36593 goto __pyx_L4_argument_unpacking_done;
36594 __pyx_L3_error:;
36595 {
36596 Py_ssize_t __pyx_temp;
36597 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
36598 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
36599 }
36600 }
36601 __Pyx_AddTraceback("pysam.libcvcf.VCF.close", __pyx_clineno, __pyx_lineno, __pyx_filename);
36602 __Pyx_RefNannyFinishContext();
36603 return NULL;
36604 __pyx_L4_argument_unpacking_done:;
36605 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_83close(__pyx_self, __pyx_v_self);
36606
36607 /* function exit code */
36608 {
36609 Py_ssize_t __pyx_temp;
36610 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
36611 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
36612 }
36613 }
36614 __Pyx_RefNannyFinishContext();
36615 return __pyx_r;
36616 }
36617
36618 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_83close(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
36619 PyObject *__pyx_r = NULL;
36620 __Pyx_RefNannyDeclarations
36621 PyObject *__pyx_t_1 = NULL;
36622 int __pyx_t_2;
36623 PyObject *__pyx_t_3 = NULL;
36624 PyObject *__pyx_t_4 = NULL;
36625 unsigned int __pyx_t_5;
36626 int __pyx_lineno = 0;
36627 const char *__pyx_filename = NULL;
36628 int __pyx_clineno = 0;
36629 __Pyx_RefNannySetupContext("close", 1);
36630
36631 /* "pysam/libcvcf.pyx":1057
36632 *
36633 * def close(self):
36634 * if self.tabixfile: # <<<<<<<<<<<<<<
36635 * self.tabixfile.close()
36636 * self.tabixfile = None
36637 */
36638 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_tabixfile); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1057, __pyx_L1_error)
36639 __Pyx_GOTREF(__pyx_t_1);
36640 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 1057, __pyx_L1_error)
36641 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
36642 if (__pyx_t_2) {
36643
36644 /* "pysam/libcvcf.pyx":1058
36645 * def close(self):
36646 * if self.tabixfile:
36647 * self.tabixfile.close() # <<<<<<<<<<<<<<
36648 * self.tabixfile = None
36649 *
36650 */
36651 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_tabixfile); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1058, __pyx_L1_error)
36652 __Pyx_GOTREF(__pyx_t_3);
36653 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_close); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1058, __pyx_L1_error)
36654 __Pyx_GOTREF(__pyx_t_4);
36655 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
36656 __pyx_t_3 = NULL;
36657 __pyx_t_5 = 0;
36658 #if CYTHON_UNPACK_METHODS
36659 if (likely(PyMethod_Check(__pyx_t_4))) {
36660 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_4);
36661 if (likely(__pyx_t_3)) {
36662 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
36663 __Pyx_INCREF(__pyx_t_3);
36664 __Pyx_INCREF(function);
36665 __Pyx_DECREF_SET(__pyx_t_4, function);
36666 __pyx_t_5 = 1;
36667 }
36668 }
36669 #endif
36670 {
36671 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
36672 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_5, 0+__pyx_t_5);
36673 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
36674 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1058, __pyx_L1_error)
36675 __Pyx_GOTREF(__pyx_t_1);
36676 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
36677 }
36678 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
36679
36680 /* "pysam/libcvcf.pyx":1059
36681 * if self.tabixfile:
36682 * self.tabixfile.close()
36683 * self.tabixfile = None # <<<<<<<<<<<<<<
36684 *
36685 * def fetch(self,
36686 */
36687 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_tabixfile, Py_None) < 0) __PYX_ERR(0, 1059, __pyx_L1_error)
36688
36689 /* "pysam/libcvcf.pyx":1057
36690 *
36691 * def close(self):
36692 * if self.tabixfile: # <<<<<<<<<<<<<<
36693 * self.tabixfile.close()
36694 * self.tabixfile = None
36695 */
36696 }
36697
36698 /* "pysam/libcvcf.pyx":1056
36699 * self.tabixfile = None
36700 *
36701 * def close(self): # <<<<<<<<<<<<<<
36702 * if self.tabixfile:
36703 * self.tabixfile.close()
36704 */
36705
36706 /* function exit code */
36707 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
36708 goto __pyx_L0;
36709 __pyx_L1_error:;
36710 __Pyx_XDECREF(__pyx_t_1);
36711 __Pyx_XDECREF(__pyx_t_3);
36712 __Pyx_XDECREF(__pyx_t_4);
36713 __Pyx_AddTraceback("pysam.libcvcf.VCF.close", __pyx_clineno, __pyx_lineno, __pyx_filename);
36714 __pyx_r = NULL;
36715 __pyx_L0:;
36716 __Pyx_XGIVEREF(__pyx_r);
36717 __Pyx_RefNannyFinishContext();
36718 return __pyx_r;
36719 }
36720
36721 /* "pysam/libcvcf.pyx":1061
36722 * self.tabixfile = None
36723 *
36724 * def fetch(self, # <<<<<<<<<<<<<<
36725 * reference=None,
36726 * start=None,
36727 */
36728
36729 /* Python wrapper */
36730 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_86fetch(PyObject *__pyx_self,
36731 #if CYTHON_METH_FASTCALL
36732 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
36733 #else
36734 PyObject *__pyx_args, PyObject *__pyx_kwds
36735 #endif
36736 ); /*proto*/
36737 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_85fetch, "VCF.fetch(self, reference=None, start=None, end=None, region=None)\n Parse a stream of VCF-formatted lines.\n Initializes class instance and return generator ");
36738 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_86fetch = {"fetch", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_86fetch, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_85fetch};
36739 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_86fetch(PyObject *__pyx_self,
36740 #if CYTHON_METH_FASTCALL
36741 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
36742 #else
36743 PyObject *__pyx_args, PyObject *__pyx_kwds
36744 #endif
36745 ) {
36746 PyObject *__pyx_v_self = 0;
36747 PyObject *__pyx_v_reference = 0;
36748 PyObject *__pyx_v_start = 0;
36749 PyObject *__pyx_v_end = 0;
36750 PyObject *__pyx_v_region = 0;
36751 #if !CYTHON_METH_FASTCALL
36752 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
36753 #endif
36754 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
36755 PyObject* values[5] = {0,0,0,0,0};
36756 int __pyx_lineno = 0;
36757 const char *__pyx_filename = NULL;
36758 int __pyx_clineno = 0;
36759 PyObject *__pyx_r = 0;
36760 __Pyx_RefNannyDeclarations
36761 __Pyx_RefNannySetupContext("fetch (wrapper)", 0);
36762 #if !CYTHON_METH_FASTCALL
36763 #if CYTHON_ASSUME_SAFE_MACROS
36764 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
36765 #else
36766 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
36767 #endif
36768 #endif
36769 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
36770 {
36771 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_reference,&__pyx_n_s_start,&__pyx_n_s_end,&__pyx_n_s_region,0};
36772
36773 /* "pysam/libcvcf.pyx":1062
36774 *
36775 * def fetch(self,
36776 * reference=None, # <<<<<<<<<<<<<<
36777 * start=None,
36778 * end=None,
36779 */
36780 values[1] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
36781
36782 /* "pysam/libcvcf.pyx":1063
36783 * def fetch(self,
36784 * reference=None,
36785 * start=None, # <<<<<<<<<<<<<<
36786 * end=None,
36787 * region=None ):
36788 */
36789 values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
36790
36791 /* "pysam/libcvcf.pyx":1064
36792 * reference=None,
36793 * start=None,
36794 * end=None, # <<<<<<<<<<<<<<
36795 * region=None ):
36796 * """ Parse a stream of VCF-formatted lines.
36797 */
36798 values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
36799
36800 /* "pysam/libcvcf.pyx":1065
36801 * start=None,
36802 * end=None,
36803 * region=None ): # <<<<<<<<<<<<<<
36804 * """ Parse a stream of VCF-formatted lines.
36805 * Initializes class instance and return generator """
36806 */
36807 values[4] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
36808 if (__pyx_kwds) {
36809 Py_ssize_t kw_args;
36810 switch (__pyx_nargs) {
36811 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
36812 CYTHON_FALLTHROUGH;
36813 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
36814 CYTHON_FALLTHROUGH;
36815 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
36816 CYTHON_FALLTHROUGH;
36817 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
36818 CYTHON_FALLTHROUGH;
36819 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
36820 CYTHON_FALLTHROUGH;
36821 case 0: break;
36822 default: goto __pyx_L5_argtuple_error;
36823 }
36824 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
36825 switch (__pyx_nargs) {
36826 case 0:
36827 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
36828 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
36829 kw_args--;
36830 }
36831 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1061, __pyx_L3_error)
36832 else goto __pyx_L5_argtuple_error;
36833 CYTHON_FALLTHROUGH;
36834 case 1:
36835 if (kw_args > 0) {
36836 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_reference);
36837 if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
36838 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1061, __pyx_L3_error)
36839 }
36840 CYTHON_FALLTHROUGH;
36841 case 2:
36842 if (kw_args > 0) {
36843 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_start);
36844 if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
36845 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1061, __pyx_L3_error)
36846 }
36847 CYTHON_FALLTHROUGH;
36848 case 3:
36849 if (kw_args > 0) {
36850 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_end);
36851 if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
36852 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1061, __pyx_L3_error)
36853 }
36854 CYTHON_FALLTHROUGH;
36855 case 4:
36856 if (kw_args > 0) {
36857 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_region);
36858 if (value) { values[4] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
36859 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1061, __pyx_L3_error)
36860 }
36861 }
36862 if (unlikely(kw_args > 0)) {
36863 const Py_ssize_t kwd_pos_args = __pyx_nargs;
36864 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "fetch") < 0)) __PYX_ERR(0, 1061, __pyx_L3_error)
36865 }
36866 } else {
36867 switch (__pyx_nargs) {
36868 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
36869 CYTHON_FALLTHROUGH;
36870 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
36871 CYTHON_FALLTHROUGH;
36872 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
36873 CYTHON_FALLTHROUGH;
36874 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
36875 CYTHON_FALLTHROUGH;
36876 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
36877 break;
36878 default: goto __pyx_L5_argtuple_error;
36879 }
36880 }
36881 __pyx_v_self = values[0];
36882 __pyx_v_reference = values[1];
36883 __pyx_v_start = values[2];
36884 __pyx_v_end = values[3];
36885 __pyx_v_region = values[4];
36886 }
36887 goto __pyx_L6_skip;
36888 __pyx_L5_argtuple_error:;
36889 __Pyx_RaiseArgtupleInvalid("fetch", 0, 1, 5, __pyx_nargs); __PYX_ERR(0, 1061, __pyx_L3_error)
36890 __pyx_L6_skip:;
36891 goto __pyx_L4_argument_unpacking_done;
36892 __pyx_L3_error:;
36893 {
36894 Py_ssize_t __pyx_temp;
36895 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
36896 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
36897 }
36898 }
36899 __Pyx_AddTraceback("pysam.libcvcf.VCF.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
36900 __Pyx_RefNannyFinishContext();
36901 return NULL;
36902 __pyx_L4_argument_unpacking_done:;
36903 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_85fetch(__pyx_self, __pyx_v_self, __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region);
36904
36905 /* "pysam/libcvcf.pyx":1061
36906 * self.tabixfile = None
36907 *
36908 * def fetch(self, # <<<<<<<<<<<<<<
36909 * reference=None,
36910 * start=None,
36911 */
36912
36913 /* function exit code */
36914 {
36915 Py_ssize_t __pyx_temp;
36916 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
36917 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
36918 }
36919 }
36920 __Pyx_RefNannyFinishContext();
36921 return __pyx_r;
36922 }
36923
36924 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_85fetch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) {
36925 PyObject *__pyx_r = NULL;
36926 __Pyx_RefNannyDeclarations
36927 PyObject *__pyx_t_1 = NULL;
36928 PyObject *__pyx_t_2 = NULL;
36929 PyObject *__pyx_t_3 = NULL;
36930 PyObject *__pyx_t_4 = NULL;
36931 int __pyx_lineno = 0;
36932 const char *__pyx_filename = NULL;
36933 int __pyx_clineno = 0;
36934 __Pyx_RefNannySetupContext("fetch", 1);
36935
36936 /* "pysam/libcvcf.pyx":1068
36937 * """ Parse a stream of VCF-formatted lines.
36938 * Initializes class instance and return generator """
36939 * return self.tabixfile.fetch( # <<<<<<<<<<<<<<
36940 * reference,
36941 * start,
36942 */
36943 __Pyx_XDECREF(__pyx_r);
36944 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_tabixfile); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1068, __pyx_L1_error)
36945 __Pyx_GOTREF(__pyx_t_1);
36946 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_fetch); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1068, __pyx_L1_error)
36947 __Pyx_GOTREF(__pyx_t_2);
36948 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
36949
36950 /* "pysam/libcvcf.pyx":1072
36951 * start,
36952 * end,
36953 * region, # <<<<<<<<<<<<<<
36954 * parser = asVCFRecord(self))
36955 *
36956 */
36957 __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1068, __pyx_L1_error)
36958 __Pyx_GOTREF(__pyx_t_1);
36959 __Pyx_INCREF(__pyx_v_reference);
36960 __Pyx_GIVEREF(__pyx_v_reference);
36961 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference)) __PYX_ERR(0, 1068, __pyx_L1_error);
36962 __Pyx_INCREF(__pyx_v_start);
36963 __Pyx_GIVEREF(__pyx_v_start);
36964 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_start)) __PYX_ERR(0, 1068, __pyx_L1_error);
36965 __Pyx_INCREF(__pyx_v_end);
36966 __Pyx_GIVEREF(__pyx_v_end);
36967 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_end)) __PYX_ERR(0, 1068, __pyx_L1_error);
36968 __Pyx_INCREF(__pyx_v_region);
36969 __Pyx_GIVEREF(__pyx_v_region);
36970 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_region)) __PYX_ERR(0, 1068, __pyx_L1_error);
36971
36972 /* "pysam/libcvcf.pyx":1073
36973 * end,
36974 * region,
36975 * parser = asVCFRecord(self)) # <<<<<<<<<<<<<<
36976 *
36977 * def validate(self, record):
36978 */
36979 __pyx_t_3 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1073, __pyx_L1_error)
36980 __Pyx_GOTREF(__pyx_t_3);
36981 __pyx_t_4 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_7libcvcf_asVCFRecord), __pyx_v_self); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1073, __pyx_L1_error)
36982 __Pyx_GOTREF(__pyx_t_4);
36983 if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_parser, __pyx_t_4) < 0) __PYX_ERR(0, 1073, __pyx_L1_error)
36984 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
36985
36986 /* "pysam/libcvcf.pyx":1068
36987 * """ Parse a stream of VCF-formatted lines.
36988 * Initializes class instance and return generator """
36989 * return self.tabixfile.fetch( # <<<<<<<<<<<<<<
36990 * reference,
36991 * start,
36992 */
36993 __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_1, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1068, __pyx_L1_error)
36994 __Pyx_GOTREF(__pyx_t_4);
36995 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
36996 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
36997 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
36998 __pyx_r = __pyx_t_4;
36999 __pyx_t_4 = 0;
37000 goto __pyx_L0;
37001
37002 /* "pysam/libcvcf.pyx":1061
37003 * self.tabixfile = None
37004 *
37005 * def fetch(self, # <<<<<<<<<<<<<<
37006 * reference=None,
37007 * start=None,
37008 */
37009
37010 /* function exit code */
37011 __pyx_L1_error:;
37012 __Pyx_XDECREF(__pyx_t_1);
37013 __Pyx_XDECREF(__pyx_t_2);
37014 __Pyx_XDECREF(__pyx_t_3);
37015 __Pyx_XDECREF(__pyx_t_4);
37016 __Pyx_AddTraceback("pysam.libcvcf.VCF.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
37017 __pyx_r = NULL;
37018 __pyx_L0:;
37019 __Pyx_XGIVEREF(__pyx_r);
37020 __Pyx_RefNannyFinishContext();
37021 return __pyx_r;
37022 }
37023
37024 /* "pysam/libcvcf.pyx":1075
37025 * parser = asVCFRecord(self))
37026 *
37027 * def validate(self, record): # <<<<<<<<<<<<<<
37028 * '''validate vcf record.
37029 *
37030 */
37031
37032 /* Python wrapper */
37033 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_88validate(PyObject *__pyx_self,
37034 #if CYTHON_METH_FASTCALL
37035 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
37036 #else
37037 PyObject *__pyx_args, PyObject *__pyx_kwds
37038 #endif
37039 ); /*proto*/
37040 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_3VCF_87validate, "VCF.validate(self, record)\nvalidate vcf record.\n\n returns a validated record.\n ");
37041 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_3VCF_88validate = {"validate", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_3VCF_88validate, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_3VCF_87validate};
37042 static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_88validate(PyObject *__pyx_self,
37043 #if CYTHON_METH_FASTCALL
37044 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
37045 #else
37046 PyObject *__pyx_args, PyObject *__pyx_kwds
37047 #endif
37048 ) {
37049 CYTHON_UNUSED PyObject *__pyx_v_self = 0;
37050 CYTHON_UNUSED PyObject *__pyx_v_record = 0;
37051 #if !CYTHON_METH_FASTCALL
37052 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
37053 #endif
37054 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
37055 PyObject* values[2] = {0,0};
37056 int __pyx_lineno = 0;
37057 const char *__pyx_filename = NULL;
37058 int __pyx_clineno = 0;
37059 PyObject *__pyx_r = 0;
37060 __Pyx_RefNannyDeclarations
37061 __Pyx_RefNannySetupContext("validate (wrapper)", 0);
37062 #if !CYTHON_METH_FASTCALL
37063 #if CYTHON_ASSUME_SAFE_MACROS
37064 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
37065 #else
37066 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
37067 #endif
37068 #endif
37069 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
37070 {
37071 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_record,0};
37072 if (__pyx_kwds) {
37073 Py_ssize_t kw_args;
37074 switch (__pyx_nargs) {
37075 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
37076 CYTHON_FALLTHROUGH;
37077 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
37078 CYTHON_FALLTHROUGH;
37079 case 0: break;
37080 default: goto __pyx_L5_argtuple_error;
37081 }
37082 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
37083 switch (__pyx_nargs) {
37084 case 0:
37085 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
37086 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
37087 kw_args--;
37088 }
37089 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1075, __pyx_L3_error)
37090 else goto __pyx_L5_argtuple_error;
37091 CYTHON_FALLTHROUGH;
37092 case 1:
37093 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_record)) != 0)) {
37094 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
37095 kw_args--;
37096 }
37097 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1075, __pyx_L3_error)
37098 else {
37099 __Pyx_RaiseArgtupleInvalid("validate", 1, 2, 2, 1); __PYX_ERR(0, 1075, __pyx_L3_error)
37100 }
37101 }
37102 if (unlikely(kw_args > 0)) {
37103 const Py_ssize_t kwd_pos_args = __pyx_nargs;
37104 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "validate") < 0)) __PYX_ERR(0, 1075, __pyx_L3_error)
37105 }
37106 } else if (unlikely(__pyx_nargs != 2)) {
37107 goto __pyx_L5_argtuple_error;
37108 } else {
37109 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
37110 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
37111 }
37112 __pyx_v_self = values[0];
37113 __pyx_v_record = values[1];
37114 }
37115 goto __pyx_L6_skip;
37116 __pyx_L5_argtuple_error:;
37117 __Pyx_RaiseArgtupleInvalid("validate", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 1075, __pyx_L3_error)
37118 __pyx_L6_skip:;
37119 goto __pyx_L4_argument_unpacking_done;
37120 __pyx_L3_error:;
37121 {
37122 Py_ssize_t __pyx_temp;
37123 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
37124 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
37125 }
37126 }
37127 __Pyx_AddTraceback("pysam.libcvcf.VCF.validate", __pyx_clineno, __pyx_lineno, __pyx_filename);
37128 __Pyx_RefNannyFinishContext();
37129 return NULL;
37130 __pyx_L4_argument_unpacking_done:;
37131 __pyx_r = __pyx_pf_5pysam_7libcvcf_3VCF_87validate(__pyx_self, __pyx_v_self, __pyx_v_record);
37132
37133 /* function exit code */
37134 {
37135 Py_ssize_t __pyx_temp;
37136 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
37137 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
37138 }
37139 }
37140 __Pyx_RefNannyFinishContext();
37141 return __pyx_r;
37142 }
37143
37144 static PyObject *__pyx_pf_5pysam_7libcvcf_3VCF_87validate(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_record) {
37145 PyObject *__pyx_r = NULL;
37146 __Pyx_RefNannyDeclarations
37147 PyObject *__pyx_t_1 = NULL;
37148 int __pyx_lineno = 0;
37149 const char *__pyx_filename = NULL;
37150 int __pyx_clineno = 0;
37151 __Pyx_RefNannySetupContext("validate", 1);
37152
37153 /* "pysam/libcvcf.pyx":1081
37154 * '''
37155 *
37156 * raise NotImplementedError("needs to be checked") # <<<<<<<<<<<<<<
37157 *
37158 * chrom, pos = record.chrom, record.pos
37159 */
37160 __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_NotImplementedError, __pyx_tuple__31, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1081, __pyx_L1_error)
37161 __Pyx_GOTREF(__pyx_t_1);
37162 __Pyx_Raise(__pyx_t_1, 0, 0, 0);
37163 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
37164 __PYX_ERR(0, 1081, __pyx_L1_error)
37165
37166 /* "pysam/libcvcf.pyx":1075
37167 * parser = asVCFRecord(self))
37168 *
37169 * def validate(self, record): # <<<<<<<<<<<<<<
37170 * '''validate vcf record.
37171 *
37172 */
37173
37174 /* function exit code */
37175 __pyx_L1_error:;
37176 __Pyx_XDECREF(__pyx_t_1);
37177 __Pyx_AddTraceback("pysam.libcvcf.VCF.validate", __pyx_clineno, __pyx_lineno, __pyx_filename);
37178 __pyx_r = NULL;
37179 __Pyx_XGIVEREF(__pyx_r);
37180 __Pyx_RefNannyFinishContext();
37181 return __pyx_r;
37182 }
37183
37184 /* "(tree fragment)":1
37185 * def __pyx_unpickle_asVCFRecord(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
37186 * cdef object __pyx_PickleError
37187 * cdef object __pyx_result
37188 */
37189
37190 /* Python wrapper */
37191 static PyObject *__pyx_pw_5pysam_7libcvcf_5__pyx_unpickle_asVCFRecord(PyObject *__pyx_self,
37192 #if CYTHON_METH_FASTCALL
37193 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
37194 #else
37195 PyObject *__pyx_args, PyObject *__pyx_kwds
37196 #endif
37197 ); /*proto*/
37198 PyDoc_STRVAR(__pyx_doc_5pysam_7libcvcf_4__pyx_unpickle_asVCFRecord, "__pyx_unpickle_asVCFRecord(__pyx_type, long __pyx_checksum, __pyx_state)");
37199 static PyMethodDef __pyx_mdef_5pysam_7libcvcf_5__pyx_unpickle_asVCFRecord = {"__pyx_unpickle_asVCFRecord", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_5__pyx_unpickle_asVCFRecord, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_4__pyx_unpickle_asVCFRecord};
37200 static PyObject *__pyx_pw_5pysam_7libcvcf_5__pyx_unpickle_asVCFRecord(PyObject *__pyx_self,
37201 #if CYTHON_METH_FASTCALL
37202 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
37203 #else
37204 PyObject *__pyx_args, PyObject *__pyx_kwds
37205 #endif
37206 ) {
37207 PyObject *__pyx_v___pyx_type = 0;
37208 long __pyx_v___pyx_checksum;
37209 PyObject *__pyx_v___pyx_state = 0;
37210 #if !CYTHON_METH_FASTCALL
37211 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
37212 #endif
37213 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
37214 PyObject* values[3] = {0,0,0};
37215 int __pyx_lineno = 0;
37216 const char *__pyx_filename = NULL;
37217 int __pyx_clineno = 0;
37218 PyObject *__pyx_r = 0;
37219 __Pyx_RefNannyDeclarations
37220 __Pyx_RefNannySetupContext("__pyx_unpickle_asVCFRecord (wrapper)", 0);
37221 #if !CYTHON_METH_FASTCALL
37222 #if CYTHON_ASSUME_SAFE_MACROS
37223 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
37224 #else
37225 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
37226 #endif
37227 #endif
37228 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
37229 {
37230 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0};
37231 if (__pyx_kwds) {
37232 Py_ssize_t kw_args;
37233 switch (__pyx_nargs) {
37234 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
37235 CYTHON_FALLTHROUGH;
37236 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
37237 CYTHON_FALLTHROUGH;
37238 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
37239 CYTHON_FALLTHROUGH;
37240 case 0: break;
37241 default: goto __pyx_L5_argtuple_error;
37242 }
37243 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
37244 switch (__pyx_nargs) {
37245 case 0:
37246 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) {
37247 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
37248 kw_args--;
37249 }
37250 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
37251 else goto __pyx_L5_argtuple_error;
37252 CYTHON_FALLTHROUGH;
37253 case 1:
37254 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) {
37255 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
37256 kw_args--;
37257 }
37258 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
37259 else {
37260 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asVCFRecord", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error)
37261 }
37262 CYTHON_FALLTHROUGH;
37263 case 2:
37264 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
37265 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
37266 kw_args--;
37267 }
37268 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
37269 else {
37270 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asVCFRecord", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error)
37271 }
37272 }
37273 if (unlikely(kw_args > 0)) {
37274 const Py_ssize_t kwd_pos_args = __pyx_nargs;
37275 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_asVCFRecord") < 0)) __PYX_ERR(1, 1, __pyx_L3_error)
37276 }
37277 } else if (unlikely(__pyx_nargs != 3)) {
37278 goto __pyx_L5_argtuple_error;
37279 } else {
37280 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
37281 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
37282 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
37283 }
37284 __pyx_v___pyx_type = values[0];
37285 __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
37286 __pyx_v___pyx_state = values[2];
37287 }
37288 goto __pyx_L6_skip;
37289 __pyx_L5_argtuple_error:;
37290 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asVCFRecord", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error)
37291 __pyx_L6_skip:;
37292 goto __pyx_L4_argument_unpacking_done;
37293 __pyx_L3_error:;
37294 {
37295 Py_ssize_t __pyx_temp;
37296 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
37297 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
37298 }
37299 }
37300 __Pyx_AddTraceback("pysam.libcvcf.__pyx_unpickle_asVCFRecord", __pyx_clineno, __pyx_lineno, __pyx_filename);
37301 __Pyx_RefNannyFinishContext();
37302 return NULL;
37303 __pyx_L4_argument_unpacking_done:;
37304 __pyx_r = __pyx_pf_5pysam_7libcvcf_4__pyx_unpickle_asVCFRecord(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state);
37305
37306 /* function exit code */
37307 {
37308 Py_ssize_t __pyx_temp;
37309 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
37310 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
37311 }
37312 }
37313 __Pyx_RefNannyFinishContext();
37314 return __pyx_r;
37315 }
37316
37317 static PyObject *__pyx_pf_5pysam_7libcvcf_4__pyx_unpickle_asVCFRecord(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) {
37318 PyObject *__pyx_v___pyx_PickleError = 0;
37319 PyObject *__pyx_v___pyx_result = 0;
37320 PyObject *__pyx_r = NULL;
37321 __Pyx_RefNannyDeclarations
37322 PyObject *__pyx_t_1 = NULL;
37323 int __pyx_t_2;
37324 PyObject *__pyx_t_3 = NULL;
37325 PyObject *__pyx_t_4 = NULL;
37326 unsigned int __pyx_t_5;
37327 int __pyx_lineno = 0;
37328 const char *__pyx_filename = NULL;
37329 int __pyx_clineno = 0;
37330 __Pyx_RefNannySetupContext("__pyx_unpickle_asVCFRecord", 1);
37331
37332 /* "(tree fragment)":4
37333 * cdef object __pyx_PickleError
37334 * cdef object __pyx_result
37335 * if __pyx_checksum not in (0xe48d6d5, 0xcc3d7cd, 0x1c28f48): # <<<<<<<<<<<<<<
37336 * from pickle import PickleError as __pyx_PickleError
37337 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe48d6d5, 0xcc3d7cd, 0x1c28f48) = (encoding, vcffile))" % __pyx_checksum
37338 */
37339 __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error)
37340 __Pyx_GOTREF(__pyx_t_1);
37341 __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__32, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error)
37342 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
37343 if (__pyx_t_2) {
37344
37345 /* "(tree fragment)":5
37346 * cdef object __pyx_result
37347 * if __pyx_checksum not in (0xe48d6d5, 0xcc3d7cd, 0x1c28f48):
37348 * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<<
37349 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe48d6d5, 0xcc3d7cd, 0x1c28f48) = (encoding, vcffile))" % __pyx_checksum
37350 * __pyx_result = asVCFRecord.__new__(__pyx_type)
37351 */
37352 __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
37353 __Pyx_GOTREF(__pyx_t_1);
37354 __Pyx_INCREF(__pyx_n_s_PickleError);
37355 __Pyx_GIVEREF(__pyx_n_s_PickleError);
37356 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error);
37357 __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error)
37358 __Pyx_GOTREF(__pyx_t_3);
37359 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
37360 __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
37361 __Pyx_GOTREF(__pyx_t_1);
37362 __Pyx_INCREF(__pyx_t_1);
37363 __pyx_v___pyx_PickleError = __pyx_t_1;
37364 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
37365 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
37366
37367 /* "(tree fragment)":6
37368 * if __pyx_checksum not in (0xe48d6d5, 0xcc3d7cd, 0x1c28f48):
37369 * from pickle import PickleError as __pyx_PickleError
37370 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe48d6d5, 0xcc3d7cd, 0x1c28f48) = (encoding, vcffile))" % __pyx_checksum # <<<<<<<<<<<<<<
37371 * __pyx_result = asVCFRecord.__new__(__pyx_type)
37372 * if __pyx_state is not None:
37373 */
37374 __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error)
37375 __Pyx_GOTREF(__pyx_t_3);
37376 __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
37377 __Pyx_GOTREF(__pyx_t_1);
37378 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
37379 __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0);
37380 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
37381 __PYX_ERR(1, 6, __pyx_L1_error)
37382
37383 /* "(tree fragment)":4
37384 * cdef object __pyx_PickleError
37385 * cdef object __pyx_result
37386 * if __pyx_checksum not in (0xe48d6d5, 0xcc3d7cd, 0x1c28f48): # <<<<<<<<<<<<<<
37387 * from pickle import PickleError as __pyx_PickleError
37388 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe48d6d5, 0xcc3d7cd, 0x1c28f48) = (encoding, vcffile))" % __pyx_checksum
37389 */
37390 }
37391
37392 /* "(tree fragment)":7
37393 * from pickle import PickleError as __pyx_PickleError
37394 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe48d6d5, 0xcc3d7cd, 0x1c28f48) = (encoding, vcffile))" % __pyx_checksum
37395 * __pyx_result = asVCFRecord.__new__(__pyx_type) # <<<<<<<<<<<<<<
37396 * if __pyx_state is not None:
37397 * __pyx_unpickle_asVCFRecord__set_state(<asVCFRecord> __pyx_result, __pyx_state)
37398 */
37399 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_7libcvcf_asVCFRecord), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error)
37400 __Pyx_GOTREF(__pyx_t_3);
37401 __pyx_t_4 = NULL;
37402 __pyx_t_5 = 0;
37403 #if CYTHON_UNPACK_METHODS
37404 if (likely(PyMethod_Check(__pyx_t_3))) {
37405 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
37406 if (likely(__pyx_t_4)) {
37407 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
37408 __Pyx_INCREF(__pyx_t_4);
37409 __Pyx_INCREF(function);
37410 __Pyx_DECREF_SET(__pyx_t_3, function);
37411 __pyx_t_5 = 1;
37412 }
37413 }
37414 #endif
37415 {
37416 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type};
37417 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
37418 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
37419 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error)
37420 __Pyx_GOTREF(__pyx_t_1);
37421 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
37422 }
37423 __pyx_v___pyx_result = __pyx_t_1;
37424 __pyx_t_1 = 0;
37425
37426 /* "(tree fragment)":8
37427 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe48d6d5, 0xcc3d7cd, 0x1c28f48) = (encoding, vcffile))" % __pyx_checksum
37428 * __pyx_result = asVCFRecord.__new__(__pyx_type)
37429 * if __pyx_state is not None: # <<<<<<<<<<<<<<
37430 * __pyx_unpickle_asVCFRecord__set_state(<asVCFRecord> __pyx_result, __pyx_state)
37431 * return __pyx_result
37432 */
37433 __pyx_t_2 = (__pyx_v___pyx_state != Py_None);
37434 if (__pyx_t_2) {
37435
37436 /* "(tree fragment)":9
37437 * __pyx_result = asVCFRecord.__new__(__pyx_type)
37438 * if __pyx_state is not None:
37439 * __pyx_unpickle_asVCFRecord__set_state(<asVCFRecord> __pyx_result, __pyx_state) # <<<<<<<<<<<<<<
37440 * return __pyx_result
37441 * cdef __pyx_unpickle_asVCFRecord__set_state(asVCFRecord __pyx_result, tuple __pyx_state):
37442 */
37443 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error)
37444 __pyx_t_1 = __pyx_f_5pysam_7libcvcf___pyx_unpickle_asVCFRecord__set_state(((struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error)
37445 __Pyx_GOTREF(__pyx_t_1);
37446 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
37447
37448 /* "(tree fragment)":8
37449 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe48d6d5, 0xcc3d7cd, 0x1c28f48) = (encoding, vcffile))" % __pyx_checksum
37450 * __pyx_result = asVCFRecord.__new__(__pyx_type)
37451 * if __pyx_state is not None: # <<<<<<<<<<<<<<
37452 * __pyx_unpickle_asVCFRecord__set_state(<asVCFRecord> __pyx_result, __pyx_state)
37453 * return __pyx_result
37454 */
37455 }
37456
37457 /* "(tree fragment)":10
37458 * if __pyx_state is not None:
37459 * __pyx_unpickle_asVCFRecord__set_state(<asVCFRecord> __pyx_result, __pyx_state)
37460 * return __pyx_result # <<<<<<<<<<<<<<
37461 * cdef __pyx_unpickle_asVCFRecord__set_state(asVCFRecord __pyx_result, tuple __pyx_state):
37462 * __pyx_result.encoding = __pyx_state[0]; __pyx_result.vcffile = __pyx_state[1]
37463 */
37464 __Pyx_XDECREF(__pyx_r);
37465 __Pyx_INCREF(__pyx_v___pyx_result);
37466 __pyx_r = __pyx_v___pyx_result;
37467 goto __pyx_L0;
37468
37469 /* "(tree fragment)":1
37470 * def __pyx_unpickle_asVCFRecord(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
37471 * cdef object __pyx_PickleError
37472 * cdef object __pyx_result
37473 */
37474
37475 /* function exit code */
37476 __pyx_L1_error:;
37477 __Pyx_XDECREF(__pyx_t_1);
37478 __Pyx_XDECREF(__pyx_t_3);
37479 __Pyx_XDECREF(__pyx_t_4);
37480 __Pyx_AddTraceback("pysam.libcvcf.__pyx_unpickle_asVCFRecord", __pyx_clineno, __pyx_lineno, __pyx_filename);
37481 __pyx_r = NULL;
37482 __pyx_L0:;
37483 __Pyx_XDECREF(__pyx_v___pyx_PickleError);
37484 __Pyx_XDECREF(__pyx_v___pyx_result);
37485 __Pyx_XGIVEREF(__pyx_r);
37486 __Pyx_RefNannyFinishContext();
37487 return __pyx_r;
37488 }
37489
37490 /* "(tree fragment)":11
37491 * __pyx_unpickle_asVCFRecord__set_state(<asVCFRecord> __pyx_result, __pyx_state)
37492 * return __pyx_result
37493 * cdef __pyx_unpickle_asVCFRecord__set_state(asVCFRecord __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
37494 * __pyx_result.encoding = __pyx_state[0]; __pyx_result.vcffile = __pyx_state[1]
37495 * if len(__pyx_state) > 2 and hasattr(__pyx_result, '__dict__'):
37496 */
37497
37498 static PyObject *__pyx_f_5pysam_7libcvcf___pyx_unpickle_asVCFRecord__set_state(struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) {
37499 PyObject *__pyx_r = NULL;
37500 __Pyx_RefNannyDeclarations
37501 PyObject *__pyx_t_1 = NULL;
37502 int __pyx_t_2;
37503 Py_ssize_t __pyx_t_3;
37504 int __pyx_t_4;
37505 PyObject *__pyx_t_5 = NULL;
37506 PyObject *__pyx_t_6 = NULL;
37507 PyObject *__pyx_t_7 = NULL;
37508 unsigned int __pyx_t_8;
37509 int __pyx_lineno = 0;
37510 const char *__pyx_filename = NULL;
37511 int __pyx_clineno = 0;
37512 __Pyx_RefNannySetupContext("__pyx_unpickle_asVCFRecord__set_state", 1);
37513
37514 /* "(tree fragment)":12
37515 * return __pyx_result
37516 * cdef __pyx_unpickle_asVCFRecord__set_state(asVCFRecord __pyx_result, tuple __pyx_state):
37517 * __pyx_result.encoding = __pyx_state[0]; __pyx_result.vcffile = __pyx_state[1] # <<<<<<<<<<<<<<
37518 * if len(__pyx_state) > 2 and hasattr(__pyx_result, '__dict__'):
37519 * __pyx_result.__dict__.update(__pyx_state[2])
37520 */
37521 if (unlikely(__pyx_v___pyx_state == Py_None)) {
37522 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
37523 __PYX_ERR(1, 12, __pyx_L1_error)
37524 }
37525 __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error)
37526 __Pyx_GOTREF(__pyx_t_1);
37527 __Pyx_GIVEREF(__pyx_t_1);
37528 __Pyx_GOTREF(__pyx_v___pyx_result->__pyx_base.encoding);
37529 __Pyx_DECREF(__pyx_v___pyx_result->__pyx_base.encoding);
37530 __pyx_v___pyx_result->__pyx_base.encoding = __pyx_t_1;
37531 __pyx_t_1 = 0;
37532 if (unlikely(__pyx_v___pyx_state == Py_None)) {
37533 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
37534 __PYX_ERR(1, 12, __pyx_L1_error)
37535 }
37536 __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error)
37537 __Pyx_GOTREF(__pyx_t_1);
37538 __Pyx_GIVEREF(__pyx_t_1);
37539 __Pyx_GOTREF(__pyx_v___pyx_result->vcffile);
37540 __Pyx_DECREF(__pyx_v___pyx_result->vcffile);
37541 __pyx_v___pyx_result->vcffile = __pyx_t_1;
37542 __pyx_t_1 = 0;
37543
37544 /* "(tree fragment)":13
37545 * cdef __pyx_unpickle_asVCFRecord__set_state(asVCFRecord __pyx_result, tuple __pyx_state):
37546 * __pyx_result.encoding = __pyx_state[0]; __pyx_result.vcffile = __pyx_state[1]
37547 * if len(__pyx_state) > 2 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
37548 * __pyx_result.__dict__.update(__pyx_state[2])
37549 */
37550 if (unlikely(__pyx_v___pyx_state == Py_None)) {
37551 PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
37552 __PYX_ERR(1, 13, __pyx_L1_error)
37553 }
37554 __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
37555 __pyx_t_4 = (__pyx_t_3 > 2);
37556 if (__pyx_t_4) {
37557 } else {
37558 __pyx_t_2 = __pyx_t_4;
37559 goto __pyx_L4_bool_binop_done;
37560 }
37561 __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
37562 __pyx_t_2 = __pyx_t_4;
37563 __pyx_L4_bool_binop_done:;
37564 if (__pyx_t_2) {
37565
37566 /* "(tree fragment)":14
37567 * __pyx_result.encoding = __pyx_state[0]; __pyx_result.vcffile = __pyx_state[1]
37568 * if len(__pyx_state) > 2 and hasattr(__pyx_result, '__dict__'):
37569 * __pyx_result.__dict__.update(__pyx_state[2]) # <<<<<<<<<<<<<<
37570 */
37571 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
37572 __Pyx_GOTREF(__pyx_t_5);
37573 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error)
37574 __Pyx_GOTREF(__pyx_t_6);
37575 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
37576 if (unlikely(__pyx_v___pyx_state == Py_None)) {
37577 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
37578 __PYX_ERR(1, 14, __pyx_L1_error)
37579 }
37580 __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 2, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
37581 __Pyx_GOTREF(__pyx_t_5);
37582 __pyx_t_7 = NULL;
37583 __pyx_t_8 = 0;
37584 #if CYTHON_UNPACK_METHODS
37585 if (likely(PyMethod_Check(__pyx_t_6))) {
37586 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6);
37587 if (likely(__pyx_t_7)) {
37588 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
37589 __Pyx_INCREF(__pyx_t_7);
37590 __Pyx_INCREF(function);
37591 __Pyx_DECREF_SET(__pyx_t_6, function);
37592 __pyx_t_8 = 1;
37593 }
37594 }
37595 #endif
37596 {
37597 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5};
37598 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
37599 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
37600 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
37601 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error)
37602 __Pyx_GOTREF(__pyx_t_1);
37603 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
37604 }
37605 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
37606
37607 /* "(tree fragment)":13
37608 * cdef __pyx_unpickle_asVCFRecord__set_state(asVCFRecord __pyx_result, tuple __pyx_state):
37609 * __pyx_result.encoding = __pyx_state[0]; __pyx_result.vcffile = __pyx_state[1]
37610 * if len(__pyx_state) > 2 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
37611 * __pyx_result.__dict__.update(__pyx_state[2])
37612 */
37613 }
37614
37615 /* "(tree fragment)":11
37616 * __pyx_unpickle_asVCFRecord__set_state(<asVCFRecord> __pyx_result, __pyx_state)
37617 * return __pyx_result
37618 * cdef __pyx_unpickle_asVCFRecord__set_state(asVCFRecord __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
37619 * __pyx_result.encoding = __pyx_state[0]; __pyx_result.vcffile = __pyx_state[1]
37620 * if len(__pyx_state) > 2 and hasattr(__pyx_result, '__dict__'):
37621 */
37622
37623 /* function exit code */
37624 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
37625 goto __pyx_L0;
37626 __pyx_L1_error:;
37627 __Pyx_XDECREF(__pyx_t_1);
37628 __Pyx_XDECREF(__pyx_t_5);
37629 __Pyx_XDECREF(__pyx_t_6);
37630 __Pyx_XDECREF(__pyx_t_7);
37631 __Pyx_AddTraceback("pysam.libcvcf.__pyx_unpickle_asVCFRecord__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename);
37632 __pyx_r = 0;
37633 __pyx_L0:;
37634 __Pyx_XGIVEREF(__pyx_r);
37635 __Pyx_RefNannyFinishContext();
37636 return __pyx_r;
37637 }
37638 static struct __pyx_vtabstruct_5pysam_7libcvcf_VCFRecord __pyx_vtable_5pysam_7libcvcf_VCFRecord;
37639
37640 static PyObject *__pyx_tp_new_5pysam_7libcvcf_VCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) {
37641 struct __pyx_obj_5pysam_7libcvcf_VCFRecord *p;
37642 PyObject *o = __Pyx_PyType_GetSlot(__pyx_ptype_5pysam_16libctabixproxies_TupleProxy, tp_new, newfunc)(t, a, k);
37643 if (unlikely(!o)) return 0;
37644 p = ((struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)o);
37645 p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy*)__pyx_vtabptr_5pysam_7libcvcf_VCFRecord;
37646 p->vcf = Py_None; Py_INCREF(Py_None);
37647 if (unlikely(__pyx_pw_5pysam_7libcvcf_9VCFRecord_3__cinit__(o, a, k) < 0)) goto bad;
37648 return o;
37649 bad:
37650 Py_DECREF(o); o = 0;
37651 return NULL;
37652 }
37653
37654 static void __pyx_tp_dealloc_5pysam_7libcvcf_VCFRecord(PyObject *o) {
37655 struct __pyx_obj_5pysam_7libcvcf_VCFRecord *p = (struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)o;
37656 #if CYTHON_USE_TP_FINALIZE
37657 if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) {
37658 if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_7libcvcf_VCFRecord) {
37659 if (PyObject_CallFinalizerFromDealloc(o)) return;
37660 }
37661 }
37662 #endif
37663 PyObject_GC_UnTrack(o);
37664 Py_CLEAR(p->vcf);
37665 #if PY_MAJOR_VERSION < 3
37666 if (!(__pyx_ptype_5pysam_16libctabixproxies_TupleProxy) || PyType_IS_GC(__pyx_ptype_5pysam_16libctabixproxies_TupleProxy)) PyObject_GC_Track(o);
37667 #else
37668 if (PyType_IS_GC(__pyx_ptype_5pysam_16libctabixproxies_TupleProxy)) PyObject_GC_Track(o);
37669 #endif
37670 if (likely(__pyx_ptype_5pysam_16libctabixproxies_TupleProxy)) __Pyx_PyType_GetSlot(__pyx_ptype_5pysam_16libctabixproxies_TupleProxy, tp_dealloc, destructor)(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_7libcvcf_VCFRecord);
37671 }
37672
37673 static int __pyx_tp_traverse_5pysam_7libcvcf_VCFRecord(PyObject *o, visitproc v, void *a) {
37674 int e;
37675 struct __pyx_obj_5pysam_7libcvcf_VCFRecord *p = (struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)o;
37676 e = ((likely(__pyx_ptype_5pysam_16libctabixproxies_TupleProxy)) ? ((__pyx_ptype_5pysam_16libctabixproxies_TupleProxy->tp_traverse) ? __pyx_ptype_5pysam_16libctabixproxies_TupleProxy->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_7libcvcf_VCFRecord)); if (e) return e;
37677 if (p->vcf) {
37678 e = (*v)(p->vcf, a); if (e) return e;
37679 }
37680 return 0;
37681 }
37682
37683 static int __pyx_tp_clear_5pysam_7libcvcf_VCFRecord(PyObject *o) {
37684 PyObject* tmp;
37685 struct __pyx_obj_5pysam_7libcvcf_VCFRecord *p = (struct __pyx_obj_5pysam_7libcvcf_VCFRecord *)o;
37686 if (likely(__pyx_ptype_5pysam_16libctabixproxies_TupleProxy)) { if (__pyx_ptype_5pysam_16libctabixproxies_TupleProxy->tp_clear) __pyx_ptype_5pysam_16libctabixproxies_TupleProxy->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_7libcvcf_VCFRecord);
37687 tmp = ((PyObject*)p->vcf);
37688 p->vcf = Py_None; Py_INCREF(Py_None);
37689 Py_XDECREF(tmp);
37690 return 0;
37691 }
37692 static PyObject *__pyx_sq_item_5pysam_7libcvcf_VCFRecord(PyObject *o, Py_ssize_t i) {
37693 PyObject *r;
37694 PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
37695 r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
37696 Py_DECREF(x);
37697 return r;
37698 }
37699
37700 static PyObject *__pyx_getprop_5pysam_7libcvcf_9VCFRecord_contig(PyObject *o, CYTHON_UNUSED void *x) {
37701 return __pyx_pw_5pysam_7libcvcf_9VCFRecord_6contig_1__get__(o);
37702 }
37703
37704 static PyObject *__pyx_getprop_5pysam_7libcvcf_9VCFRecord_pos(PyObject *o, CYTHON_UNUSED void *x) {
37705 return __pyx_pw_5pysam_7libcvcf_9VCFRecord_3pos_1__get__(o);
37706 }
37707
37708 static PyObject *__pyx_getprop_5pysam_7libcvcf_9VCFRecord_id(PyObject *o, CYTHON_UNUSED void *x) {
37709 return __pyx_pw_5pysam_7libcvcf_9VCFRecord_2id_1__get__(o);
37710 }
37711
37712 static PyObject *__pyx_getprop_5pysam_7libcvcf_9VCFRecord_ref(PyObject *o, CYTHON_UNUSED void *x) {
37713 return __pyx_pw_5pysam_7libcvcf_9VCFRecord_3ref_1__get__(o);
37714 }
37715
37716 static PyObject *__pyx_getprop_5pysam_7libcvcf_9VCFRecord_alt(PyObject *o, CYTHON_UNUSED void *x) {
37717 return __pyx_pw_5pysam_7libcvcf_9VCFRecord_3alt_1__get__(o);
37718 }
37719
37720 static PyObject *__pyx_getprop_5pysam_7libcvcf_9VCFRecord_qual(PyObject *o, CYTHON_UNUSED void *x) {
37721 return __pyx_pw_5pysam_7libcvcf_9VCFRecord_4qual_1__get__(o);
37722 }
37723
37724 static PyObject *__pyx_getprop_5pysam_7libcvcf_9VCFRecord_filter(PyObject *o, CYTHON_UNUSED void *x) {
37725 return __pyx_pw_5pysam_7libcvcf_9VCFRecord_6filter_1__get__(o);
37726 }
37727
37728 static PyObject *__pyx_getprop_5pysam_7libcvcf_9VCFRecord_info(PyObject *o, CYTHON_UNUSED void *x) {
37729 return __pyx_pw_5pysam_7libcvcf_9VCFRecord_4info_1__get__(o);
37730 }
37731
37732 static PyObject *__pyx_getprop_5pysam_7libcvcf_9VCFRecord_format(PyObject *o, CYTHON_UNUSED void *x) {
37733 return __pyx_pw_5pysam_7libcvcf_9VCFRecord_6format_1__get__(o);
37734 }
37735
37736 static PyObject *__pyx_getprop_5pysam_7libcvcf_9VCFRecord_samples(PyObject *o, CYTHON_UNUSED void *x) {
37737 return __pyx_pw_5pysam_7libcvcf_9VCFRecord_7samples_1__get__(o);
37738 }
37739
37740 static PyMethodDef __pyx_methods_5pysam_7libcvcf_VCFRecord[] = {
37741 {"error", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_9VCFRecord_5error, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_9VCFRecord_4error},
37742 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_9VCFRecord_11__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_9VCFRecord_10__reduce_cython__},
37743 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_9VCFRecord_13__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_9VCFRecord_12__setstate_cython__},
37744 {0, 0, 0, 0}
37745 };
37746
37747 static struct PyGetSetDef __pyx_getsets_5pysam_7libcvcf_VCFRecord[] = {
37748 {(char *)"contig", __pyx_getprop_5pysam_7libcvcf_9VCFRecord_contig, 0, (char *)0, 0},
37749 {(char *)"pos", __pyx_getprop_5pysam_7libcvcf_9VCFRecord_pos, 0, (char *)0, 0},
37750 {(char *)"id", __pyx_getprop_5pysam_7libcvcf_9VCFRecord_id, 0, (char *)0, 0},
37751 {(char *)"ref", __pyx_getprop_5pysam_7libcvcf_9VCFRecord_ref, 0, (char *)0, 0},
37752 {(char *)"alt", __pyx_getprop_5pysam_7libcvcf_9VCFRecord_alt, 0, (char *)0, 0},
37753 {(char *)"qual", __pyx_getprop_5pysam_7libcvcf_9VCFRecord_qual, 0, (char *)0, 0},
37754 {(char *)"filter", __pyx_getprop_5pysam_7libcvcf_9VCFRecord_filter, 0, (char *)0, 0},
37755 {(char *)"info", __pyx_getprop_5pysam_7libcvcf_9VCFRecord_info, 0, (char *)0, 0},
37756 {(char *)"format", __pyx_getprop_5pysam_7libcvcf_9VCFRecord_format, 0, (char *)0, 0},
37757 {(char *)"samples", __pyx_getprop_5pysam_7libcvcf_9VCFRecord_samples, 0, (char *)0, 0},
37758 {0, 0, 0, 0, 0}
37759 };
37760 #if CYTHON_USE_TYPE_SPECS
37761 static PyType_Slot __pyx_type_5pysam_7libcvcf_VCFRecord_slots[] = {
37762 {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_7libcvcf_VCFRecord},
37763 {Py_sq_length, (void *)__pyx_pw_5pysam_7libcvcf_9VCFRecord_7__len__},
37764 {Py_sq_item, (void *)__pyx_sq_item_5pysam_7libcvcf_VCFRecord},
37765 {Py_mp_length, (void *)__pyx_pw_5pysam_7libcvcf_9VCFRecord_7__len__},
37766 {Py_mp_subscript, (void *)__pyx_pw_5pysam_7libcvcf_9VCFRecord_9__getitem__},
37767 {Py_tp_doc, (void *)PyDoc_STR("VCFRecord(vcf)\nvcf record.\n\n initialized from data and vcf meta\n ")},
37768 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_7libcvcf_VCFRecord},
37769 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_7libcvcf_VCFRecord},
37770 {Py_tp_methods, (void *)__pyx_methods_5pysam_7libcvcf_VCFRecord},
37771 {Py_tp_getset, (void *)__pyx_getsets_5pysam_7libcvcf_VCFRecord},
37772 {Py_tp_init, (void *)__pyx_pw_5pysam_7libcvcf_9VCFRecord_1__init__},
37773 {Py_tp_new, (void *)__pyx_tp_new_5pysam_7libcvcf_VCFRecord},
37774 {0, 0},
37775 };
37776 static PyType_Spec __pyx_type_5pysam_7libcvcf_VCFRecord_spec = {
37777 "pysam.libcvcf.VCFRecord",
37778 sizeof(struct __pyx_obj_5pysam_7libcvcf_VCFRecord),
37779 0,
37780 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE,
37781 __pyx_type_5pysam_7libcvcf_VCFRecord_slots,
37782 };
37783 #else
37784
37785 static PySequenceMethods __pyx_tp_as_sequence_VCFRecord = {
37786 __pyx_pw_5pysam_7libcvcf_9VCFRecord_7__len__, /*sq_length*/
37787 0, /*sq_concat*/
37788 0, /*sq_repeat*/
37789 __pyx_sq_item_5pysam_7libcvcf_VCFRecord, /*sq_item*/
37790 0, /*sq_slice*/
37791 0, /*sq_ass_item*/
37792 0, /*sq_ass_slice*/
37793 0, /*sq_contains*/
37794 0, /*sq_inplace_concat*/
37795 0, /*sq_inplace_repeat*/
37796 };
37797
37798 static PyMappingMethods __pyx_tp_as_mapping_VCFRecord = {
37799 __pyx_pw_5pysam_7libcvcf_9VCFRecord_7__len__, /*mp_length*/
37800 __pyx_pw_5pysam_7libcvcf_9VCFRecord_9__getitem__, /*mp_subscript*/
37801 0, /*mp_ass_subscript*/
37802 };
37803
37804 static PyTypeObject __pyx_type_5pysam_7libcvcf_VCFRecord = {
37805 PyVarObject_HEAD_INIT(0, 0)
37806 "pysam.libcvcf.""VCFRecord", /*tp_name*/
37807 sizeof(struct __pyx_obj_5pysam_7libcvcf_VCFRecord), /*tp_basicsize*/
37808 0, /*tp_itemsize*/
37809 __pyx_tp_dealloc_5pysam_7libcvcf_VCFRecord, /*tp_dealloc*/
37810 #if PY_VERSION_HEX < 0x030800b4
37811 0, /*tp_print*/
37812 #endif
37813 #if PY_VERSION_HEX >= 0x030800b4
37814 0, /*tp_vectorcall_offset*/
37815 #endif
37816 0, /*tp_getattr*/
37817 0, /*tp_setattr*/
37818 #if PY_MAJOR_VERSION < 3
37819 0, /*tp_compare*/
37820 #endif
37821 #if PY_MAJOR_VERSION >= 3
37822 0, /*tp_as_async*/
37823 #endif
37824 0, /*tp_repr*/
37825 0, /*tp_as_number*/
37826 &__pyx_tp_as_sequence_VCFRecord, /*tp_as_sequence*/
37827 &__pyx_tp_as_mapping_VCFRecord, /*tp_as_mapping*/
37828 0, /*tp_hash*/
37829 0, /*tp_call*/
37830 0, /*tp_str*/
37831 0, /*tp_getattro*/
37832 0, /*tp_setattro*/
37833 0, /*tp_as_buffer*/
37834 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE, /*tp_flags*/
37835 PyDoc_STR("VCFRecord(vcf)\nvcf record.\n\n initialized from data and vcf meta\n "), /*tp_doc*/
37836 __pyx_tp_traverse_5pysam_7libcvcf_VCFRecord, /*tp_traverse*/
37837 __pyx_tp_clear_5pysam_7libcvcf_VCFRecord, /*tp_clear*/
37838 0, /*tp_richcompare*/
37839 0, /*tp_weaklistoffset*/
37840 0, /*tp_iter*/
37841 0, /*tp_iternext*/
37842 __pyx_methods_5pysam_7libcvcf_VCFRecord, /*tp_methods*/
37843 0, /*tp_members*/
37844 __pyx_getsets_5pysam_7libcvcf_VCFRecord, /*tp_getset*/
37845 0, /*tp_base*/
37846 0, /*tp_dict*/
37847 0, /*tp_descr_get*/
37848 0, /*tp_descr_set*/
37849 #if !CYTHON_USE_TYPE_SPECS
37850 0, /*tp_dictoffset*/
37851 #endif
37852 __pyx_pw_5pysam_7libcvcf_9VCFRecord_1__init__, /*tp_init*/
37853 0, /*tp_alloc*/
37854 __pyx_tp_new_5pysam_7libcvcf_VCFRecord, /*tp_new*/
37855 0, /*tp_free*/
37856 0, /*tp_is_gc*/
37857 0, /*tp_bases*/
37858 0, /*tp_mro*/
37859 0, /*tp_cache*/
37860 0, /*tp_subclasses*/
37861 0, /*tp_weaklist*/
37862 0, /*tp_del*/
37863 0, /*tp_version_tag*/
37864 #if PY_VERSION_HEX >= 0x030400a1
37865 #if CYTHON_USE_TP_FINALIZE
37866 0, /*tp_finalize*/
37867 #else
37868 NULL, /*tp_finalize*/
37869 #endif
37870 #endif
37871 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
37872 0, /*tp_vectorcall*/
37873 #endif
37874 #if __PYX_NEED_TP_PRINT_SLOT == 1
37875 0, /*tp_print*/
37876 #endif
37877 #if PY_VERSION_HEX >= 0x030C0000
37878 0, /*tp_watched*/
37879 #endif
37880 #if PY_VERSION_HEX >= 0x030d00A4
37881 0, /*tp_versions_used*/
37882 #endif
37883 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
37884 0, /*tp_pypy_flags*/
37885 #endif
37886 };
37887 #endif
37888 static struct __pyx_vtabstruct_5pysam_7libcvcf_asVCFRecord __pyx_vtable_5pysam_7libcvcf_asVCFRecord;
37889
37890 static PyObject *__pyx_tp_new_5pysam_7libcvcf_asVCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) {
37891 struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *p;
37892 PyObject *o = __Pyx_PyType_GetSlot(__pyx_ptype_5pysam_9libctabix_Parser, tp_new, newfunc)(t, a, k);
37893 if (unlikely(!o)) return 0;
37894 p = ((struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *)o);
37895 p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_Parser*)__pyx_vtabptr_5pysam_7libcvcf_asVCFRecord;
37896 p->vcffile = Py_None; Py_INCREF(Py_None);
37897 return o;
37898 }
37899
37900 static void __pyx_tp_dealloc_5pysam_7libcvcf_asVCFRecord(PyObject *o) {
37901 struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *)o;
37902 #if CYTHON_USE_TP_FINALIZE
37903 if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) {
37904 if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_7libcvcf_asVCFRecord) {
37905 if (PyObject_CallFinalizerFromDealloc(o)) return;
37906 }
37907 }
37908 #endif
37909 PyObject_GC_UnTrack(o);
37910 Py_CLEAR(p->vcffile);
37911 #if PY_MAJOR_VERSION < 3
37912 if (!(__pyx_ptype_5pysam_9libctabix_Parser) || PyType_IS_GC(__pyx_ptype_5pysam_9libctabix_Parser)) PyObject_GC_Track(o);
37913 #else
37914 if (PyType_IS_GC(__pyx_ptype_5pysam_9libctabix_Parser)) PyObject_GC_Track(o);
37915 #endif
37916 if (likely(__pyx_ptype_5pysam_9libctabix_Parser)) __Pyx_PyType_GetSlot(__pyx_ptype_5pysam_9libctabix_Parser, tp_dealloc, destructor)(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_7libcvcf_asVCFRecord);
37917 }
37918
37919 static int __pyx_tp_traverse_5pysam_7libcvcf_asVCFRecord(PyObject *o, visitproc v, void *a) {
37920 int e;
37921 struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *)o;
37922 e = ((likely(__pyx_ptype_5pysam_9libctabix_Parser)) ? ((__pyx_ptype_5pysam_9libctabix_Parser->tp_traverse) ? __pyx_ptype_5pysam_9libctabix_Parser->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_7libcvcf_asVCFRecord)); if (e) return e;
37923 if (p->vcffile) {
37924 e = (*v)(p->vcffile, a); if (e) return e;
37925 }
37926 return 0;
37927 }
37928
37929 static int __pyx_tp_clear_5pysam_7libcvcf_asVCFRecord(PyObject *o) {
37930 PyObject* tmp;
37931 struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_7libcvcf_asVCFRecord *)o;
37932 if (likely(__pyx_ptype_5pysam_9libctabix_Parser)) { if (__pyx_ptype_5pysam_9libctabix_Parser->tp_clear) __pyx_ptype_5pysam_9libctabix_Parser->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_7libcvcf_asVCFRecord);
37933 tmp = ((PyObject*)p->vcffile);
37934 p->vcffile = Py_None; Py_INCREF(Py_None);
37935 Py_XDECREF(tmp);
37936 return 0;
37937 }
37938
37939 static PyMethodDef __pyx_methods_5pysam_7libcvcf_asVCFRecord[] = {
37940 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_11asVCFRecord_3__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_11asVCFRecord_2__reduce_cython__},
37941 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_7libcvcf_11asVCFRecord_5__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_7libcvcf_11asVCFRecord_4__setstate_cython__},
37942 {0, 0, 0, 0}
37943 };
37944 #if CYTHON_USE_TYPE_SPECS
37945 static PyType_Slot __pyx_type_5pysam_7libcvcf_asVCFRecord_slots[] = {
37946 {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_7libcvcf_asVCFRecord},
37947 {Py_tp_doc, (void *)PyDoc_STR("asVCFRecord(vcffile)\nconverts a :term:`tabix row` into a VCF record.")},
37948 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_7libcvcf_asVCFRecord},
37949 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_7libcvcf_asVCFRecord},
37950 {Py_tp_methods, (void *)__pyx_methods_5pysam_7libcvcf_asVCFRecord},
37951 {Py_tp_init, (void *)__pyx_pw_5pysam_7libcvcf_11asVCFRecord_1__init__},
37952 {Py_tp_new, (void *)__pyx_tp_new_5pysam_7libcvcf_asVCFRecord},
37953 {0, 0},
37954 };
37955 static PyType_Spec __pyx_type_5pysam_7libcvcf_asVCFRecord_spec = {
37956 "pysam.libcvcf.asVCFRecord",
37957 sizeof(struct __pyx_obj_5pysam_7libcvcf_asVCFRecord),
37958 0,
37959 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE,
37960 __pyx_type_5pysam_7libcvcf_asVCFRecord_slots,
37961 };
37962 #else
37963
37964 static PyTypeObject __pyx_type_5pysam_7libcvcf_asVCFRecord = {
37965 PyVarObject_HEAD_INIT(0, 0)
37966 "pysam.libcvcf.""asVCFRecord", /*tp_name*/
37967 sizeof(struct __pyx_obj_5pysam_7libcvcf_asVCFRecord), /*tp_basicsize*/
37968 0, /*tp_itemsize*/
37969 __pyx_tp_dealloc_5pysam_7libcvcf_asVCFRecord, /*tp_dealloc*/
37970 #if PY_VERSION_HEX < 0x030800b4
37971 0, /*tp_print*/
37972 #endif
37973 #if PY_VERSION_HEX >= 0x030800b4
37974 0, /*tp_vectorcall_offset*/
37975 #endif
37976 0, /*tp_getattr*/
37977 0, /*tp_setattr*/
37978 #if PY_MAJOR_VERSION < 3
37979 0, /*tp_compare*/
37980 #endif
37981 #if PY_MAJOR_VERSION >= 3
37982 0, /*tp_as_async*/
37983 #endif
37984 0, /*tp_repr*/
37985 0, /*tp_as_number*/
37986 0, /*tp_as_sequence*/
37987 0, /*tp_as_mapping*/
37988 0, /*tp_hash*/
37989 0, /*tp_call*/
37990 0, /*tp_str*/
37991 0, /*tp_getattro*/
37992 0, /*tp_setattro*/
37993 0, /*tp_as_buffer*/
37994 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE, /*tp_flags*/
37995 PyDoc_STR("asVCFRecord(vcffile)\nconverts a :term:`tabix row` into a VCF record."), /*tp_doc*/
37996 __pyx_tp_traverse_5pysam_7libcvcf_asVCFRecord, /*tp_traverse*/
37997 __pyx_tp_clear_5pysam_7libcvcf_asVCFRecord, /*tp_clear*/
37998 0, /*tp_richcompare*/
37999 0, /*tp_weaklistoffset*/
38000 0, /*tp_iter*/
38001 0, /*tp_iternext*/
38002 __pyx_methods_5pysam_7libcvcf_asVCFRecord, /*tp_methods*/
38003 0, /*tp_members*/
38004 0, /*tp_getset*/
38005 0, /*tp_base*/
38006 0, /*tp_dict*/
38007 0, /*tp_descr_get*/
38008 0, /*tp_descr_set*/
38009 #if !CYTHON_USE_TYPE_SPECS
38010 0, /*tp_dictoffset*/
38011 #endif
38012 __pyx_pw_5pysam_7libcvcf_11asVCFRecord_1__init__, /*tp_init*/
38013 0, /*tp_alloc*/
38014 __pyx_tp_new_5pysam_7libcvcf_asVCFRecord, /*tp_new*/
38015 0, /*tp_free*/
38016 0, /*tp_is_gc*/
38017 0, /*tp_bases*/
38018 0, /*tp_mro*/
38019 0, /*tp_cache*/
38020 0, /*tp_subclasses*/
38021 0, /*tp_weaklist*/
38022 0, /*tp_del*/
38023 0, /*tp_version_tag*/
38024 #if PY_VERSION_HEX >= 0x030400a1
38025 #if CYTHON_USE_TP_FINALIZE
38026 0, /*tp_finalize*/
38027 #else
38028 NULL, /*tp_finalize*/
38029 #endif
38030 #endif
38031 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
38032 0, /*tp_vectorcall*/
38033 #endif
38034 #if __PYX_NEED_TP_PRINT_SLOT == 1
38035 0, /*tp_print*/
38036 #endif
38037 #if PY_VERSION_HEX >= 0x030C0000
38038 0, /*tp_watched*/
38039 #endif
38040 #if PY_VERSION_HEX >= 0x030d00A4
38041 0, /*tp_versions_used*/
38042 #endif
38043 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
38044 0, /*tp_pypy_flags*/
38045 #endif
38046 };
38047 #endif
38048
38049 #if CYTHON_USE_FREELISTS
38050 static struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse *__pyx_freelist_5pysam_7libcvcf___pyx_scope_struct___parse[8];
38051 static int __pyx_freecount_5pysam_7libcvcf___pyx_scope_struct___parse = 0;
38052 #endif
38053
38054 static PyObject *__pyx_tp_new_5pysam_7libcvcf___pyx_scope_struct___parse(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
38055 PyObject *o;
38056 #if CYTHON_COMPILING_IN_LIMITED_API
38057 allocfunc alloc_func = (allocfunc)PyType_GetSlot(t, Py_tp_alloc);
38058 o = alloc_func(t, 0);
38059 #else
38060 #if CYTHON_USE_FREELISTS
38061 if (likely((int)(__pyx_freecount_5pysam_7libcvcf___pyx_scope_struct___parse > 0) & (int)(t->tp_basicsize == sizeof(struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse)))) {
38062 o = (PyObject*)__pyx_freelist_5pysam_7libcvcf___pyx_scope_struct___parse[--__pyx_freecount_5pysam_7libcvcf___pyx_scope_struct___parse];
38063 memset(o, 0, sizeof(struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse));
38064 (void) PyObject_INIT(o, t);
38065 PyObject_GC_Track(o);
38066 } else
38067 #endif
38068 {
38069 o = (*t->tp_alloc)(t, 0);
38070 if (unlikely(!o)) return 0;
38071 }
38072 #endif
38073 return o;
38074 }
38075
38076 static void __pyx_tp_dealloc_5pysam_7libcvcf___pyx_scope_struct___parse(PyObject *o) {
38077 struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse *p = (struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse *)o;
38078 #if CYTHON_USE_TP_FINALIZE
38079 if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) {
38080 if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_7libcvcf___pyx_scope_struct___parse) {
38081 if (PyObject_CallFinalizerFromDealloc(o)) return;
38082 }
38083 }
38084 #endif
38085 PyObject_GC_UnTrack(o);
38086 Py_CLEAR(p->__pyx_v_d);
38087 Py_CLEAR(p->__pyx_v_line);
38088 Py_CLEAR(p->__pyx_v_self);
38089 Py_CLEAR(p->__pyx_v_stream);
38090 Py_CLEAR(p->__pyx_t_0);
38091 #if CYTHON_USE_FREELISTS
38092 if (((int)(__pyx_freecount_5pysam_7libcvcf___pyx_scope_struct___parse < 8) & (int)(Py_TYPE(o)->tp_basicsize == sizeof(struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse)))) {
38093 __pyx_freelist_5pysam_7libcvcf___pyx_scope_struct___parse[__pyx_freecount_5pysam_7libcvcf___pyx_scope_struct___parse++] = ((struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse *)o);
38094 } else
38095 #endif
38096 {
38097 #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY
38098 (*Py_TYPE(o)->tp_free)(o);
38099 #else
38100 {
38101 freefunc tp_free = (freefunc)PyType_GetSlot(Py_TYPE(o), Py_tp_free);
38102 if (tp_free) tp_free(o);
38103 }
38104 #endif
38105 }
38106 }
38107
38108 static int __pyx_tp_traverse_5pysam_7libcvcf___pyx_scope_struct___parse(PyObject *o, visitproc v, void *a) {
38109 int e;
38110 struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse *p = (struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse *)o;
38111 if (p->__pyx_v_d) {
38112 e = (*v)(p->__pyx_v_d, a); if (e) return e;
38113 }
38114 if (p->__pyx_v_line) {
38115 e = (*v)(p->__pyx_v_line, a); if (e) return e;
38116 }
38117 if (p->__pyx_v_self) {
38118 e = (*v)(p->__pyx_v_self, a); if (e) return e;
38119 }
38120 if (p->__pyx_v_stream) {
38121 e = (*v)(p->__pyx_v_stream, a); if (e) return e;
38122 }
38123 if (p->__pyx_t_0) {
38124 e = (*v)(p->__pyx_t_0, a); if (e) return e;
38125 }
38126 return 0;
38127 }
38128 #if CYTHON_USE_TYPE_SPECS
38129 static PyType_Slot __pyx_type_5pysam_7libcvcf___pyx_scope_struct___parse_slots[] = {
38130 {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_7libcvcf___pyx_scope_struct___parse},
38131 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_7libcvcf___pyx_scope_struct___parse},
38132 {Py_tp_new, (void *)__pyx_tp_new_5pysam_7libcvcf___pyx_scope_struct___parse},
38133 {0, 0},
38134 };
38135 static PyType_Spec __pyx_type_5pysam_7libcvcf___pyx_scope_struct___parse_spec = {
38136 "pysam.libcvcf.__pyx_scope_struct___parse",
38137 sizeof(struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse),
38138 0,
38139 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE,
38140 __pyx_type_5pysam_7libcvcf___pyx_scope_struct___parse_slots,
38141 };
38142 #else
38143
38144 static PyTypeObject __pyx_type_5pysam_7libcvcf___pyx_scope_struct___parse = {
38145 PyVarObject_HEAD_INIT(0, 0)
38146 "pysam.libcvcf.""__pyx_scope_struct___parse", /*tp_name*/
38147 sizeof(struct __pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse), /*tp_basicsize*/
38148 0, /*tp_itemsize*/
38149 __pyx_tp_dealloc_5pysam_7libcvcf___pyx_scope_struct___parse, /*tp_dealloc*/
38150 #if PY_VERSION_HEX < 0x030800b4
38151 0, /*tp_print*/
38152 #endif
38153 #if PY_VERSION_HEX >= 0x030800b4
38154 0, /*tp_vectorcall_offset*/
38155 #endif
38156 0, /*tp_getattr*/
38157 0, /*tp_setattr*/
38158 #if PY_MAJOR_VERSION < 3
38159 0, /*tp_compare*/
38160 #endif
38161 #if PY_MAJOR_VERSION >= 3
38162 0, /*tp_as_async*/
38163 #endif
38164 0, /*tp_repr*/
38165 0, /*tp_as_number*/
38166 0, /*tp_as_sequence*/
38167 0, /*tp_as_mapping*/
38168 0, /*tp_hash*/
38169 0, /*tp_call*/
38170 0, /*tp_str*/
38171 0, /*tp_getattro*/
38172 0, /*tp_setattro*/
38173 0, /*tp_as_buffer*/
38174 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE, /*tp_flags*/
38175 0, /*tp_doc*/
38176 __pyx_tp_traverse_5pysam_7libcvcf___pyx_scope_struct___parse, /*tp_traverse*/
38177 0, /*tp_clear*/
38178 0, /*tp_richcompare*/
38179 0, /*tp_weaklistoffset*/
38180 0, /*tp_iter*/
38181 0, /*tp_iternext*/
38182 0, /*tp_methods*/
38183 0, /*tp_members*/
38184 0, /*tp_getset*/
38185 0, /*tp_base*/
38186 0, /*tp_dict*/
38187 0, /*tp_descr_get*/
38188 0, /*tp_descr_set*/
38189 #if !CYTHON_USE_TYPE_SPECS
38190 0, /*tp_dictoffset*/
38191 #endif
38192 0, /*tp_init*/
38193 0, /*tp_alloc*/
38194 __pyx_tp_new_5pysam_7libcvcf___pyx_scope_struct___parse, /*tp_new*/
38195 0, /*tp_free*/
38196 0, /*tp_is_gc*/
38197 0, /*tp_bases*/
38198 0, /*tp_mro*/
38199 0, /*tp_cache*/
38200 0, /*tp_subclasses*/
38201 0, /*tp_weaklist*/
38202 0, /*tp_del*/
38203 0, /*tp_version_tag*/
38204 #if PY_VERSION_HEX >= 0x030400a1
38205 #if CYTHON_USE_TP_FINALIZE
38206 0, /*tp_finalize*/
38207 #else
38208 NULL, /*tp_finalize*/
38209 #endif
38210 #endif
38211 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
38212 0, /*tp_vectorcall*/
38213 #endif
38214 #if __PYX_NEED_TP_PRINT_SLOT == 1
38215 0, /*tp_print*/
38216 #endif
38217 #if PY_VERSION_HEX >= 0x030C0000
38218 0, /*tp_watched*/
38219 #endif
38220 #if PY_VERSION_HEX >= 0x030d00A4
38221 0, /*tp_versions_used*/
38222 #endif
38223 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
38224 0, /*tp_pypy_flags*/
38225 #endif
38226 };
38227 #endif
38228
38229 static PyMethodDef __pyx_methods[] = {
38230 {0, 0, 0, 0}
38231 };
38232 #ifndef CYTHON_SMALL_CODE
38233 #if defined(__clang__)
38234 #define CYTHON_SMALL_CODE
38235 #elif defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3))
38236 #define CYTHON_SMALL_CODE __attribute__((cold))
38237 #else
38238 #define CYTHON_SMALL_CODE
38239 #endif
38240 #endif
38241 /* #### Code section: pystring_table ### */
38242
38243 static int __Pyx_CreateStringTabAndInitStrings(void) {
38244 __Pyx_StringTabEntry __pyx_string_tab[] = {
38245 {&__pyx_kp_u_, __pyx_k_, sizeof(__pyx_k_), 0, 1, 0, 0},
38246 {&__pyx_kp_b_0, __pyx_k_0, sizeof(__pyx_k_0), 0, 0, 0, 0},
38247 {&__pyx_kp_u_0, __pyx_k_0, sizeof(__pyx_k_0), 0, 1, 0, 0},
38248 {&__pyx_n_u_A, __pyx_k_A, sizeof(__pyx_k_A), 0, 1, 0, 1},
38249 {&__pyx_n_u_ACGTN, __pyx_k_ACGTN, sizeof(__pyx_k_ACGTN), 0, 1, 0, 1},
38250 {&__pyx_kp_u_ACGTN_2, __pyx_k_ACGTN_2, sizeof(__pyx_k_ACGTN_2), 0, 1, 0, 0},
38251 {&__pyx_n_u_ALT, __pyx_k_ALT, sizeof(__pyx_k_ALT), 0, 1, 0, 1},
38252 {&__pyx_n_s_AssertionError, __pyx_k_AssertionError, sizeof(__pyx_k_AssertionError), 0, 0, 1, 1},
38253 {&__pyx_n_s_BADLY_FORMATTED_FORMAT_STRING, __pyx_k_BADLY_FORMATTED_FORMAT_STRING, sizeof(__pyx_k_BADLY_FORMATTED_FORMAT_STRING), 0, 0, 1, 1},
38254 {&__pyx_kp_u_BADLY_FORMATTED_FORMAT_STRING_Fo, __pyx_k_BADLY_FORMATTED_FORMAT_STRING_Fo, sizeof(__pyx_k_BADLY_FORMATTED_FORMAT_STRING_Fo), 0, 1, 0, 0},
38255 {&__pyx_n_s_BADLY_FORMATTED_HEADING, __pyx_k_BADLY_FORMATTED_HEADING, sizeof(__pyx_k_BADLY_FORMATTED_HEADING), 0, 0, 1, 1},
38256 {&__pyx_kp_u_BADLY_FORMATTED_HEADING_Did_not, __pyx_k_BADLY_FORMATTED_HEADING_Did_not, sizeof(__pyx_k_BADLY_FORMATTED_HEADING_Did_not), 0, 1, 0, 0},
38257 {&__pyx_kp_u_BAD_CHR_TAG_Error_calculating_ch, __pyx_k_BAD_CHR_TAG_Error_calculating_ch, sizeof(__pyx_k_BAD_CHR_TAG_Error_calculating_ch), 0, 1, 0, 0},
38258 {&__pyx_n_s_BAD_GENOTYPE, __pyx_k_BAD_GENOTYPE, sizeof(__pyx_k_BAD_GENOTYPE), 0, 0, 1, 1},
38259 {&__pyx_kp_u_BAD_GENOTYPE_Cannot_parse_genoty, __pyx_k_BAD_GENOTYPE_Cannot_parse_genoty, sizeof(__pyx_k_BAD_GENOTYPE_Cannot_parse_genoty), 0, 1, 0, 0},
38260 {&__pyx_n_s_BAD_NUMBER_OF_COLUMNS, __pyx_k_BAD_NUMBER_OF_COLUMNS, sizeof(__pyx_k_BAD_NUMBER_OF_COLUMNS), 0, 0, 1, 1},
38261 {&__pyx_kp_u_BAD_NUMBER_OF_COLUMNS_Wrong_numb, __pyx_k_BAD_NUMBER_OF_COLUMNS_Wrong_numb, sizeof(__pyx_k_BAD_NUMBER_OF_COLUMNS_Wrong_numb), 0, 1, 0, 0},
38262 {&__pyx_n_s_BAD_NUMBER_OF_PARAMETERS, __pyx_k_BAD_NUMBER_OF_PARAMETERS, sizeof(__pyx_k_BAD_NUMBER_OF_PARAMETERS), 0, 0, 1, 1},
38263 {&__pyx_kp_u_BAD_NUMBER_OF_PARAMETERS_Found_u, __pyx_k_BAD_NUMBER_OF_PARAMETERS_Found_u, sizeof(__pyx_k_BAD_NUMBER_OF_PARAMETERS_Found_u), 0, 1, 0, 0},
38264 {&__pyx_n_s_BAD_NUMBER_OF_VALUES, __pyx_k_BAD_NUMBER_OF_VALUES, sizeof(__pyx_k_BAD_NUMBER_OF_VALUES), 0, 0, 1, 1},
38265 {&__pyx_kp_u_BAD_NUMBER_OF_VALUES_Found_too_m, __pyx_k_BAD_NUMBER_OF_VALUES_Found_too_m, sizeof(__pyx_k_BAD_NUMBER_OF_VALUES_Found_too_m), 0, 1, 0, 0},
38266 {&__pyx_n_u_CHROM, __pyx_k_CHROM, sizeof(__pyx_k_CHROM), 0, 1, 0, 1},
38267 {&__pyx_kp_u_Can_only_handle_v3_3_and_v4_0_VC, __pyx_k_Can_only_handle_v3_3_and_v4_0_VC, sizeof(__pyx_k_Can_only_handle_v3_3_and_v4_0_VC), 0, 1, 0, 0},
38268 {&__pyx_n_u_Character, __pyx_k_Character, sizeof(__pyx_k_Character), 0, 1, 0, 1},
38269 {&__pyx_kp_u_Conditional_genotype_quality, __pyx_k_Conditional_genotype_quality, sizeof(__pyx_k_Conditional_genotype_quality), 0, 1, 0, 0},
38270 {&__pyx_n_u_D, __pyx_k_D, sizeof(__pyx_k_D), 0, 1, 0, 1},
38271 {&__pyx_n_u_DP, __pyx_k_DP, sizeof(__pyx_k_DP), 0, 1, 0, 1},
38272 {&__pyx_kp_u_Description, __pyx_k_Description, sizeof(__pyx_k_Description), 0, 1, 0, 0},
38273 {&__pyx_n_u_Description_2, __pyx_k_Description_2, sizeof(__pyx_k_Description_2), 0, 1, 0, 1},
38274 {&__pyx_kp_u_Don_t_understand_region_string_s, __pyx_k_Don_t_understand_region_string_s, sizeof(__pyx_k_Don_t_understand_region_string_s), 0, 1, 0, 0},
38275 {&__pyx_n_u_EC, __pyx_k_EC, sizeof(__pyx_k_EC), 0, 1, 0, 1},
38276 {&__pyx_n_s_ERROR_FLAG_HAS_VALUE, __pyx_k_ERROR_FLAG_HAS_VALUE, sizeof(__pyx_k_ERROR_FLAG_HAS_VALUE), 0, 0, 1, 1},
38277 {&__pyx_kp_u_ERROR_FLAG_HAS_VALUE_Flag_fields, __pyx_k_ERROR_FLAG_HAS_VALUE_Flag_fields, sizeof(__pyx_k_ERROR_FLAG_HAS_VALUE_Flag_fields), 0, 1, 0, 0},
38278 {&__pyx_n_s_ERROR_FORMAT_NOT_CHAR, __pyx_k_ERROR_FORMAT_NOT_CHAR, sizeof(__pyx_k_ERROR_FORMAT_NOT_CHAR), 0, 0, 1, 1},
38279 {&__pyx_kp_u_ERROR_FORMAT_NOT_CHAR_Eexpected, __pyx_k_ERROR_FORMAT_NOT_CHAR_Eexpected, sizeof(__pyx_k_ERROR_FORMAT_NOT_CHAR_Eexpected), 0, 1, 0, 0},
38280 {&__pyx_n_s_ERROR_FORMAT_NOT_INTEGER, __pyx_k_ERROR_FORMAT_NOT_INTEGER, sizeof(__pyx_k_ERROR_FORMAT_NOT_INTEGER), 0, 0, 1, 1},
38281 {&__pyx_kp_u_ERROR_FORMAT_NOT_INTEGER_Expecte, __pyx_k_ERROR_FORMAT_NOT_INTEGER_Expecte, sizeof(__pyx_k_ERROR_FORMAT_NOT_INTEGER_Expecte), 0, 1, 0, 0},
38282 {&__pyx_n_s_ERROR_FORMAT_NOT_NUMERICAL, __pyx_k_ERROR_FORMAT_NOT_NUMERICAL, sizeof(__pyx_k_ERROR_FORMAT_NOT_NUMERICAL), 0, 0, 1, 1},
38283 {&__pyx_kp_u_ERROR_FORMAT_NOT_NUMERICAL_Expec, __pyx_k_ERROR_FORMAT_NOT_NUMERICAL_Expec, sizeof(__pyx_k_ERROR_FORMAT_NOT_NUMERICAL_Expec), 0, 1, 0, 0},
38284 {&__pyx_n_s_ERROR_INFO_STRING, __pyx_k_ERROR_INFO_STRING, sizeof(__pyx_k_ERROR_INFO_STRING), 0, 0, 1, 1},
38285 {&__pyx_kp_u_ERROR_INFO_STRING_Error_while_pa, __pyx_k_ERROR_INFO_STRING_Error_while_pa, sizeof(__pyx_k_ERROR_INFO_STRING_Error_while_pa), 0, 1, 0, 0},
38286 {&__pyx_n_s_ERROR_TRAILING_DATA, __pyx_k_ERROR_TRAILING_DATA, sizeof(__pyx_k_ERROR_TRAILING_DATA), 0, 0, 1, 1},
38287 {&__pyx_kp_u_ERROR_TRAILING_DATA_Numerical_fi, __pyx_k_ERROR_TRAILING_DATA_Numerical_fi, sizeof(__pyx_k_ERROR_TRAILING_DATA_Numerical_fi), 0, 1, 0, 0},
38288 {&__pyx_n_s_ERROR_UNKNOWN_KEY, __pyx_k_ERROR_UNKNOWN_KEY, sizeof(__pyx_k_ERROR_UNKNOWN_KEY), 0, 0, 1, 1},
38289 {&__pyx_kp_u_ERROR_UNKNOWN_KEY_Unknown_key_s, __pyx_k_ERROR_UNKNOWN_KEY_Unknown_key_s, sizeof(__pyx_k_ERROR_UNKNOWN_KEY_Unknown_key_s), 0, 1, 0, 0},
38290 {&__pyx_n_u_Error, __pyx_k_Error, sizeof(__pyx_k_Error), 0, 1, 0, 1},
38291 {&__pyx_kp_u_Expected_alternate_allel_counts, __pyx_k_Expected_alternate_allel_counts, sizeof(__pyx_k_Expected_alternate_allel_counts), 0, 1, 0, 0},
38292 {&__pyx_n_u_FILTER, __pyx_k_FILTER, sizeof(__pyx_k_FILTER), 0, 1, 0, 1},
38293 {&__pyx_n_s_FILTER_NOT_DEFINED, __pyx_k_FILTER_NOT_DEFINED, sizeof(__pyx_k_FILTER_NOT_DEFINED), 0, 0, 1, 1},
38294 {&__pyx_kp_u_FILTER_NOT_DEFINED_Identifier_s, __pyx_k_FILTER_NOT_DEFINED_Identifier_s, sizeof(__pyx_k_FILTER_NOT_DEFINED_Identifier_s), 0, 1, 0, 0},
38295 {&__pyx_n_s_FORMAT, __pyx_k_FORMAT, sizeof(__pyx_k_FORMAT), 0, 0, 1, 1},
38296 {&__pyx_n_u_FORMAT, __pyx_k_FORMAT, sizeof(__pyx_k_FORMAT), 0, 1, 0, 1},
38297 {&__pyx_n_s_FORMAT_MISSING_QUOTES, __pyx_k_FORMAT_MISSING_QUOTES, sizeof(__pyx_k_FORMAT_MISSING_QUOTES), 0, 0, 1, 1},
38298 {&__pyx_kp_u_FORMAT_MISSING_QUOTES_Descriptio, __pyx_k_FORMAT_MISSING_QUOTES_Descriptio, sizeof(__pyx_k_FORMAT_MISSING_QUOTES_Descriptio), 0, 1, 0, 0},
38299 {&__pyx_n_s_FORMAT_NOT_DEFINED, __pyx_k_FORMAT_NOT_DEFINED, sizeof(__pyx_k_FORMAT_NOT_DEFINED), 0, 0, 1, 1},
38300 {&__pyx_kp_u_FORMAT_NOT_DEFINED_Identifier_s, __pyx_k_FORMAT_NOT_DEFINED_Identifier_s, sizeof(__pyx_k_FORMAT_NOT_DEFINED_Identifier_s), 0, 1, 0, 0},
38301 {&__pyx_n_u_FT, __pyx_k_FT, sizeof(__pyx_k_FT), 0, 1, 0, 1},
38302 {&__pyx_n_u_Flag, __pyx_k_Flag, sizeof(__pyx_k_Flag), 0, 1, 0, 1},
38303 {&__pyx_n_u_Float, __pyx_k_Float, sizeof(__pyx_k_Float), 0, 1, 0, 1},
38304 {&__pyx_n_u_G, __pyx_k_G, sizeof(__pyx_k_G), 0, 1, 0, 1},
38305 {&__pyx_n_u_GL, __pyx_k_GL, sizeof(__pyx_k_GL), 0, 1, 0, 1},
38306 {&__pyx_n_u_GLE, __pyx_k_GLE, sizeof(__pyx_k_GLE), 0, 1, 0, 1},
38307 {&__pyx_n_u_GP, __pyx_k_GP, sizeof(__pyx_k_GP), 0, 1, 0, 1},
38308 {&__pyx_n_u_GQ, __pyx_k_GQ, sizeof(__pyx_k_GQ), 0, 1, 0, 1},
38309 {&__pyx_n_u_GT, __pyx_k_GT, sizeof(__pyx_k_GT), 0, 1, 0, 1},
38310 {&__pyx_n_s_GTdata, __pyx_k_GTdata, sizeof(__pyx_k_GTdata), 0, 0, 1, 1},
38311 {&__pyx_n_s_GTstring, __pyx_k_GTstring, sizeof(__pyx_k_GTstring), 0, 0, 1, 1},
38312 {&__pyx_n_u_Genotype, __pyx_k_Genotype, sizeof(__pyx_k_Genotype), 0, 1, 0, 1},
38313 {&__pyx_kp_u_Genotype_Quality, __pyx_k_Genotype_Quality, sizeof(__pyx_k_Genotype_Quality), 0, 1, 0, 0},
38314 {&__pyx_kp_u_Genotype_likelihoods, __pyx_k_Genotype_likelihoods, sizeof(__pyx_k_Genotype_likelihoods), 0, 1, 0, 0},
38315 {&__pyx_kp_u_Genotype_posterior_probabilities, __pyx_k_Genotype_posterior_probabilities, sizeof(__pyx_k_Genotype_posterior_probabilities), 0, 1, 0, 0},
38316 {&__pyx_n_s_HEADING_NOT_SEPARATED_BY_TABS, __pyx_k_HEADING_NOT_SEPARATED_BY_TABS, sizeof(__pyx_k_HEADING_NOT_SEPARATED_BY_TABS), 0, 0, 1, 1},
38317 {&__pyx_kp_u_HEADING_NOT_SEPARATED_BY_TABS_He, __pyx_k_HEADING_NOT_SEPARATED_BY_TABS_He, sizeof(__pyx_k_HEADING_NOT_SEPARATED_BY_TABS_He), 0, 1, 0, 0},
38318 {&__pyx_n_u_HQ, __pyx_k_HQ, sizeof(__pyx_k_HQ), 0, 1, 0, 1},
38319 {&__pyx_kp_u_Haplotype_Quality, __pyx_k_Haplotype_Quality, sizeof(__pyx_k_Haplotype_Quality), 0, 1, 0, 0},
38320 {&__pyx_n_u_I, __pyx_k_I, sizeof(__pyx_k_I), 0, 1, 0, 1},
38321 {&__pyx_kp_u_ID, __pyx_k_ID, sizeof(__pyx_k_ID), 0, 1, 0, 0},
38322 {&__pyx_n_u_ID_2, __pyx_k_ID_2, sizeof(__pyx_k_ID_2), 0, 1, 0, 1},
38323 {&__pyx_n_u_INFO, __pyx_k_INFO, sizeof(__pyx_k_INFO), 0, 1, 0, 1},
38324 {&__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_k_Incompatible_checksums_0x_x_vs_0, sizeof(__pyx_k_Incompatible_checksums_0x_x_vs_0), 0, 0, 1, 0},
38325 {&__pyx_n_u_Integer, __pyx_k_Integer, sizeof(__pyx_k_Integer), 0, 1, 0, 1},
38326 {&__pyx_kp_u_Invalid_error_string_s, __pyx_k_Invalid_error_string_s, sizeof(__pyx_k_Invalid_error_string_s), 0, 1, 0, 0},
38327 {&__pyx_n_s_KeyError, __pyx_k_KeyError, sizeof(__pyx_k_KeyError), 0, 0, 1, 1},
38328 {&__pyx_n_s_MISSING_INDEL_ALLELE_REF_BASE, __pyx_k_MISSING_INDEL_ALLELE_REF_BASE, sizeof(__pyx_k_MISSING_INDEL_ALLELE_REF_BASE), 0, 0, 1, 1},
38329 {&__pyx_kp_u_MISSING_INDEL_ALLELE_REF_BASE_In, __pyx_k_MISSING_INDEL_ALLELE_REF_BASE_In, sizeof(__pyx_k_MISSING_INDEL_ALLELE_REF_BASE_In), 0, 1, 0, 0},
38330 {&__pyx_n_s_MISSING_REF, __pyx_k_MISSING_REF, sizeof(__pyx_k_MISSING_REF), 0, 0, 1, 1},
38331 {&__pyx_kp_u_MISSING_REF_Reference_allele_mis, __pyx_k_MISSING_REF_Reference_allele_mis, sizeof(__pyx_k_MISSING_REF_Reference_allele_mis), 0, 1, 0, 0},
38332 {&__pyx_n_u_MQ, __pyx_k_MQ, sizeof(__pyx_k_MQ), 0, 1, 0, 1},
38333 {&__pyx_n_s_MemoryError, __pyx_k_MemoryError, sizeof(__pyx_k_MemoryError), 0, 0, 1, 1},
38334 {&__pyx_n_u_N, __pyx_k_N, sizeof(__pyx_k_N), 0, 1, 0, 1},
38335 {&__pyx_n_s_NT_ALLELES, __pyx_k_NT_ALLELES, sizeof(__pyx_k_NT_ALLELES), 0, 0, 1, 1},
38336 {&__pyx_n_s_NT_GENOTYPES, __pyx_k_NT_GENOTYPES, sizeof(__pyx_k_NT_GENOTYPES), 0, 0, 1, 1},
38337 {&__pyx_n_s_NT_NR_ALLELES, __pyx_k_NT_NR_ALLELES, sizeof(__pyx_k_NT_NR_ALLELES), 0, 0, 1, 1},
38338 {&__pyx_n_s_NT_NUMBER, __pyx_k_NT_NUMBER, sizeof(__pyx_k_NT_NUMBER), 0, 0, 1, 1},
38339 {&__pyx_n_s_NT_PHASED_GENOTYPES, __pyx_k_NT_PHASED_GENOTYPES, sizeof(__pyx_k_NT_PHASED_GENOTYPES), 0, 0, 1, 1},
38340 {&__pyx_n_s_NT_UNKNOWN, __pyx_k_NT_UNKNOWN, sizeof(__pyx_k_NT_UNKNOWN), 0, 0, 1, 1},
38341 {&__pyx_n_s_NotImplementedError, __pyx_k_NotImplementedError, sizeof(__pyx_k_NotImplementedError), 0, 0, 1, 1},
38342 {&__pyx_kp_u_Number, __pyx_k_Number, sizeof(__pyx_k_Number), 0, 1, 0, 0},
38343 {&__pyx_n_u_Number_2, __pyx_k_Number_2, sizeof(__pyx_k_Number_2), 0, 1, 0, 1},
38344 {&__pyx_n_b_PASS, __pyx_k_PASS, sizeof(__pyx_k_PASS), 0, 0, 0, 1},
38345 {&__pyx_n_u_PASS, __pyx_k_PASS, sizeof(__pyx_k_PASS), 0, 1, 0, 1},
38346 {&__pyx_n_u_PL, __pyx_k_PL, sizeof(__pyx_k_PL), 0, 1, 0, 1},
38347 {&__pyx_n_u_POS, __pyx_k_POS, sizeof(__pyx_k_POS), 0, 1, 0, 1},
38348 {&__pyx_n_s_POS_NOT_NUMERICAL, __pyx_k_POS_NOT_NUMERICAL, sizeof(__pyx_k_POS_NOT_NUMERICAL), 0, 0, 1, 1},
38349 {&__pyx_kp_u_POS_NOT_NUMERICAL_Position_colum, __pyx_k_POS_NOT_NUMERICAL_Position_colum, sizeof(__pyx_k_POS_NOT_NUMERICAL_Position_colum), 0, 1, 0, 0},
38350 {&__pyx_n_s_POS_NOT_POSITIVE, __pyx_k_POS_NOT_POSITIVE, sizeof(__pyx_k_POS_NOT_POSITIVE), 0, 0, 1, 1},
38351 {&__pyx_kp_u_POS_NOT_POSITIVE_Position_field, __pyx_k_POS_NOT_POSITIVE_Position_field, sizeof(__pyx_k_POS_NOT_POSITIVE_Position_field), 0, 1, 0, 0},
38352 {&__pyx_n_u_PQ, __pyx_k_PQ, sizeof(__pyx_k_PQ), 0, 1, 0, 1},
38353 {&__pyx_n_u_PS, __pyx_k_PS, sizeof(__pyx_k_PS), 0, 1, 0, 1},
38354 {&__pyx_kp_u_Phase_set, __pyx_k_Phase_set, sizeof(__pyx_k_Phase_set), 0, 1, 0, 0},
38355 {&__pyx_kp_u_Phasing_quality, __pyx_k_Phasing_quality, sizeof(__pyx_k_Phasing_quality), 0, 1, 0, 0},
38356 {&__pyx_kp_u_Phred_scaled_genotype_likelihood, __pyx_k_Phred_scaled_genotype_likelihood, sizeof(__pyx_k_Phred_scaled_genotype_likelihood), 0, 1, 0, 0},
38357 {&__pyx_n_s_PickleError, __pyx_k_PickleError, sizeof(__pyx_k_PickleError), 0, 0, 1, 1},
38358 {&__pyx_n_u_QUAL, __pyx_k_QUAL, sizeof(__pyx_k_QUAL), 0, 1, 0, 1},
38359 {&__pyx_n_s_QUAL_NOT_NUMERICAL, __pyx_k_QUAL_NOT_NUMERICAL, sizeof(__pyx_k_QUAL_NOT_NUMERICAL), 0, 0, 1, 1},
38360 {&__pyx_kp_u_QUAL_NOT_NUMERICAL_Quality_field, __pyx_k_QUAL_NOT_NUMERICAL_Quality_field, sizeof(__pyx_k_QUAL_NOT_NUMERICAL_Quality_field), 0, 1, 0, 0},
38361 {&__pyx_n_u_REF, __pyx_k_REF, sizeof(__pyx_k_REF), 0, 1, 0, 1},
38362 {&__pyx_kp_u_RMS_mapping_quality, __pyx_k_RMS_mapping_quality, sizeof(__pyx_k_RMS_mapping_quality), 0, 1, 0, 0},
38363 {&__pyx_kp_u_Read_depth_at_this_position_for, __pyx_k_Read_depth_at_this_position_for, sizeof(__pyx_k_Read_depth_at_this_position_for), 0, 1, 0, 0},
38364 {&__pyx_kp_u_Required_key_s_not_found_in_data, __pyx_k_Required_key_s_not_found_in_data, sizeof(__pyx_k_Required_key_s_not_found_in_data), 0, 1, 0, 0},
38365 {&__pyx_kp_u_Sample_Genotype_Filter, __pyx_k_Sample_Genotype_Filter, sizeof(__pyx_k_Sample_Genotype_Filter), 0, 1, 0, 0},
38366 {&__pyx_n_s_StopIteration, __pyx_k_StopIteration, sizeof(__pyx_k_StopIteration), 0, 0, 1, 1},
38367 {&__pyx_n_u_String, __pyx_k_String, sizeof(__pyx_k_String), 0, 1, 0, 1},
38368 {&__pyx_n_s_Tabixfile, __pyx_k_Tabixfile, sizeof(__pyx_k_Tabixfile), 0, 0, 1, 1},
38369 {&__pyx_kp_u_Type, __pyx_k_Type, sizeof(__pyx_k_Type), 0, 1, 0, 0},
38370 {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1},
38371 {&__pyx_n_u_Type_2, __pyx_k_Type_2, sizeof(__pyx_k_Type_2), 0, 1, 0, 1},
38372 {&__pyx_n_s_UNKNOWN_CHAR_IN_REF, __pyx_k_UNKNOWN_CHAR_IN_REF, sizeof(__pyx_k_UNKNOWN_CHAR_IN_REF), 0, 0, 1, 1},
38373 {&__pyx_kp_u_UNKNOWN_CHAR_IN_REF_Unknown_char, __pyx_k_UNKNOWN_CHAR_IN_REF_Unknown_char, sizeof(__pyx_k_UNKNOWN_CHAR_IN_REF_Unknown_char), 0, 1, 0, 0},
38374 {&__pyx_n_s_UNKNOWN_FORMAT_STRING, __pyx_k_UNKNOWN_FORMAT_STRING, sizeof(__pyx_k_UNKNOWN_FORMAT_STRING), 0, 0, 1, 1},
38375 {&__pyx_kp_u_UNKNOWN_FORMAT_STRING_Unknown_fi, __pyx_k_UNKNOWN_FORMAT_STRING_Unknown_fi, sizeof(__pyx_k_UNKNOWN_FORMAT_STRING_Unknown_fi), 0, 1, 0, 0},
38376 {&__pyx_kp_u_Undefined_tag, __pyx_k_Undefined_tag, sizeof(__pyx_k_Undefined_tag), 0, 1, 0, 0},
38377 {&__pyx_kp_u_Unknown_number_type_encountered, __pyx_k_Unknown_number_type_encountered, sizeof(__pyx_k_Unknown_number_type_encountered), 0, 1, 0, 0},
38378 {&__pyx_n_s_V33_BAD_ALLELE, __pyx_k_V33_BAD_ALLELE, sizeof(__pyx_k_V33_BAD_ALLELE), 0, 0, 1, 1},
38379 {&__pyx_kp_u_V33_BAD_ALLELE_Cannot_interpret, __pyx_k_V33_BAD_ALLELE_Cannot_interpret, sizeof(__pyx_k_V33_BAD_ALLELE_Cannot_interpret), 0, 1, 0, 0},
38380 {&__pyx_n_s_V33_BAD_REF, __pyx_k_V33_BAD_REF, sizeof(__pyx_k_V33_BAD_REF), 0, 0, 1, 1},
38381 {&__pyx_kp_u_V33_BAD_REF_Reference_should_be, __pyx_k_V33_BAD_REF_Reference_should_be, sizeof(__pyx_k_V33_BAD_REF_Reference_should_be), 0, 1, 0, 0},
38382 {&__pyx_n_s_V33_UNMATCHED_DELETION, __pyx_k_V33_UNMATCHED_DELETION, sizeof(__pyx_k_V33_UNMATCHED_DELETION), 0, 0, 1, 1},
38383 {&__pyx_kp_u_V33_UNMATCHED_DELETION_Deleted_s, __pyx_k_V33_UNMATCHED_DELETION_Deleted_s, sizeof(__pyx_k_V33_UNMATCHED_DELETION_Deleted_s), 0, 1, 0, 0},
38384 {&__pyx_n_s_V40_BAD_ALLELE, __pyx_k_V40_BAD_ALLELE, sizeof(__pyx_k_V40_BAD_ALLELE), 0, 0, 1, 1},
38385 {&__pyx_kp_u_V40_BAD_ALLELE_Bad_allele_found, __pyx_k_V40_BAD_ALLELE_Bad_allele_found, sizeof(__pyx_k_V40_BAD_ALLELE_Bad_allele_found), 0, 1, 0, 0},
38386 {&__pyx_n_s_V40_FORMAT_MUST_HAVE_NAMED_FIELD, __pyx_k_V40_FORMAT_MUST_HAVE_NAMED_FIELD, sizeof(__pyx_k_V40_FORMAT_MUST_HAVE_NAMED_FIELD), 0, 0, 1, 1},
38387 {&__pyx_kp_u_V40_FORMAT_MUST_HAVE_NAMED_FIELD_2, __pyx_k_V40_FORMAT_MUST_HAVE_NAMED_FIELD_2, sizeof(__pyx_k_V40_FORMAT_MUST_HAVE_NAMED_FIELD_2), 0, 1, 0, 0},
38388 {&__pyx_n_s_V40_MISSING_ANGLE_BRACKETS, __pyx_k_V40_MISSING_ANGLE_BRACKETS, sizeof(__pyx_k_V40_MISSING_ANGLE_BRACKETS), 0, 0, 1, 1},
38389 {&__pyx_kp_u_V40_MISSING_ANGLE_BRACKETS_Forma, __pyx_k_V40_MISSING_ANGLE_BRACKETS_Forma, sizeof(__pyx_k_V40_MISSING_ANGLE_BRACKETS_Forma), 0, 1, 0, 0},
38390 {&__pyx_n_s_VCF, __pyx_k_VCF, sizeof(__pyx_k_VCF), 0, 0, 1, 1},
38391 {&__pyx_n_u_VCF, __pyx_k_VCF, sizeof(__pyx_k_VCF), 0, 1, 0, 1},
38392 {&__pyx_n_s_VCFRecord, __pyx_k_VCFRecord, sizeof(__pyx_k_VCFRecord), 0, 0, 1, 1},
38393 {&__pyx_n_u_VCFRecord, __pyx_k_VCFRecord, sizeof(__pyx_k_VCFRecord), 0, 1, 0, 1},
38394 {&__pyx_n_s_VCFRecord___reduce_cython, __pyx_k_VCFRecord___reduce_cython, sizeof(__pyx_k_VCFRecord___reduce_cython), 0, 0, 1, 1},
38395 {&__pyx_n_s_VCFRecord___setstate_cython, __pyx_k_VCFRecord___setstate_cython, sizeof(__pyx_k_VCFRecord___setstate_cython), 0, 0, 1, 1},
38396 {&__pyx_n_s_VCFRecord_error, __pyx_k_VCFRecord_error, sizeof(__pyx_k_VCFRecord_error), 0, 0, 1, 1},
38397 {&__pyx_n_s_VCF___del, __pyx_k_VCF___del, sizeof(__pyx_k_VCF___del), 0, 0, 1, 1},
38398 {&__pyx_n_s_VCF___init, __pyx_k_VCF___init, sizeof(__pyx_k_VCF___init), 0, 0, 1, 1},
38399 {&__pyx_n_s_VCF__add_definition, __pyx_k_VCF__add_definition, sizeof(__pyx_k_VCF__add_definition), 0, 0, 1, 1},
38400 {&__pyx_n_s_VCF__parse, __pyx_k_VCF__parse, sizeof(__pyx_k_VCF__parse), 0, 0, 1, 1},
38401 {&__pyx_n_s_VCF__parse_header, __pyx_k_VCF__parse_header, sizeof(__pyx_k_VCF__parse_header), 0, 0, 1, 1},
38402 {&__pyx_n_s_VCF_close, __pyx_k_VCF_close, sizeof(__pyx_k_VCF_close), 0, 0, 1, 1},
38403 {&__pyx_n_s_VCF_compare_calls, __pyx_k_VCF_compare_calls, sizeof(__pyx_k_VCF_compare_calls), 0, 0, 1, 1},
38404 {&__pyx_n_s_VCF_connect, __pyx_k_VCF_connect, sizeof(__pyx_k_VCF_connect), 0, 0, 1, 1},
38405 {&__pyx_n_s_VCF_convertGT, __pyx_k_VCF_convertGT, sizeof(__pyx_k_VCF_convertGT), 0, 0, 1, 1},
38406 {&__pyx_n_s_VCF_convertGTback, __pyx_k_VCF_convertGTback, sizeof(__pyx_k_VCF_convertGTback), 0, 0, 1, 1},
38407 {&__pyx_n_s_VCF_enter_default_format, __pyx_k_VCF_enter_default_format, sizeof(__pyx_k_VCF_enter_default_format), 0, 0, 1, 1},
38408 {&__pyx_n_s_VCF_error, __pyx_k_VCF_error, sizeof(__pyx_k_VCF_error), 0, 0, 1, 1},
38409 {&__pyx_n_s_VCF_fetch, __pyx_k_VCF_fetch, sizeof(__pyx_k_VCF_fetch), 0, 0, 1, 1},
38410 {&__pyx_n_s_VCF_format_format, __pyx_k_VCF_format_format, sizeof(__pyx_k_VCF_format_format), 0, 0, 1, 1},
38411 {&__pyx_n_s_VCF_format_formatdata, __pyx_k_VCF_format_formatdata, sizeof(__pyx_k_VCF_format_formatdata), 0, 0, 1, 1},
38412 {&__pyx_n_s_VCF_get_expected, __pyx_k_VCF_get_expected, sizeof(__pyx_k_VCF_get_expected), 0, 0, 1, 1},
38413 {&__pyx_n_s_VCF_getfilter, __pyx_k_VCF_getfilter, sizeof(__pyx_k_VCF_getfilter), 0, 0, 1, 1},
38414 {&__pyx_n_s_VCF_getformat, __pyx_k_VCF_getformat, sizeof(__pyx_k_VCF_getformat), 0, 0, 1, 1},
38415 {&__pyx_n_s_VCF_getheader, __pyx_k_VCF_getheader, sizeof(__pyx_k_VCF_getheader), 0, 0, 1, 1},
38416 {&__pyx_n_s_VCF_getinfo, __pyx_k_VCF_getinfo, sizeof(__pyx_k_VCF_getinfo), 0, 0, 1, 1},
38417 {&__pyx_n_s_VCF_getsamples, __pyx_k_VCF_getsamples, sizeof(__pyx_k_VCF_getsamples), 0, 0, 1, 1},
38418 {&__pyx_n_s_VCF_ignoreerror, __pyx_k_VCF_ignoreerror, sizeof(__pyx_k_VCF_ignoreerror), 0, 0, 1, 1},
38419 {&__pyx_n_s_VCF_inregion, __pyx_k_VCF_inregion, sizeof(__pyx_k_VCF_inregion), 0, 0, 1, 1},
38420 {&__pyx_n_s_VCF_parse, __pyx_k_VCF_parse, sizeof(__pyx_k_VCF_parse), 0, 0, 1, 1},
38421 {&__pyx_n_s_VCF_parse_data, __pyx_k_VCF_parse_data, sizeof(__pyx_k_VCF_parse_data), 0, 0, 1, 1},
38422 {&__pyx_n_s_VCF_parse_format, __pyx_k_VCF_parse_format, sizeof(__pyx_k_VCF_parse_format), 0, 0, 1, 1},
38423 {&__pyx_n_s_VCF_parse_formatdata, __pyx_k_VCF_parse_formatdata, sizeof(__pyx_k_VCF_parse_formatdata), 0, 0, 1, 1},
38424 {&__pyx_n_s_VCF_parse_header, __pyx_k_VCF_parse_header, sizeof(__pyx_k_VCF_parse_header), 0, 0, 1, 1},
38425 {&__pyx_n_s_VCF_parse_heading, __pyx_k_VCF_parse_heading, sizeof(__pyx_k_VCF_parse_heading), 0, 0, 1, 1},
38426 {&__pyx_kp_u_VCF_says, __pyx_k_VCF_says, sizeof(__pyx_k_VCF_says), 0, 1, 0, 0},
38427 {&__pyx_n_s_VCF_setfilter, __pyx_k_VCF_setfilter, sizeof(__pyx_k_VCF_setfilter), 0, 0, 1, 1},
38428 {&__pyx_n_s_VCF_setformat, __pyx_k_VCF_setformat, sizeof(__pyx_k_VCF_setformat), 0, 0, 1, 1},
38429 {&__pyx_n_s_VCF_setheader, __pyx_k_VCF_setheader, sizeof(__pyx_k_VCF_setheader), 0, 0, 1, 1},
38430 {&__pyx_n_s_VCF_setinfo, __pyx_k_VCF_setinfo, sizeof(__pyx_k_VCF_setinfo), 0, 0, 1, 1},
38431 {&__pyx_n_s_VCF_setreference, __pyx_k_VCF_setreference, sizeof(__pyx_k_VCF_setreference), 0, 0, 1, 1},
38432 {&__pyx_n_s_VCF_setregions, __pyx_k_VCF_setregions, sizeof(__pyx_k_VCF_setregions), 0, 0, 1, 1},
38433 {&__pyx_n_s_VCF_setsamples, __pyx_k_VCF_setsamples, sizeof(__pyx_k_VCF_setsamples), 0, 0, 1, 1},
38434 {&__pyx_n_s_VCF_setversion, __pyx_k_VCF_setversion, sizeof(__pyx_k_VCF_setversion), 0, 0, 1, 1},
38435 {&__pyx_n_s_VCF_validate, __pyx_k_VCF_validate, sizeof(__pyx_k_VCF_validate), 0, 0, 1, 1},
38436 {&__pyx_n_s_VCF_warnerror, __pyx_k_VCF_warnerror, sizeof(__pyx_k_VCF_warnerror), 0, 0, 1, 1},
38437 {&__pyx_n_s_VCF_write, __pyx_k_VCF_write, sizeof(__pyx_k_VCF_write), 0, 0, 1, 1},
38438 {&__pyx_n_s_VCF_write_data, __pyx_k_VCF_write_data, sizeof(__pyx_k_VCF_write_data), 0, 0, 1, 1},
38439 {&__pyx_n_s_VCF_write_header, __pyx_k_VCF_write_header, sizeof(__pyx_k_VCF_write_header), 0, 0, 1, 1},
38440 {&__pyx_n_s_VCF_write_heading, __pyx_k_VCF_write_heading, sizeof(__pyx_k_VCF_write_heading), 0, 0, 1, 1},
38441 {&__pyx_n_s_VCF_writeheader, __pyx_k_VCF_writeheader, sizeof(__pyx_k_VCF_writeheader), 0, 0, 1, 1},
38442 {&__pyx_kp_u_VCFv3_3, __pyx_k_VCFv3_3, sizeof(__pyx_k_VCFv3_3), 0, 1, 0, 0},
38443 {&__pyx_kp_u_VCFv4_0, __pyx_k_VCFv4_0, sizeof(__pyx_k_VCFv4_0), 0, 1, 0, 0},
38444 {&__pyx_kp_u_VCFv4_1, __pyx_k_VCFv4_1, sizeof(__pyx_k_VCFv4_1), 0, 1, 0, 0},
38445 {&__pyx_kp_u_VCFv4_2, __pyx_k_VCFv4_2, sizeof(__pyx_k_VCFv4_2), 0, 1, 0, 0},
38446 {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1},
38447 {&__pyx_n_s_WRONG_REF, __pyx_k_WRONG_REF, sizeof(__pyx_k_WRONG_REF), 0, 0, 1, 1},
38448 {&__pyx_kp_u_WRONG_REF_Wrong_reference_s, __pyx_k_WRONG_REF_Wrong_reference_s, sizeof(__pyx_k_WRONG_REF_Wrong_reference_s), 0, 1, 0, 0},
38449 {&__pyx_n_u_Warning, __pyx_k_Warning, sizeof(__pyx_k_Warning), 0, 1, 0, 1},
38450 {&__pyx_n_s_ZERO_FOR_NON_FLAG_FIELD, __pyx_k_ZERO_FOR_NON_FLAG_FIELD, sizeof(__pyx_k_ZERO_FOR_NON_FLAG_FIELD), 0, 0, 1, 1},
38451 {&__pyx_kp_u_ZERO_FOR_NON_FLAG_FIELD_number_s, __pyx_k_ZERO_FOR_NON_FLAG_FIELD_number_s, sizeof(__pyx_k_ZERO_FOR_NON_FLAG_FIELD_number_s), 0, 1, 0, 0},
38452 {&__pyx_n_s_ZERO_LENGTH_ALLELE, __pyx_k_ZERO_LENGTH_ALLELE, sizeof(__pyx_k_ZERO_LENGTH_ALLELE), 0, 0, 1, 1},
38453 {&__pyx_kp_u_ZERO_LENGTH_ALLELE_Found_zero_le, __pyx_k_ZERO_LENGTH_ALLELE_Found_zero_le, sizeof(__pyx_k_ZERO_LENGTH_ALLELE_Found_zero_le), 0, 1, 0, 0},
38454 {&__pyx_kp_u__10, __pyx_k__10, sizeof(__pyx_k__10), 0, 1, 0, 0},
38455 {&__pyx_kp_u__11, __pyx_k__11, sizeof(__pyx_k__11), 0, 1, 0, 0},
38456 {&__pyx_kp_u__12, __pyx_k__12, sizeof(__pyx_k__12), 0, 1, 0, 0},
38457 {&__pyx_kp_u__13, __pyx_k__13, sizeof(__pyx_k__13), 0, 1, 0, 0},
38458 {&__pyx_n_s__139, __pyx_k__139, sizeof(__pyx_k__139), 0, 0, 1, 1},
38459 {&__pyx_kp_u__14, __pyx_k__14, sizeof(__pyx_k__14), 0, 1, 0, 0},
38460 {&__pyx_kp_u__15, __pyx_k__15, sizeof(__pyx_k__15), 0, 1, 0, 0},
38461 {&__pyx_kp_u__16, __pyx_k__16, sizeof(__pyx_k__16), 0, 1, 0, 0},
38462 {&__pyx_kp_u__19, __pyx_k__19, sizeof(__pyx_k__19), 0, 1, 0, 0},
38463 {&__pyx_kp_u__2, __pyx_k__2, sizeof(__pyx_k__2), 0, 1, 0, 0},
38464 {&__pyx_kp_u__23, __pyx_k__23, sizeof(__pyx_k__23), 0, 1, 0, 0},
38465 {&__pyx_kp_u__24, __pyx_k__24, sizeof(__pyx_k__24), 0, 1, 0, 0},
38466 {&__pyx_kp_u__25, __pyx_k__25, sizeof(__pyx_k__25), 0, 1, 0, 0},
38467 {&__pyx_kp_u__27, __pyx_k__27, sizeof(__pyx_k__27), 0, 1, 0, 0},
38468 {&__pyx_kp_u__3, __pyx_k__3, sizeof(__pyx_k__3), 0, 1, 0, 0},
38469 {&__pyx_n_s__33, __pyx_k__33, sizeof(__pyx_k__33), 0, 0, 1, 1},
38470 {&__pyx_kp_u__34, __pyx_k__34, sizeof(__pyx_k__34), 0, 1, 0, 0},
38471 {&__pyx_kp_u__4, __pyx_k__4, sizeof(__pyx_k__4), 0, 1, 0, 0},
38472 {&__pyx_kp_b__5, __pyx_k__5, sizeof(__pyx_k__5), 0, 0, 0, 0},
38473 {&__pyx_kp_u__5, __pyx_k__5, sizeof(__pyx_k__5), 0, 1, 0, 0},
38474 {&__pyx_kp_u__6, __pyx_k__6, sizeof(__pyx_k__6), 0, 1, 0, 0},
38475 {&__pyx_kp_u__7, __pyx_k__7, sizeof(__pyx_k__7), 0, 1, 0, 0},
38476 {&__pyx_kp_u__8, __pyx_k__8, sizeof(__pyx_k__8), 0, 1, 0, 0},
38477 {&__pyx_n_s_a, __pyx_k_a, sizeof(__pyx_k_a), 0, 0, 1, 1},
38478 {&__pyx_n_s_add, __pyx_k_add, sizeof(__pyx_k_add), 0, 0, 1, 1},
38479 {&__pyx_n_s_add_definition, __pyx_k_add_definition, sizeof(__pyx_k_add_definition), 0, 0, 1, 1},
38480 {&__pyx_n_s_addn, __pyx_k_addn, sizeof(__pyx_k_addn), 0, 0, 1, 1},
38481 {&__pyx_n_s_addns, __pyx_k_addns, sizeof(__pyx_k_addns), 0, 0, 1, 1},
38482 {&__pyx_n_s_all, __pyx_k_all, sizeof(__pyx_k_all), 0, 0, 1, 1},
38483 {&__pyx_n_s_allele, __pyx_k_allele, sizeof(__pyx_k_allele), 0, 0, 1, 1},
38484 {&__pyx_n_s_alleleRegEx, __pyx_k_alleleRegEx, sizeof(__pyx_k_alleleRegEx), 0, 0, 1, 1},
38485 {&__pyx_kp_u_alleles, __pyx_k_alleles, sizeof(__pyx_k_alleles), 0, 1, 0, 0},
38486 {&__pyx_n_s_alt, __pyx_k_alt, sizeof(__pyx_k_alt), 0, 0, 1, 1},
38487 {&__pyx_n_u_alt, __pyx_k_alt, sizeof(__pyx_k_alt), 0, 1, 0, 1},
38488 {&__pyx_n_s_alt1, __pyx_k_alt1, sizeof(__pyx_k_alt1), 0, 0, 1, 1},
38489 {&__pyx_n_s_alt2, __pyx_k_alt2, sizeof(__pyx_k_alt2), 0, 0, 1, 1},
38490 {&__pyx_n_s_append, __pyx_k_append, sizeof(__pyx_k_append), 0, 0, 1, 1},
38491 {&__pyx_n_s_args, __pyx_k_args, sizeof(__pyx_k_args), 0, 0, 1, 1},
38492 {&__pyx_n_s_asVCFRecord, __pyx_k_asVCFRecord, sizeof(__pyx_k_asVCFRecord), 0, 0, 1, 1},
38493 {&__pyx_n_s_asVCFRecord___reduce_cython, __pyx_k_asVCFRecord___reduce_cython, sizeof(__pyx_k_asVCFRecord___reduce_cython), 0, 0, 1, 1},
38494 {&__pyx_n_s_asVCFRecord___setstate_cython, __pyx_k_asVCFRecord___setstate_cython, sizeof(__pyx_k_asVCFRecord___setstate_cython), 0, 0, 1, 1},
38495 {&__pyx_n_u_ascii, __pyx_k_ascii, sizeof(__pyx_k_ascii), 0, 1, 0, 1},
38496 {&__pyx_n_s_asyncio_coroutines, __pyx_k_asyncio_coroutines, sizeof(__pyx_k_asyncio_coroutines), 0, 0, 1, 1},
38497 {&__pyx_n_s_bisect, __pyx_k_bisect, sizeof(__pyx_k_bisect), 0, 0, 1, 1},
38498 {&__pyx_n_s_blurp, __pyx_k_blurp, sizeof(__pyx_k_blurp), 0, 0, 1, 1},
38499 {&__pyx_n_s_c, __pyx_k_c, sizeof(__pyx_k_c), 0, 0, 1, 1},
38500 {&__pyx_n_s_chrom, __pyx_k_chrom, sizeof(__pyx_k_chrom), 0, 0, 1, 1},
38501 {&__pyx_n_u_chrom, __pyx_k_chrom, sizeof(__pyx_k_chrom), 0, 1, 0, 1},
38502 {&__pyx_n_s_class_getitem, __pyx_k_class_getitem, sizeof(__pyx_k_class_getitem), 0, 0, 1, 1},
38503 {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1},
38504 {&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1},
38505 {&__pyx_n_s_collections, __pyx_k_collections, sizeof(__pyx_k_collections), 0, 0, 1, 1},
38506 {&__pyx_n_s_cols, __pyx_k_cols, sizeof(__pyx_k_cols), 0, 0, 1, 1},
38507 {&__pyx_n_s_compare_calls, __pyx_k_compare_calls, sizeof(__pyx_k_compare_calls), 0, 0, 1, 1},
38508 {&__pyx_n_s_compile, __pyx_k_compile, sizeof(__pyx_k_compile), 0, 0, 1, 1},
38509 {&__pyx_n_s_connect, __pyx_k_connect, sizeof(__pyx_k_connect), 0, 0, 1, 1},
38510 {&__pyx_n_s_convertGT, __pyx_k_convertGT, sizeof(__pyx_k_convertGT), 0, 0, 1, 1},
38511 {&__pyx_n_s_convertGTback, __pyx_k_convertGTback, sizeof(__pyx_k_convertGTback), 0, 0, 1, 1},
38512 {&__pyx_n_s_copy, __pyx_k_copy, sizeof(__pyx_k_copy), 0, 0, 1, 1},
38513 {&__pyx_n_s_copy_2, __pyx_k_copy_2, sizeof(__pyx_k_copy_2), 0, 0, 1, 1},
38514 {&__pyx_n_s_d, __pyx_k_d, sizeof(__pyx_k_d), 0, 0, 1, 1},
38515 {&__pyx_n_s_data, __pyx_k_data, sizeof(__pyx_k_data), 0, 0, 1, 1},
38516 {&__pyx_n_s_datagenerator, __pyx_k_datagenerator, sizeof(__pyx_k_datagenerator), 0, 0, 1, 1},
38517 {&__pyx_n_s_deepcopy, __pyx_k_deepcopy, sizeof(__pyx_k_deepcopy), 0, 0, 1, 1},
38518 {&__pyx_n_s_defaultdict, __pyx_k_defaultdict, sizeof(__pyx_k_defaultdict), 0, 0, 1, 1},
38519 {&__pyx_n_s_del, __pyx_k_del, sizeof(__pyx_k_del), 0, 0, 1, 1},
38520 {&__pyx_kp_u_deletion_is, __pyx_k_deletion_is, sizeof(__pyx_k_deletion_is), 0, 1, 0, 0},
38521 {&__pyx_n_u_descr, __pyx_k_descr, sizeof(__pyx_k_descr), 0, 1, 0, 1},
38522 {&__pyx_n_s_description, __pyx_k_description, sizeof(__pyx_k_description), 0, 0, 1, 1},
38523 {&__pyx_n_s_dict, __pyx_k_dict, sizeof(__pyx_k_dict), 0, 0, 1, 1},
38524 {&__pyx_n_s_dict_2, __pyx_k_dict_2, sizeof(__pyx_k_dict_2), 0, 0, 1, 1},
38525 {&__pyx_n_s_dict_3, __pyx_k_dict_3, sizeof(__pyx_k_dict_3), 0, 0, 1, 1},
38526 {&__pyx_kp_u_disable, __pyx_k_disable, sizeof(__pyx_k_disable), 0, 1, 0, 0},
38527 {&__pyx_n_s_doc, __pyx_k_doc, sizeof(__pyx_k_doc), 0, 0, 1, 1},
38528 {&__pyx_n_s_elts, __pyx_k_elts, sizeof(__pyx_k_elts), 0, 0, 1, 1},
38529 {&__pyx_kp_u_enable, __pyx_k_enable, sizeof(__pyx_k_enable), 0, 1, 0, 0},
38530 {&__pyx_n_s_encoding, __pyx_k_encoding, sizeof(__pyx_k_encoding), 0, 0, 1, 1},
38531 {&__pyx_n_s_end, __pyx_k_end, sizeof(__pyx_k_end), 0, 0, 1, 1},
38532 {&__pyx_n_s_endswith, __pyx_k_endswith, sizeof(__pyx_k_endswith), 0, 0, 1, 1},
38533 {&__pyx_n_s_enter_default_format, __pyx_k_enter_default_format, sizeof(__pyx_k_enter_default_format), 0, 0, 1, 1},
38534 {&__pyx_n_s_enumerate, __pyx_k_enumerate, sizeof(__pyx_k_enumerate), 0, 0, 1, 1},
38535 {&__pyx_n_s_err, __pyx_k_err, sizeof(__pyx_k_err), 0, 0, 1, 1},
38536 {&__pyx_n_s_error, __pyx_k_error, sizeof(__pyx_k_error), 0, 0, 1, 1},
38537 {&__pyx_n_s_errorlabel, __pyx_k_errorlabel, sizeof(__pyx_k_errorlabel), 0, 0, 1, 1},
38538 {&__pyx_n_s_errors, __pyx_k_errors, sizeof(__pyx_k_errors), 0, 0, 1, 1},
38539 {&__pyx_n_s_errorstring, __pyx_k_errorstring, sizeof(__pyx_k_errorstring), 0, 0, 1, 1},
38540 {&__pyx_n_s_errwarn, __pyx_k_errwarn, sizeof(__pyx_k_errwarn), 0, 0, 1, 1},
38541 {&__pyx_kp_u_expected, __pyx_k_expected, sizeof(__pyx_k_expected), 0, 1, 0, 0},
38542 {&__pyx_kp_u_expected_2, __pyx_k_expected_2, sizeof(__pyx_k_expected_2), 0, 1, 0, 0},
38543 {&__pyx_kp_u_expected_3, __pyx_k_expected_3, sizeof(__pyx_k_expected_3), 0, 1, 0, 0},
38544 {&__pyx_n_s_expected_4, __pyx_k_expected_4, sizeof(__pyx_k_expected_4), 0, 0, 1, 1},
38545 {&__pyx_n_s_f, __pyx_k_f, sizeof(__pyx_k_f), 0, 0, 1, 1},
38546 {&__pyx_n_s_fa, __pyx_k_fa, sizeof(__pyx_k_fa), 0, 0, 1, 1},
38547 {&__pyx_n_s_faref, __pyx_k_faref, sizeof(__pyx_k_faref), 0, 0, 1, 1},
38548 {&__pyx_n_s_faref_leftflank, __pyx_k_faref_leftflank, sizeof(__pyx_k_faref_leftflank), 0, 0, 1, 1},
38549 {&__pyx_n_s_fetch, __pyx_k_fetch, sizeof(__pyx_k_fetch), 0, 0, 1, 1},
38550 {&__pyx_n_u_fileformat, __pyx_k_fileformat, sizeof(__pyx_k_fileformat), 0, 1, 0, 1},
38551 {&__pyx_kp_u_fileformat_VCFv, __pyx_k_fileformat_VCFv, sizeof(__pyx_k_fileformat_VCFv), 0, 1, 0, 0},
38552 {&__pyx_n_s_filename, __pyx_k_filename, sizeof(__pyx_k_filename), 0, 0, 1, 1},
38553 {&__pyx_n_s_filter, __pyx_k_filter, sizeof(__pyx_k_filter), 0, 0, 1, 1},
38554 {&__pyx_n_s_filter_2, __pyx_k_filter_2, sizeof(__pyx_k_filter_2), 0, 0, 1, 1},
38555 {&__pyx_n_u_filter_2, __pyx_k_filter_2, sizeof(__pyx_k_filter_2), 0, 1, 0, 1},
38556 {&__pyx_n_s_find, __pyx_k_find, sizeof(__pyx_k_find), 0, 0, 1, 1},
38557 {&__pyx_n_s_first, __pyx_k_first, sizeof(__pyx_k_first), 0, 0, 1, 1},
38558 {&__pyx_n_s_fmt, __pyx_k_fmt, sizeof(__pyx_k_fmt), 0, 0, 1, 1},
38559 {&__pyx_kp_u_for, __pyx_k_for, sizeof(__pyx_k_for), 0, 1, 0, 0},
38560 {&__pyx_n_s_format, __pyx_k_format, sizeof(__pyx_k_format), 0, 0, 1, 1},
38561 {&__pyx_n_u_format, __pyx_k_format, sizeof(__pyx_k_format), 0, 1, 0, 1},
38562 {&__pyx_n_s_format_2, __pyx_k_format_2, sizeof(__pyx_k_format_2), 0, 0, 1, 1},
38563 {&__pyx_n_s_format_format, __pyx_k_format_format, sizeof(__pyx_k_format_format), 0, 0, 1, 1},
38564 {&__pyx_n_s_format_formatdata, __pyx_k_format_formatdata, sizeof(__pyx_k_format_formatdata), 0, 0, 1, 1},
38565 {&__pyx_n_s_formatdict, __pyx_k_formatdict, sizeof(__pyx_k_formatdict), 0, 0, 1, 1},
38566 {&__pyx_kp_u_found, __pyx_k_found, sizeof(__pyx_k_found), 0, 1, 0, 0},
38567 {&__pyx_kp_u_gc, __pyx_k_gc, sizeof(__pyx_k_gc), 0, 1, 0, 0},
38568 {&__pyx_kp_u_genotypes, __pyx_k_genotypes, sizeof(__pyx_k_genotypes), 0, 1, 0, 0},
38569 {&__pyx_n_s_get, __pyx_k_get, sizeof(__pyx_k_get), 0, 0, 1, 1},
38570 {&__pyx_n_s_get_expected, __pyx_k_get_expected, sizeof(__pyx_k_get_expected), 0, 0, 1, 1},
38571 {&__pyx_n_s_get_sequence, __pyx_k_get_sequence, sizeof(__pyx_k_get_sequence), 0, 0, 1, 1},
38572 {&__pyx_n_s_getfilter, __pyx_k_getfilter, sizeof(__pyx_k_getfilter), 0, 0, 1, 1},
38573 {&__pyx_n_s_getformat, __pyx_k_getformat, sizeof(__pyx_k_getformat), 0, 0, 1, 1},
38574 {&__pyx_n_s_getheader, __pyx_k_getheader, sizeof(__pyx_k_getheader), 0, 0, 1, 1},
38575 {&__pyx_n_s_getinfo, __pyx_k_getinfo, sizeof(__pyx_k_getinfo), 0, 0, 1, 1},
38576 {&__pyx_n_s_getsamples, __pyx_k_getsamples, sizeof(__pyx_k_getsamples), 0, 0, 1, 1},
38577 {&__pyx_n_s_getstate, __pyx_k_getstate, sizeof(__pyx_k_getstate), 0, 0, 1, 1},
38578 {&__pyx_kp_u_got, __pyx_k_got, sizeof(__pyx_k_got), 0, 1, 0, 0},
38579 {&__pyx_n_s_gts, __pyx_k_gts, sizeof(__pyx_k_gts), 0, 0, 1, 1},
38580 {&__pyx_n_s_gtsRegEx, __pyx_k_gtsRegEx, sizeof(__pyx_k_gtsRegEx), 0, 0, 1, 1},
38581 {&__pyx_n_s_have_deletions, __pyx_k_have_deletions, sizeof(__pyx_k_have_deletions), 0, 0, 1, 1},
38582 {&__pyx_n_s_header, __pyx_k_header, sizeof(__pyx_k_header), 0, 0, 1, 1},
38583 {&__pyx_n_s_header_2, __pyx_k_header_2, sizeof(__pyx_k_header_2), 0, 0, 1, 1},
38584 {&__pyx_n_s_headings, __pyx_k_headings, sizeof(__pyx_k_headings), 0, 0, 1, 1},
38585 {&__pyx_n_s_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 0, 1, 1},
38586 {&__pyx_kp_u_id, __pyx_k_id, sizeof(__pyx_k_id), 0, 1, 0, 0},
38587 {&__pyx_n_s_id_2, __pyx_k_id_2, sizeof(__pyx_k_id_2), 0, 0, 1, 1},
38588 {&__pyx_n_u_id_2, __pyx_k_id_2, sizeof(__pyx_k_id_2), 0, 1, 0, 1},
38589 {&__pyx_kp_u_id_numbertype_number_type_descri, __pyx_k_id_numbertype_number_type_descri, sizeof(__pyx_k_id_numbertype_number_type_descri), 0, 1, 0, 0},
38590 {&__pyx_n_s_idx, __pyx_k_idx, sizeof(__pyx_k_idx), 0, 0, 1, 1},
38591 {&__pyx_n_s_ielts, __pyx_k_ielts, sizeof(__pyx_k_ielts), 0, 0, 1, 1},
38592 {&__pyx_n_s_ignored_errors, __pyx_k_ignored_errors, sizeof(__pyx_k_ignored_errors), 0, 0, 1, 1},
38593 {&__pyx_n_s_ignoreerror, __pyx_k_ignoreerror, sizeof(__pyx_k_ignoreerror), 0, 0, 1, 1},
38594 {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1},
38595 {&__pyx_kp_u_in_line, __pyx_k_in_line, sizeof(__pyx_k_in_line), 0, 1, 0, 0},
38596 {&__pyx_n_s_info, __pyx_k_info, sizeof(__pyx_k_info), 0, 0, 1, 1},
38597 {&__pyx_n_s_info_2, __pyx_k_info_2, sizeof(__pyx_k_info_2), 0, 0, 1, 1},
38598 {&__pyx_n_u_info_2, __pyx_k_info_2, sizeof(__pyx_k_info_2), 0, 1, 0, 1},
38599 {&__pyx_n_s_init, __pyx_k_init, sizeof(__pyx_k_init), 0, 0, 1, 1},
38600 {&__pyx_n_s_init_subclass, __pyx_k_init_subclass, sizeof(__pyx_k_init_subclass), 0, 0, 1, 1},
38601 {&__pyx_n_s_initializing, __pyx_k_initializing, sizeof(__pyx_k_initializing), 0, 0, 1, 1},
38602 {&__pyx_n_s_inregion, __pyx_k_inregion, sizeof(__pyx_k_inregion), 0, 0, 1, 1},
38603 {&__pyx_n_s_is_coroutine, __pyx_k_is_coroutine, sizeof(__pyx_k_is_coroutine), 0, 0, 1, 1},
38604 {&__pyx_kp_u_isenabled, __pyx_k_isenabled, sizeof(__pyx_k_isenabled), 0, 1, 0, 0},
38605 {&__pyx_n_s_itemgetter, __pyx_k_itemgetter, sizeof(__pyx_k_itemgetter), 0, 0, 1, 1},
38606 {&__pyx_n_s_itervalues, __pyx_k_itervalues, sizeof(__pyx_k_itervalues), 0, 0, 1, 1},
38607 {&__pyx_n_s_join, __pyx_k_join, sizeof(__pyx_k_join), 0, 0, 1, 1},
38608 {&__pyx_n_s_k, __pyx_k_k, sizeof(__pyx_k_k), 0, 0, 1, 1},
38609 {&__pyx_n_s_key, __pyx_k_key, sizeof(__pyx_k_key), 0, 0, 1, 1},
38610 {&__pyx_n_s_keys, __pyx_k_keys, sizeof(__pyx_k_keys), 0, 0, 1, 1},
38611 {&__pyx_n_s_l, __pyx_k_l, sizeof(__pyx_k_l), 0, 0, 1, 1},
38612 {&__pyx_n_s_label, __pyx_k_label, sizeof(__pyx_k_label), 0, 0, 1, 1},
38613 {&__pyx_n_s_last, __pyx_k_last, sizeof(__pyx_k_last), 0, 0, 1, 1},
38614 {&__pyx_n_s_last_line, __pyx_k_last_line, sizeof(__pyx_k_last_line), 0, 0, 1, 1},
38615 {&__pyx_n_s_left, __pyx_k_left, sizeof(__pyx_k_left), 0, 0, 1, 1},
38616 {&__pyx_n_s_leftalign, __pyx_k_leftalign, sizeof(__pyx_k_leftalign), 0, 0, 1, 1},
38617 {&__pyx_n_s_leftalign_2, __pyx_k_leftalign_2, sizeof(__pyx_k_leftalign_2), 0, 0, 1, 1},
38618 {&__pyx_n_s_line, __pyx_k_line, sizeof(__pyx_k_line), 0, 0, 1, 1},
38619 {&__pyx_n_s_line_2, __pyx_k_line_2, sizeof(__pyx_k_line_2), 0, 0, 1, 1},
38620 {&__pyx_n_s_lineno, __pyx_k_lineno, sizeof(__pyx_k_lineno), 0, 0, 1, 1},
38621 {&__pyx_n_s_lineparse, __pyx_k_lineparse, sizeof(__pyx_k_lineparse), 0, 0, 1, 1},
38622 {&__pyx_n_s_lines, __pyx_k_lines, sizeof(__pyx_k_lines), 0, 0, 1, 1},
38623 {&__pyx_n_s_lines_2, __pyx_k_lines_2, sizeof(__pyx_k_lines_2), 0, 0, 1, 1},
38624 {&__pyx_n_s_longest, __pyx_k_longest, sizeof(__pyx_k_longest), 0, 0, 1, 1},
38625 {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
38626 {&__pyx_n_s_map, __pyx_k_map, sizeof(__pyx_k_map), 0, 0, 1, 1},
38627 {&__pyx_n_s_match, __pyx_k_match, sizeof(__pyx_k_match), 0, 0, 1, 1},
38628 {&__pyx_n_s_metaclass, __pyx_k_metaclass, sizeof(__pyx_k_metaclass), 0, 0, 1, 1},
38629 {&__pyx_n_s_min, __pyx_k_min, sizeof(__pyx_k_min), 0, 0, 1, 1},
38630 {&__pyx_n_u_missing, __pyx_k_missing, sizeof(__pyx_k_missing), 0, 1, 0, 1},
38631 {&__pyx_n_s_missingvalue, __pyx_k_missingvalue, sizeof(__pyx_k_missingvalue), 0, 0, 1, 1},
38632 {&__pyx_n_s_module, __pyx_k_module, sizeof(__pyx_k_module), 0, 0, 1, 1},
38633 {&__pyx_n_s_movable, __pyx_k_movable, sizeof(__pyx_k_movable), 0, 0, 1, 1},
38634 {&__pyx_n_s_mro_entries, __pyx_k_mro_entries, sizeof(__pyx_k_mro_entries), 0, 0, 1, 1},
38635 {&__pyx_n_s_n, __pyx_k_n, sizeof(__pyx_k_n), 0, 0, 1, 1},
38636 {&__pyx_n_s_na, __pyx_k_na, sizeof(__pyx_k_na), 0, 0, 1, 1},
38637 {&__pyx_n_s_name, __pyx_k_name, sizeof(__pyx_k_name), 0, 0, 1, 1},
38638 {&__pyx_n_s_namedtuple, __pyx_k_namedtuple, sizeof(__pyx_k_namedtuple), 0, 0, 1, 1},
38639 {&__pyx_kp_u_needs_to_be_checked, __pyx_k_needs_to_be_checked, sizeof(__pyx_k_needs_to_be_checked), 0, 1, 0, 0},
38640 {&__pyx_n_s_new, __pyx_k_new, sizeof(__pyx_k_new), 0, 0, 1, 1},
38641 {&__pyx_n_s_newalts, __pyx_k_newalts, sizeof(__pyx_k_newalts), 0, 0, 1, 1},
38642 {&__pyx_n_s_nmb, __pyx_k_nmb, sizeof(__pyx_k_nmb), 0, 0, 1, 1},
38643 {&__pyx_kp_s_no_default___reduce___due_to_non, __pyx_k_no_default___reduce___due_to_non, sizeof(__pyx_k_no_default___reduce___due_to_non), 0, 0, 1, 0},
38644 {&__pyx_kp_u_nonref_alleles, __pyx_k_nonref_alleles, sizeof(__pyx_k_nonref_alleles), 0, 1, 0, 0},
38645 {&__pyx_n_s_number, __pyx_k_number, sizeof(__pyx_k_number), 0, 0, 1, 1},
38646 {&__pyx_n_u_number, __pyx_k_number, sizeof(__pyx_k_number), 0, 1, 0, 1},
38647 {&__pyx_n_s_numbertype, __pyx_k_numbertype, sizeof(__pyx_k_numbertype), 0, 0, 1, 1},
38648 {&__pyx_n_s_object, __pyx_k_object, sizeof(__pyx_k_object), 0, 0, 1, 1},
38649 {&__pyx_n_s_operator, __pyx_k_operator, sizeof(__pyx_k_operator), 0, 0, 1, 1},
38650 {&__pyx_n_s_opt, __pyx_k_opt, sizeof(__pyx_k_opt), 0, 0, 1, 1},
38651 {&__pyx_kp_u_output, __pyx_k_output, sizeof(__pyx_k_output), 0, 1, 0, 0},
38652 {&__pyx_n_s_output_2, __pyx_k_output_2, sizeof(__pyx_k_output_2), 0, 0, 1, 1},
38653 {&__pyx_kp_u_parameters_got, __pyx_k_parameters_got, sizeof(__pyx_k_parameters_got), 0, 1, 0, 0},
38654 {&__pyx_n_s_parse, __pyx_k_parse, sizeof(__pyx_k_parse), 0, 0, 1, 1},
38655 {&__pyx_n_s_parse_2, __pyx_k_parse_2, sizeof(__pyx_k_parse_2), 0, 0, 1, 1},
38656 {&__pyx_n_s_parse_data, __pyx_k_parse_data, sizeof(__pyx_k_parse_data), 0, 0, 1, 1},
38657 {&__pyx_n_s_parse_format, __pyx_k_parse_format, sizeof(__pyx_k_parse_format), 0, 0, 1, 1},
38658 {&__pyx_n_s_parse_formatdata, __pyx_k_parse_formatdata, sizeof(__pyx_k_parse_formatdata), 0, 0, 1, 1},
38659 {&__pyx_n_s_parse_header, __pyx_k_parse_header, sizeof(__pyx_k_parse_header), 0, 0, 1, 1},
38660 {&__pyx_n_s_parse_header_2, __pyx_k_parse_header_2, sizeof(__pyx_k_parse_header_2), 0, 0, 1, 1},
38661 {&__pyx_n_s_parse_heading, __pyx_k_parse_heading, sizeof(__pyx_k_parse_heading), 0, 0, 1, 1},
38662 {&__pyx_n_s_parse_regions, __pyx_k_parse_regions, sizeof(__pyx_k_parse_regions), 0, 0, 1, 1},
38663 {&__pyx_n_s_parser, __pyx_k_parser, sizeof(__pyx_k_parser), 0, 0, 1, 1},
38664 {&__pyx_kp_u_phased_genotypes, __pyx_k_phased_genotypes, sizeof(__pyx_k_phased_genotypes), 0, 1, 0, 0},
38665 {&__pyx_n_s_pickle, __pyx_k_pickle, sizeof(__pyx_k_pickle), 0, 0, 1, 1},
38666 {&__pyx_n_s_pos, __pyx_k_pos, sizeof(__pyx_k_pos), 0, 0, 1, 1},
38667 {&__pyx_n_u_pos, __pyx_k_pos, sizeof(__pyx_k_pos), 0, 1, 0, 1},
38668 {&__pyx_n_s_pos1, __pyx_k_pos1, sizeof(__pyx_k_pos1), 0, 0, 1, 1},
38669 {&__pyx_n_s_pos2, __pyx_k_pos2, sizeof(__pyx_k_pos2), 0, 0, 1, 1},
38670 {&__pyx_n_s_prepare, __pyx_k_prepare, sizeof(__pyx_k_prepare), 0, 0, 1, 1},
38671 {&__pyx_n_s_pysam, __pyx_k_pysam, sizeof(__pyx_k_pysam), 0, 0, 1, 1},
38672 {&__pyx_n_s_pysam_libcvcf, __pyx_k_pysam_libcvcf, sizeof(__pyx_k_pysam_libcvcf), 0, 0, 1, 1},
38673 {&__pyx_kp_s_pysam_libcvcf_pyx, __pyx_k_pysam_libcvcf_pyx, sizeof(__pyx_k_pysam_libcvcf_pyx), 0, 0, 1, 0},
38674 {&__pyx_n_s_pyx_PickleError, __pyx_k_pyx_PickleError, sizeof(__pyx_k_pyx_PickleError), 0, 0, 1, 1},
38675 {&__pyx_n_s_pyx_checksum, __pyx_k_pyx_checksum, sizeof(__pyx_k_pyx_checksum), 0, 0, 1, 1},
38676 {&__pyx_n_s_pyx_result, __pyx_k_pyx_result, sizeof(__pyx_k_pyx_result), 0, 0, 1, 1},
38677 {&__pyx_n_s_pyx_state, __pyx_k_pyx_state, sizeof(__pyx_k_pyx_state), 0, 0, 1, 1},
38678 {&__pyx_n_s_pyx_type, __pyx_k_pyx_type, sizeof(__pyx_k_pyx_type), 0, 0, 1, 1},
38679 {&__pyx_n_s_pyx_unpickle_asVCFRecord, __pyx_k_pyx_unpickle_asVCFRecord, sizeof(__pyx_k_pyx_unpickle_asVCFRecord), 0, 0, 1, 1},
38680 {&__pyx_n_s_pyx_vtable, __pyx_k_pyx_vtable, sizeof(__pyx_k_pyx_vtable), 0, 0, 1, 1},
38681 {&__pyx_n_s_qual, __pyx_k_qual, sizeof(__pyx_k_qual), 0, 0, 1, 1},
38682 {&__pyx_n_u_qual, __pyx_k_qual, sizeof(__pyx_k_qual), 0, 1, 0, 1},
38683 {&__pyx_n_s_qualname, __pyx_k_qualname, sizeof(__pyx_k_qualname), 0, 0, 1, 1},
38684 {&__pyx_n_s_r, __pyx_k_r, sizeof(__pyx_k_r), 0, 0, 1, 1},
38685 {&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1},
38686 {&__pyx_n_s_re, __pyx_k_re, sizeof(__pyx_k_re), 0, 0, 1, 1},
38687 {&__pyx_n_s_record, __pyx_k_record, sizeof(__pyx_k_record), 0, 0, 1, 1},
38688 {&__pyx_n_s_reduce, __pyx_k_reduce, sizeof(__pyx_k_reduce), 0, 0, 1, 1},
38689 {&__pyx_n_s_reduce_cython, __pyx_k_reduce_cython, sizeof(__pyx_k_reduce_cython), 0, 0, 1, 1},
38690 {&__pyx_n_s_reduce_ex, __pyx_k_reduce_ex, sizeof(__pyx_k_reduce_ex), 0, 0, 1, 1},
38691 {&__pyx_n_s_ref, __pyx_k_ref, sizeof(__pyx_k_ref), 0, 0, 1, 1},
38692 {&__pyx_n_u_ref, __pyx_k_ref, sizeof(__pyx_k_ref), 0, 1, 0, 1},
38693 {&__pyx_n_s_ref1, __pyx_k_ref1, sizeof(__pyx_k_ref1), 0, 0, 1, 1},
38694 {&__pyx_n_s_ref2, __pyx_k_ref2, sizeof(__pyx_k_ref2), 0, 0, 1, 1},
38695 {&__pyx_n_s_reference, __pyx_k_reference, sizeof(__pyx_k_reference), 0, 0, 1, 1},
38696 {&__pyx_n_s_reference_2, __pyx_k_reference_2, sizeof(__pyx_k_reference_2), 0, 0, 1, 1},
38697 {&__pyx_kp_u_reference_is, __pyx_k_reference_is, sizeof(__pyx_k_reference_is), 0, 1, 0, 0},
38698 {&__pyx_kp_u_reference_is_2, __pyx_k_reference_is_2, sizeof(__pyx_k_reference_is_2), 0, 1, 0, 0},
38699 {&__pyx_n_s_region, __pyx_k_region, sizeof(__pyx_k_region), 0, 0, 1, 1},
38700 {&__pyx_n_s_regions, __pyx_k_regions, sizeof(__pyx_k_regions), 0, 0, 1, 1},
38701 {&__pyx_n_s_regions_2, __pyx_k_regions_2, sizeof(__pyx_k_regions_2), 0, 0, 1, 1},
38702 {&__pyx_n_s_replace, __pyx_k_replace, sizeof(__pyx_k_replace), 0, 0, 1, 1},
38703 {&__pyx_n_s_required, __pyx_k_required, sizeof(__pyx_k_required), 0, 0, 1, 1},
38704 {&__pyx_n_s_required_2, __pyx_k_required_2, sizeof(__pyx_k_required_2), 0, 0, 1, 1},
38705 {&__pyx_n_s_rest, __pyx_k_rest, sizeof(__pyx_k_rest), 0, 0, 1, 1},
38706 {&__pyx_n_s_result, __pyx_k_result, sizeof(__pyx_k_result), 0, 0, 1, 1},
38707 {&__pyx_n_s_s, __pyx_k_s, sizeof(__pyx_k_s), 0, 0, 1, 1},
38708 {&__pyx_n_s_sample, __pyx_k_sample, sizeof(__pyx_k_sample), 0, 0, 1, 1},
38709 {&__pyx_n_s_sample2column, __pyx_k_sample2column, sizeof(__pyx_k_sample2column), 0, 0, 1, 1},
38710 {&__pyx_n_s_samples, __pyx_k_samples, sizeof(__pyx_k_samples), 0, 0, 1, 1},
38711 {&__pyx_kp_u_samples_2, __pyx_k_samples_2, sizeof(__pyx_k_samples_2), 0, 1, 0, 0},
38712 {&__pyx_n_s_samples_3, __pyx_k_samples_3, sizeof(__pyx_k_samples_3), 0, 0, 1, 1},
38713 {&__pyx_n_s_sdata, __pyx_k_sdata, sizeof(__pyx_k_sdata), 0, 0, 1, 1},
38714 {&__pyx_n_s_self, __pyx_k_self, sizeof(__pyx_k_self), 0, 0, 1, 1},
38715 {&__pyx_n_s_send, __pyx_k_send, sizeof(__pyx_k_send), 0, 0, 1, 1},
38716 {&__pyx_n_s_separator, __pyx_k_separator, sizeof(__pyx_k_separator), 0, 0, 1, 1},
38717 {&__pyx_n_s_sequence, __pyx_k_sequence, sizeof(__pyx_k_sequence), 0, 0, 1, 1},
38718 {&__pyx_n_s_set_name, __pyx_k_set_name, sizeof(__pyx_k_set_name), 0, 0, 1, 1},
38719 {&__pyx_n_s_setfilter, __pyx_k_setfilter, sizeof(__pyx_k_setfilter), 0, 0, 1, 1},
38720 {&__pyx_n_s_setformat, __pyx_k_setformat, sizeof(__pyx_k_setformat), 0, 0, 1, 1},
38721 {&__pyx_n_s_setheader, __pyx_k_setheader, sizeof(__pyx_k_setheader), 0, 0, 1, 1},
38722 {&__pyx_n_s_setinfo, __pyx_k_setinfo, sizeof(__pyx_k_setinfo), 0, 0, 1, 1},
38723 {&__pyx_n_s_setreference, __pyx_k_setreference, sizeof(__pyx_k_setreference), 0, 0, 1, 1},
38724 {&__pyx_n_s_setregions, __pyx_k_setregions, sizeof(__pyx_k_setregions), 0, 0, 1, 1},
38725 {&__pyx_n_s_setsamples, __pyx_k_setsamples, sizeof(__pyx_k_setsamples), 0, 0, 1, 1},
38726 {&__pyx_n_s_setstate, __pyx_k_setstate, sizeof(__pyx_k_setstate), 0, 0, 1, 1},
38727 {&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 0, 0, 1, 1},
38728 {&__pyx_n_s_setversion, __pyx_k_setversion, sizeof(__pyx_k_setversion), 0, 0, 1, 1},
38729 {&__pyx_n_s_shortest, __pyx_k_shortest, sizeof(__pyx_k_shortest), 0, 0, 1, 1},
38730 {&__pyx_n_s_spec, __pyx_k_spec, sizeof(__pyx_k_spec), 0, 0, 1, 1},
38731 {&__pyx_n_s_split, __pyx_k_split, sizeof(__pyx_k_split), 0, 0, 1, 1},
38732 {&__pyx_n_s_start, __pyx_k_start, sizeof(__pyx_k_start), 0, 0, 1, 1},
38733 {&__pyx_n_s_startswith, __pyx_k_startswith, sizeof(__pyx_k_startswith), 0, 0, 1, 1},
38734 {&__pyx_n_s_state, __pyx_k_state, sizeof(__pyx_k_state), 0, 0, 1, 1},
38735 {&__pyx_kp_u_sth_entry_not_found, __pyx_k_sth_entry_not_found, sizeof(__pyx_k_sth_entry_not_found), 0, 1, 0, 0},
38736 {&__pyx_n_s_stream, __pyx_k_stream, sizeof(__pyx_k_stream), 0, 0, 1, 1},
38737 {&__pyx_n_s_string, __pyx_k_string, sizeof(__pyx_k_string), 0, 0, 1, 1},
38738 {&__pyx_kp_s_stringsource, __pyx_k_stringsource, sizeof(__pyx_k_stringsource), 0, 0, 1, 0},
38739 {&__pyx_n_s_strip, __pyx_k_strip, sizeof(__pyx_k_strip), 0, 0, 1, 1},
38740 {&__pyx_n_s_super, __pyx_k_super, sizeof(__pyx_k_super), 0, 0, 1, 1},
38741 {&__pyx_n_s_sys, __pyx_k_sys, sizeof(__pyx_k_sys), 0, 0, 1, 1},
38742 {&__pyx_n_s_t, __pyx_k_t, sizeof(__pyx_k_t), 0, 0, 1, 1},
38743 {&__pyx_n_s_tabixfile, __pyx_k_tabixfile, sizeof(__pyx_k_tabixfile), 0, 0, 1, 1},
38744 {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
38745 {&__pyx_n_s_throw, __pyx_k_throw, sizeof(__pyx_k_throw), 0, 0, 1, 1},
38746 {&__pyx_n_s_type, __pyx_k_type, sizeof(__pyx_k_type), 0, 0, 1, 1},
38747 {&__pyx_n_u_type, __pyx_k_type, sizeof(__pyx_k_type), 0, 1, 0, 1},
38748 {&__pyx_n_s_update, __pyx_k_update, sizeof(__pyx_k_update), 0, 0, 1, 1},
38749 {&__pyx_n_s_upper, __pyx_k_upper, sizeof(__pyx_k_upper), 0, 0, 1, 1},
38750 {&__pyx_n_s_use_setstate, __pyx_k_use_setstate, sizeof(__pyx_k_use_setstate), 0, 0, 1, 1},
38751 {&__pyx_n_s_v, __pyx_k_v, sizeof(__pyx_k_v), 0, 0, 1, 1},
38752 {&__pyx_n_s_validate, __pyx_k_validate, sizeof(__pyx_k_validate), 0, 0, 1, 1},
38753 {&__pyx_n_s_value, __pyx_k_value, sizeof(__pyx_k_value), 0, 0, 1, 1},
38754 {&__pyx_n_s_values, __pyx_k_values, sizeof(__pyx_k_values), 0, 0, 1, 1},
38755 {&__pyx_kp_u_values_in_element, __pyx_k_values_in_element, sizeof(__pyx_k_values_in_element), 0, 1, 0, 0},
38756 {&__pyx_n_s_var, __pyx_k_var, sizeof(__pyx_k_var), 0, 0, 1, 1},
38757 {&__pyx_n_s_vcf, __pyx_k_vcf, sizeof(__pyx_k_vcf), 0, 0, 1, 1},
38758 {&__pyx_n_s_vcffile, __pyx_k_vcffile, sizeof(__pyx_k_vcffile), 0, 0, 1, 1},
38759 {&__pyx_n_s_version, __pyx_k_version, sizeof(__pyx_k_version), 0, 0, 1, 1},
38760 {&__pyx_n_s_version_2, __pyx_k_version_2, sizeof(__pyx_k_version_2), 0, 0, 1, 1},
38761 {&__pyx_n_s_warn_errors, __pyx_k_warn_errors, sizeof(__pyx_k_warn_errors), 0, 0, 1, 1},
38762 {&__pyx_n_s_warnerror, __pyx_k_warnerror, sizeof(__pyx_k_warnerror), 0, 0, 1, 1},
38763 {&__pyx_n_s_write, __pyx_k_write, sizeof(__pyx_k_write), 0, 0, 1, 1},
38764 {&__pyx_n_s_write_data, __pyx_k_write_data, sizeof(__pyx_k_write_data), 0, 0, 1, 1},
38765 {&__pyx_n_s_write_header, __pyx_k_write_header, sizeof(__pyx_k_write_header), 0, 0, 1, 1},
38766 {&__pyx_n_s_write_heading, __pyx_k_write_heading, sizeof(__pyx_k_write_heading), 0, 0, 1, 1},
38767 {&__pyx_n_s_writeheader, __pyx_k_writeheader, sizeof(__pyx_k_writeheader), 0, 0, 1, 1},
38768 {&__pyx_n_s_x, __pyx_k_x, sizeof(__pyx_k_x), 0, 0, 1, 1},
38769 {&__pyx_n_s_y, __pyx_k_y, sizeof(__pyx_k_y), 0, 0, 1, 1},
38770 {&__pyx_n_s_zip, __pyx_k_zip, sizeof(__pyx_k_zip), 0, 0, 1, 1},
38771 {0, 0, 0, 0, 0, 0, 0}
38772 };
38773 return __Pyx_InitStrings(__pyx_string_tab);
38774 }
38775 /* #### Code section: cached_builtins ### */
38776 static CYTHON_SMALL_CODE int __Pyx_InitCachedBuiltins(void) {
38777 __pyx_builtin_object = __Pyx_GetBuiltinName(__pyx_n_s_object); if (!__pyx_builtin_object) __PYX_ERR(0, 253, __pyx_L1_error)
38778 __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) __PYX_ERR(0, 87, __pyx_L1_error)
38779 __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 224, __pyx_L1_error)
38780 __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(1, 2, __pyx_L1_error)
38781 __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) __PYX_ERR(0, 493, __pyx_L1_error)
38782 __pyx_builtin_map = __Pyx_GetBuiltinName(__pyx_n_s_map); if (!__pyx_builtin_map) __PYX_ERR(0, 500, __pyx_L1_error)
38783 __pyx_builtin_AssertionError = __Pyx_GetBuiltinName(__pyx_n_s_AssertionError); if (!__pyx_builtin_AssertionError) __PYX_ERR(0, 539, __pyx_L1_error)
38784 __pyx_builtin_min = __Pyx_GetBuiltinName(__pyx_n_s_min); if (!__pyx_builtin_min) __PYX_ERR(0, 837, __pyx_L1_error)
38785 __pyx_builtin_zip = __Pyx_GetBuiltinName(__pyx_n_s_zip); if (!__pyx_builtin_zip) __PYX_ERR(0, 877, __pyx_L1_error)
38786 __pyx_builtin_StopIteration = __Pyx_GetBuiltinName(__pyx_n_s_StopIteration); if (!__pyx_builtin_StopIteration) __PYX_ERR(0, 937, __pyx_L1_error)
38787 __pyx_builtin_KeyError = __Pyx_GetBuiltinName(__pyx_n_s_KeyError); if (!__pyx_builtin_KeyError) __PYX_ERR(0, 1000, __pyx_L1_error)
38788 __pyx_builtin_NotImplementedError = __Pyx_GetBuiltinName(__pyx_n_s_NotImplementedError); if (!__pyx_builtin_NotImplementedError) __PYX_ERR(0, 1081, __pyx_L1_error)
38789 __pyx_builtin_MemoryError = __Pyx_GetBuiltinName(__pyx_n_s_MemoryError); if (!__pyx_builtin_MemoryError) __PYX_ERR(3, 120, __pyx_L1_error)
38790 return 0;
38791 __pyx_L1_error:;
38792 return -1;
38793 }
38794 /* #### Code section: cached_constants ### */
38795
38796 static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) {
38797 __Pyx_RefNannyDeclarations
38798 __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
38799
38800 /* "pysam/libcvcf.pyx":337
38801 * if _copy != None:
38802 * self._leftalign = _copy._leftalign
38803 * self._header = _copy._header[:] # <<<<<<<<<<<<<<
38804 * self._version = _copy._version
38805 * self._info = copy.deepcopy(_copy._info)
38806 */
38807 __pyx_slice__9 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__9)) __PYX_ERR(0, 337, __pyx_L1_error)
38808 __Pyx_GOTREF(__pyx_slice__9);
38809 __Pyx_GIVEREF(__pyx_slice__9);
38810
38811 /* "pysam/libcvcf.pyx":372
38812 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
38813 * format += ">"
38814 * format = format[1:-1] # <<<<<<<<<<<<<<
38815 * data = {'id':None,'number':None,'type':None,'descr':None}
38816 * idx = 0
38817 */
38818 __pyx_slice__17 = PySlice_New(__pyx_int_1, __pyx_int_neg_1, Py_None); if (unlikely(!__pyx_slice__17)) __PYX_ERR(0, 372, __pyx_L1_error)
38819 __Pyx_GOTREF(__pyx_slice__17);
38820 __Pyx_GIVEREF(__pyx_slice__17);
38821
38822 /* "pysam/libcvcf.pyx":377
38823 * while len(format.strip())>0:
38824 * elts = format.strip().split(',')
38825 * first, rest = elts[0], ','.join(elts[1:]) # <<<<<<<<<<<<<<
38826 * if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
38827 * if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
38828 */
38829 __pyx_slice__18 = PySlice_New(__pyx_int_1, Py_None, Py_None); if (unlikely(!__pyx_slice__18)) __PYX_ERR(0, 377, __pyx_L1_error)
38830 __Pyx_GOTREF(__pyx_slice__18);
38831 __Pyx_GIVEREF(__pyx_slice__18);
38832
38833 /* "pysam/libcvcf.pyx":391
38834 * elts = first.split('=') + [rest]
38835 * data['descr'] = elts[1]
38836 * rest = '"'.join(elts[2:]) # <<<<<<<<<<<<<<
38837 * if rest.startswith(','): rest = rest[1:]
38838 * else:
38839 */
38840 __pyx_slice__20 = PySlice_New(__pyx_int_2, Py_None, Py_None); if (unlikely(!__pyx_slice__20)) __PYX_ERR(0, 391, __pyx_L1_error)
38841 __Pyx_GOTREF(__pyx_slice__20);
38842 __Pyx_GIVEREF(__pyx_slice__20);
38843
38844 /* "pysam/libcvcf.pyx":512
38845 * # snip off trailing missing data
38846 * while len(output) > 1:
38847 * last = output[-1].replace(',','').replace('.','') # <<<<<<<<<<<<<<
38848 * if len(last)>0: break
38849 * output = output[:-1]
38850 */
38851 __pyx_tuple__21 = PyTuple_Pack(2, __pyx_kp_u__2, __pyx_kp_u_); if (unlikely(!__pyx_tuple__21)) __PYX_ERR(0, 512, __pyx_L1_error)
38852 __Pyx_GOTREF(__pyx_tuple__21);
38853 __Pyx_GIVEREF(__pyx_tuple__21);
38854 __pyx_tuple__22 = PyTuple_Pack(2, __pyx_kp_u__5, __pyx_kp_u_); if (unlikely(!__pyx_tuple__22)) __PYX_ERR(0, 512, __pyx_L1_error)
38855 __Pyx_GOTREF(__pyx_tuple__22);
38856 __Pyx_GIVEREF(__pyx_tuple__22);
38857
38858 /* "pysam/libcvcf.pyx":602
38859 * self.error(line,self.BADLY_FORMATTED_HEADING,err)
38860 *
38861 * self._samples = headings[9:] # <<<<<<<<<<<<<<
38862 * self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] )
38863 *
38864 */
38865 __pyx_slice__26 = PySlice_New(__pyx_int_9, Py_None, Py_None); if (unlikely(!__pyx_slice__26)) __PYX_ERR(0, 602, __pyx_L1_error)
38866 __Pyx_GOTREF(__pyx_slice__26);
38867 __Pyx_GIVEREF(__pyx_slice__26);
38868
38869 /* "pysam/libcvcf.pyx":835
38870 * if not movable:
38871 * break
38872 * ref = ref[:-1] # <<<<<<<<<<<<<<
38873 * alt = [allele[:-1] for allele in alt]
38874 * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
38875 */
38876 __pyx_slice__28 = PySlice_New(Py_None, __pyx_int_neg_1, Py_None); if (unlikely(!__pyx_slice__28)) __PYX_ERR(0, 835, __pyx_L1_error)
38877 __Pyx_GOTREF(__pyx_slice__28);
38878 __Pyx_GIVEREF(__pyx_slice__28);
38879
38880 /* "pysam/libcvcf.pyx":988
38881 *
38882 * def setversion(self, version):
38883 * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") # <<<<<<<<<<<<<<
38884 * self._version = version
38885 *
38886 */
38887 __pyx_tuple__30 = PyTuple_Pack(1, __pyx_kp_u_Can_only_handle_v3_3_and_v4_0_VC); if (unlikely(!__pyx_tuple__30)) __PYX_ERR(0, 988, __pyx_L1_error)
38888 __Pyx_GOTREF(__pyx_tuple__30);
38889 __Pyx_GIVEREF(__pyx_tuple__30);
38890
38891 /* "pysam/libcvcf.pyx":1081
38892 * '''
38893 *
38894 * raise NotImplementedError("needs to be checked") # <<<<<<<<<<<<<<
38895 *
38896 * chrom, pos = record.chrom, record.pos
38897 */
38898 __pyx_tuple__31 = PyTuple_Pack(1, __pyx_kp_u_needs_to_be_checked); if (unlikely(!__pyx_tuple__31)) __PYX_ERR(0, 1081, __pyx_L1_error)
38899 __Pyx_GOTREF(__pyx_tuple__31);
38900 __Pyx_GIVEREF(__pyx_tuple__31);
38901
38902 /* "(tree fragment)":4
38903 * cdef object __pyx_PickleError
38904 * cdef object __pyx_result
38905 * if __pyx_checksum not in (0xe48d6d5, 0xcc3d7cd, 0x1c28f48): # <<<<<<<<<<<<<<
38906 * from pickle import PickleError as __pyx_PickleError
38907 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe48d6d5, 0xcc3d7cd, 0x1c28f48) = (encoding, vcffile))" % __pyx_checksum
38908 */
38909 __pyx_tuple__32 = PyTuple_Pack(3, __pyx_int_239654613, __pyx_int_214161357, __pyx_int_29527880); if (unlikely(!__pyx_tuple__32)) __PYX_ERR(1, 4, __pyx_L1_error)
38910 __Pyx_GOTREF(__pyx_tuple__32);
38911 __Pyx_GIVEREF(__pyx_tuple__32);
38912
38913 /* "pysam/libcvcf.pyx":64
38914 * import pysam
38915 *
38916 * gtsRegEx = re.compile("[|/\\\\]") # <<<<<<<<<<<<<<
38917 * alleleRegEx = re.compile('^[ACGTN]+$')
38918 *
38919 */
38920 __pyx_tuple__35 = PyTuple_Pack(1, __pyx_kp_u__34); if (unlikely(!__pyx_tuple__35)) __PYX_ERR(0, 64, __pyx_L1_error)
38921 __Pyx_GOTREF(__pyx_tuple__35);
38922 __Pyx_GIVEREF(__pyx_tuple__35);
38923
38924 /* "pysam/libcvcf.pyx":65
38925 *
38926 * gtsRegEx = re.compile("[|/\\\\]")
38927 * alleleRegEx = re.compile('^[ACGTN]+$') # <<<<<<<<<<<<<<
38928 *
38929 * # Utility function. Uses 0-based coordinates
38930 */
38931 __pyx_tuple__36 = PyTuple_Pack(1, __pyx_kp_u_ACGTN_2); if (unlikely(!__pyx_tuple__36)) __PYX_ERR(0, 65, __pyx_L1_error)
38932 __Pyx_GOTREF(__pyx_tuple__36);
38933 __Pyx_GIVEREF(__pyx_tuple__36);
38934
38935 /* "pysam/libcvcf.pyx":68
38936 *
38937 * # Utility function. Uses 0-based coordinates
38938 * def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<<
38939 * # obtain sequence from .fa file, without truncation
38940 * if end<=start: return ""
38941 */
38942 __pyx_tuple__37 = PyTuple_Pack(5, __pyx_n_s_chrom, __pyx_n_s_start, __pyx_n_s_end, __pyx_n_s_fa, __pyx_n_s_sequence); if (unlikely(!__pyx_tuple__37)) __PYX_ERR(0, 68, __pyx_L1_error)
38943 __Pyx_GOTREF(__pyx_tuple__37);
38944 __Pyx_GIVEREF(__pyx_tuple__37);
38945 __pyx_codeobj__38 = (PyObject*)__Pyx_PyCode_New(4, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__37, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_get_sequence, 68, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__38)) __PYX_ERR(0, 68, __pyx_L1_error)
38946
38947 /* "pysam/libcvcf.pyx":78
38948 *
38949 * # Utility function. Parses a region string
38950 * def parse_regions( string ): # <<<<<<<<<<<<<<
38951 * result = []
38952 * for r in string.split(','):
38953 */
38954 __pyx_tuple__39 = PyTuple_Pack(8, __pyx_n_s_string, __pyx_n_s_result, __pyx_n_s_r, __pyx_n_s_elts, __pyx_n_s_chrom, __pyx_n_s_start, __pyx_n_s_end, __pyx_n_s_ielts); if (unlikely(!__pyx_tuple__39)) __PYX_ERR(0, 78, __pyx_L1_error)
38955 __Pyx_GOTREF(__pyx_tuple__39);
38956 __Pyx_GIVEREF(__pyx_tuple__39);
38957 __pyx_codeobj__40 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 8, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__39, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_parse_regions, 78, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__40)) __PYX_ERR(0, 78, __pyx_L1_error)
38958
38959 /* "pysam/libcvcf.pyx":96
38960 *
38961 *
38962 * FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue') # <<<<<<<<<<<<<<
38963 *
38964 * ###########################################################################################################
38965 */
38966 __pyx_tuple__41 = PyTuple_Pack(2, __pyx_n_u_FORMAT, __pyx_kp_u_id_numbertype_number_type_descri); if (unlikely(!__pyx_tuple__41)) __PYX_ERR(0, 96, __pyx_L1_error)
38967 __Pyx_GOTREF(__pyx_tuple__41);
38968 __Pyx_GIVEREF(__pyx_tuple__41);
38969
38970 /* "pysam/libcvcf.pyx":134
38971 * self.encoding = vcf.encoding
38972 *
38973 * def error(self, line, error, opt=None): # <<<<<<<<<<<<<<
38974 * '''raise error.'''
38975 * # pass to vcf file for error handling
38976 */
38977 __pyx_tuple__42 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_line, __pyx_n_s_error, __pyx_n_s_opt); if (unlikely(!__pyx_tuple__42)) __PYX_ERR(0, 134, __pyx_L1_error)
38978 __Pyx_GOTREF(__pyx_tuple__42);
38979 __Pyx_GIVEREF(__pyx_tuple__42);
38980 __pyx_codeobj__43 = (PyObject*)__Pyx_PyCode_New(4, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__42, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_error, 134, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__43)) __PYX_ERR(0, 134, __pyx_L1_error)
38981 __pyx_tuple__44 = PyTuple_Pack(1, Py_None); if (unlikely(!__pyx_tuple__44)) __PYX_ERR(0, 134, __pyx_L1_error)
38982 __Pyx_GOTREF(__pyx_tuple__44);
38983 __Pyx_GIVEREF(__pyx_tuple__44);
38984
38985 /* "(tree fragment)":1
38986 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
38987 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
38988 * def __setstate_cython__(self, __pyx_state):
38989 */
38990 __pyx_tuple__45 = PyTuple_Pack(1, __pyx_n_s_self); if (unlikely(!__pyx_tuple__45)) __PYX_ERR(1, 1, __pyx_L1_error)
38991 __Pyx_GOTREF(__pyx_tuple__45);
38992 __Pyx_GIVEREF(__pyx_tuple__45);
38993 __pyx_codeobj__46 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__45, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__46)) __PYX_ERR(1, 1, __pyx_L1_error)
38994
38995 /* "(tree fragment)":3
38996 * def __reduce_cython__(self):
38997 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
38998 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
38999 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
39000 */
39001 __pyx_tuple__47 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_pyx_state); if (unlikely(!__pyx_tuple__47)) __PYX_ERR(1, 3, __pyx_L1_error)
39002 __Pyx_GOTREF(__pyx_tuple__47);
39003 __Pyx_GIVEREF(__pyx_tuple__47);
39004 __pyx_codeobj__48 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__47, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__48)) __PYX_ERR(1, 3, __pyx_L1_error)
39005
39006 /* "(tree fragment)":1
39007 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
39008 * cdef tuple state
39009 * cdef object _dict
39010 */
39011 __pyx_tuple__49 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_state, __pyx_n_s_dict_2, __pyx_n_s_use_setstate); if (unlikely(!__pyx_tuple__49)) __PYX_ERR(1, 1, __pyx_L1_error)
39012 __Pyx_GOTREF(__pyx_tuple__49);
39013 __Pyx_GIVEREF(__pyx_tuple__49);
39014 __pyx_codeobj__50 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__49, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__50)) __PYX_ERR(1, 1, __pyx_L1_error)
39015
39016 /* "(tree fragment)":16
39017 * else:
39018 * return __pyx_unpickle_asVCFRecord, (type(self), 0xe48d6d5, state)
39019 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
39020 * __pyx_unpickle_asVCFRecord__set_state(self, __pyx_state)
39021 */
39022 __pyx_codeobj__51 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__47, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__51)) __PYX_ERR(1, 16, __pyx_L1_error)
39023
39024 /* "pysam/libcvcf.pyx":253
39025 * return r
39026 *
39027 * class VCF(object): # <<<<<<<<<<<<<<
39028 *
39029 * # types
39030 */
39031 __pyx_tuple__52 = PyTuple_Pack(1, __pyx_builtin_object); if (unlikely(!__pyx_tuple__52)) __PYX_ERR(0, 253, __pyx_L1_error)
39032 __Pyx_GOTREF(__pyx_tuple__52);
39033 __Pyx_GIVEREF(__pyx_tuple__52);
39034 __pyx_tuple__53 = PyTuple_Pack(1, __pyx_builtin_object); if (unlikely(!__pyx_tuple__53)) __PYX_ERR(0, 253, __pyx_L1_error)
39035 __Pyx_GOTREF(__pyx_tuple__53);
39036 __Pyx_GIVEREF(__pyx_tuple__53);
39037
39038 /* "pysam/libcvcf.pyx":330
39039 * _lines = None
39040 *
39041 * def __init__(self, _copy=None, reference=None, regions=None, # <<<<<<<<<<<<<<
39042 * lines=None, leftalign=False):
39043 * # make error identifiers accessible by name
39044 */
39045 __pyx_tuple__54 = PyTuple_Pack(7, __pyx_n_s_self, __pyx_n_s_copy, __pyx_n_s_reference, __pyx_n_s_regions, __pyx_n_s_lines, __pyx_n_s_leftalign, __pyx_n_s_id_2); if (unlikely(!__pyx_tuple__54)) __PYX_ERR(0, 330, __pyx_L1_error)
39046 __Pyx_GOTREF(__pyx_tuple__54);
39047 __Pyx_GIVEREF(__pyx_tuple__54);
39048 __pyx_codeobj__55 = (PyObject*)__Pyx_PyCode_New(6, 0, 0, 7, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__54, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_init, 330, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__55)) __PYX_ERR(0, 330, __pyx_L1_error)
39049 __pyx_tuple__56 = PyTuple_Pack(5, Py_None, Py_None, Py_None, Py_None, ((PyObject *)Py_False)); if (unlikely(!__pyx_tuple__56)) __PYX_ERR(0, 330, __pyx_L1_error)
39050 __Pyx_GOTREF(__pyx_tuple__56);
39051 __Pyx_GIVEREF(__pyx_tuple__56);
39052
39053 /* "pysam/libcvcf.pyx":355
39054 * self.tabixfile = None
39055 *
39056 * def error(self,line,error,opt=None): # <<<<<<<<<<<<<<
39057 * if error in self._ignored_errors: return
39058 * errorlabel, errorstring = self._errors[error].split(':')
39059 */
39060 __pyx_tuple__57 = PyTuple_Pack(7, __pyx_n_s_self, __pyx_n_s_line, __pyx_n_s_error, __pyx_n_s_opt, __pyx_n_s_errorlabel, __pyx_n_s_errorstring, __pyx_n_s_errwarn); if (unlikely(!__pyx_tuple__57)) __PYX_ERR(0, 355, __pyx_L1_error)
39061 __Pyx_GOTREF(__pyx_tuple__57);
39062 __Pyx_GIVEREF(__pyx_tuple__57);
39063 __pyx_codeobj__58 = (PyObject*)__Pyx_PyCode_New(4, 0, 0, 7, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__57, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_error, 355, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__58)) __PYX_ERR(0, 355, __pyx_L1_error)
39064
39065 /* "pysam/libcvcf.pyx":364
39066 * raise ValueError(errorstring)
39067 *
39068 * def parse_format(self,line,format,filter=False): # <<<<<<<<<<<<<<
39069 * if self._version == 40:
39070 * if not format.startswith('<'):
39071 */
39072 __pyx_tuple__59 = PyTuple_Pack(11, __pyx_n_s_self, __pyx_n_s_line, __pyx_n_s_format, __pyx_n_s_filter_2, __pyx_n_s_data, __pyx_n_s_idx, __pyx_n_s_elts, __pyx_n_s_first, __pyx_n_s_rest, __pyx_n_s_n, __pyx_n_s_t); if (unlikely(!__pyx_tuple__59)) __PYX_ERR(0, 364, __pyx_L1_error)
39073 __Pyx_GOTREF(__pyx_tuple__59);
39074 __Pyx_GIVEREF(__pyx_tuple__59);
39075 __pyx_codeobj__60 = (PyObject*)__Pyx_PyCode_New(4, 0, 0, 11, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__59, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_parse_format, 364, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__60)) __PYX_ERR(0, 364, __pyx_L1_error)
39076 __pyx_tuple__61 = PyTuple_Pack(1, ((PyObject *)Py_False)); if (unlikely(!__pyx_tuple__61)) __PYX_ERR(0, 364, __pyx_L1_error)
39077 __Pyx_GOTREF(__pyx_tuple__61);
39078 __Pyx_GIVEREF(__pyx_tuple__61);
39079
39080 /* "pysam/libcvcf.pyx":436
39081 * return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
39082 *
39083 * def format_format( self, fmt, filter=False ): # <<<<<<<<<<<<<<
39084 * values = [('ID',fmt.id)]
39085 * if fmt.number != None and not filter:
39086 */
39087 __pyx_tuple__62 = PyTuple_Pack(10, __pyx_n_s_self, __pyx_n_s_fmt, __pyx_n_s_filter_2, __pyx_n_s_values, __pyx_n_s_nmb, __pyx_n_s_format, __pyx_n_s_k, __pyx_n_s_v, __pyx_n_s_k, __pyx_n_s_v); if (unlikely(!__pyx_tuple__62)) __PYX_ERR(0, 436, __pyx_L1_error)
39088 __Pyx_GOTREF(__pyx_tuple__62);
39089 __Pyx_GIVEREF(__pyx_tuple__62);
39090 __pyx_codeobj__63 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 10, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__62, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_format_format, 436, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__63)) __PYX_ERR(0, 436, __pyx_L1_error)
39091
39092 /* "pysam/libcvcf.pyx":456
39093 * return format
39094 *
39095 * def get_expected(self, format, formatdict, alt): # <<<<<<<<<<<<<<
39096 * fmt = formatdict[format]
39097 * if fmt.numbertype == self.NT_UNKNOWN: return -1
39098 */
39099 __pyx_tuple__64 = PyTuple_Pack(5, __pyx_n_s_self, __pyx_n_s_format, __pyx_n_s_formatdict, __pyx_n_s_alt, __pyx_n_s_fmt); if (unlikely(!__pyx_tuple__64)) __PYX_ERR(0, 456, __pyx_L1_error)
39100 __Pyx_GOTREF(__pyx_tuple__64);
39101 __Pyx_GIVEREF(__pyx_tuple__64);
39102 __pyx_codeobj__65 = (PyObject*)__Pyx_PyCode_New(4, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_get_expected, 456, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__65)) __PYX_ERR(0, 456, __pyx_L1_error)
39103
39104 /* "pysam/libcvcf.pyx":467
39105 *
39106 *
39107 * def _add_definition(self, formatdict, key, data, line ): # <<<<<<<<<<<<<<
39108 * if key in formatdict: return
39109 * self.error(line,self.ERROR_UNKNOWN_KEY,key)
39110 */
39111 __pyx_tuple__66 = PyTuple_Pack(5, __pyx_n_s_self, __pyx_n_s_formatdict, __pyx_n_s_key, __pyx_n_s_data, __pyx_n_s_line); if (unlikely(!__pyx_tuple__66)) __PYX_ERR(0, 467, __pyx_L1_error)
39112 __Pyx_GOTREF(__pyx_tuple__66);
39113 __Pyx_GIVEREF(__pyx_tuple__66);
39114 __pyx_codeobj__67 = (PyObject*)__Pyx_PyCode_New(5, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_add_definition, 467, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__67)) __PYX_ERR(0, 467, __pyx_L1_error)
39115
39116 /* "pysam/libcvcf.pyx":484
39117 *
39118 * # todo: trim trailing missing values
39119 * def format_formatdata( self, data, format, key=True, value=True, separator=":" ): # <<<<<<<<<<<<<<
39120 * output, sdata = [], []
39121 * if type(data) == type([]): # for FORMAT field, make data with dummy values
39122 */
39123 __pyx_tuple__68 = PyTuple_Pack(13, __pyx_n_s_self, __pyx_n_s_data, __pyx_n_s_format, __pyx_n_s_key, __pyx_n_s_value, __pyx_n_s_separator, __pyx_n_s_output_2, __pyx_n_s_sdata, __pyx_n_s_d, __pyx_n_s_k, __pyx_n_s_idx, __pyx_n_s_v, __pyx_n_s_last); if (unlikely(!__pyx_tuple__68)) __PYX_ERR(0, 484, __pyx_L1_error)
39124 __Pyx_GOTREF(__pyx_tuple__68);
39125 __Pyx_GIVEREF(__pyx_tuple__68);
39126 __pyx_codeobj__69 = (PyObject*)__Pyx_PyCode_New(6, 0, 0, 13, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__68, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_format_formatdata, 484, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__69)) __PYX_ERR(0, 484, __pyx_L1_error)
39127 __pyx_tuple__70 = PyTuple_Pack(3, ((PyObject *)Py_True), ((PyObject *)Py_True), ((PyObject*)__pyx_kp_u__3)); if (unlikely(!__pyx_tuple__70)) __PYX_ERR(0, 484, __pyx_L1_error)
39128 __Pyx_GOTREF(__pyx_tuple__70);
39129 __Pyx_GIVEREF(__pyx_tuple__70);
39130
39131 /* "pysam/libcvcf.pyx":518
39132 *
39133 *
39134 * def enter_default_format(self): # <<<<<<<<<<<<<<
39135 * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
39136 * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
39137 */
39138 __pyx_tuple__71 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_f); if (unlikely(!__pyx_tuple__71)) __PYX_ERR(0, 518, __pyx_L1_error)
39139 __Pyx_GOTREF(__pyx_tuple__71);
39140 __Pyx_GIVEREF(__pyx_tuple__71);
39141 __pyx_codeobj__72 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__71, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_enter_default_format, 518, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__72)) __PYX_ERR(0, 518, __pyx_L1_error)
39142
39143 /* "pysam/libcvcf.pyx":537
39144 * self._format[f.id] = f
39145 *
39146 * def parse_header(self, line): # <<<<<<<<<<<<<<
39147 *
39148 * assert line.startswith('##')
39149 */
39150 __pyx_tuple__73 = PyTuple_Pack(6, __pyx_n_s_self, __pyx_n_s_line, __pyx_n_s_elts, __pyx_n_s_key, __pyx_n_s_value, __pyx_n_s_f); if (unlikely(!__pyx_tuple__73)) __PYX_ERR(0, 537, __pyx_L1_error)
39151 __Pyx_GOTREF(__pyx_tuple__73);
39152 __Pyx_GIVEREF(__pyx_tuple__73);
39153 __pyx_codeobj__74 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 6, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__73, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_parse_header, 537, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__74)) __PYX_ERR(0, 537, __pyx_L1_error)
39154
39155 /* "pysam/libcvcf.pyx":570
39156 *
39157 *
39158 * def write_header( self, stream ): # <<<<<<<<<<<<<<
39159 * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
39160 * for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
39161 */
39162 __pyx_tuple__75 = PyTuple_Pack(7, __pyx_n_s_self, __pyx_n_s_stream, __pyx_n_s_key, __pyx_n_s_value, __pyx_n_s_var, __pyx_n_s_label, __pyx_n_s_f); if (unlikely(!__pyx_tuple__75)) __PYX_ERR(0, 570, __pyx_L1_error)
39163 __Pyx_GOTREF(__pyx_tuple__75);
39164 __Pyx_GIVEREF(__pyx_tuple__75);
39165 __pyx_codeobj__76 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 7, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_write_header, 570, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__76)) __PYX_ERR(0, 570, __pyx_L1_error)
39166
39167 /* "pysam/libcvcf.pyx":577
39168 *
39169 *
39170 * def parse_heading( self, line ): # <<<<<<<<<<<<<<
39171 * assert line.startswith('#')
39172 * assert not line.startswith('##')
39173 */
39174 __pyx_tuple__77 = PyTuple_Pack(8, __pyx_n_s_self, __pyx_n_s_line, __pyx_n_s_headings, __pyx_n_s_i, __pyx_n_s_s, __pyx_n_s_err, __pyx_n_s_x, __pyx_n_s_y); if (unlikely(!__pyx_tuple__77)) __PYX_ERR(0, 577, __pyx_L1_error)
39175 __Pyx_GOTREF(__pyx_tuple__77);
39176 __Pyx_GIVEREF(__pyx_tuple__77);
39177 __pyx_codeobj__78 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 8, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_parse_heading, 577, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__78)) __PYX_ERR(0, 577, __pyx_L1_error)
39178
39179 /* "pysam/libcvcf.pyx":605
39180 * self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] )
39181 *
39182 * def write_heading( self, stream ): # <<<<<<<<<<<<<<
39183 * stream.write("#" + "\t".join(self._required + self._samples) + "\n")
39184 *
39185 */
39186 __pyx_tuple__79 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_stream); if (unlikely(!__pyx_tuple__79)) __PYX_ERR(0, 605, __pyx_L1_error)
39187 __Pyx_GOTREF(__pyx_tuple__79);
39188 __Pyx_GIVEREF(__pyx_tuple__79);
39189 __pyx_codeobj__80 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__79, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_write_heading, 605, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__80)) __PYX_ERR(0, 605, __pyx_L1_error)
39190
39191 /* "pysam/libcvcf.pyx":608
39192 * stream.write("#" + "\t".join(self._required + self._samples) + "\n")
39193 *
39194 * def convertGT(self, GTstring): # <<<<<<<<<<<<<<
39195 * if GTstring == ".": return ["."]
39196 * try:
39197 */
39198 __pyx_tuple__81 = PyTuple_Pack(3, __pyx_n_s_self, __pyx_n_s_GTstring, __pyx_n_s_gts); if (unlikely(!__pyx_tuple__81)) __PYX_ERR(0, 608, __pyx_L1_error)
39199 __Pyx_GOTREF(__pyx_tuple__81);
39200 __Pyx_GIVEREF(__pyx_tuple__81);
39201 __pyx_codeobj__82 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 3, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__81, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_convertGT, 608, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__82)) __PYX_ERR(0, 608, __pyx_L1_error)
39202
39203 /* "pysam/libcvcf.pyx":620
39204 * return [".","|","."]
39205 *
39206 * def convertGTback(self, GTdata): # <<<<<<<<<<<<<<
39207 * return ''.join(map(str,GTdata))
39208 *
39209 */
39210 __pyx_tuple__83 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_GTdata); if (unlikely(!__pyx_tuple__83)) __PYX_ERR(0, 620, __pyx_L1_error)
39211 __Pyx_GOTREF(__pyx_tuple__83);
39212 __Pyx_GIVEREF(__pyx_tuple__83);
39213 __pyx_codeobj__84 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__83, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_convertGTback, 620, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__84)) __PYX_ERR(0, 620, __pyx_L1_error)
39214
39215 /* "pysam/libcvcf.pyx":623
39216 * return ''.join(map(str,GTdata))
39217 *
39218 * def parse_formatdata( self, key, value, formatdict, line ): # <<<<<<<<<<<<<<
39219 * # To do: check that the right number of values is present
39220 * f = formatdict.get(key,None)
39221 */
39222 __pyx_tuple__85 = PyTuple_Pack(9, __pyx_n_s_self, __pyx_n_s_key, __pyx_n_s_value, __pyx_n_s_formatdict, __pyx_n_s_line, __pyx_n_s_f, __pyx_n_s_values, __pyx_n_s_idx, __pyx_n_s_v); if (unlikely(!__pyx_tuple__85)) __PYX_ERR(0, 623, __pyx_L1_error)
39223 __Pyx_GOTREF(__pyx_tuple__85);
39224 __Pyx_GIVEREF(__pyx_tuple__85);
39225 __pyx_codeobj__86 = (PyObject*)__Pyx_PyCode_New(5, 0, 0, 9, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__85, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_parse_formatdata, 623, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__86)) __PYX_ERR(0, 623, __pyx_L1_error)
39226
39227 /* "pysam/libcvcf.pyx":665
39228 * self.error(line,self.ERROR_INFO_STRING)
39229 *
39230 * def inregion(self, chrom, pos): # <<<<<<<<<<<<<<
39231 * if not self._regions: return True
39232 * for r in self._regions:
39233 */
39234 __pyx_tuple__87 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_chrom, __pyx_n_s_pos, __pyx_n_s_r); if (unlikely(!__pyx_tuple__87)) __PYX_ERR(0, 665, __pyx_L1_error)
39235 __Pyx_GOTREF(__pyx_tuple__87);
39236 __Pyx_GIVEREF(__pyx_tuple__87);
39237 __pyx_codeobj__88 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__87, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_inregion, 665, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__88)) __PYX_ERR(0, 665, __pyx_L1_error)
39238
39239 /* "pysam/libcvcf.pyx":671
39240 * return False
39241 *
39242 * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<<
39243 * cols = line.split('\t')
39244 * if len(cols) != len(self._samples)+9:
39245 */
39246 __pyx_tuple__89 = PyTuple_Pack(48, __pyx_n_s_self, __pyx_n_s_line, __pyx_n_s_lineparse, __pyx_n_s_cols, __pyx_n_s_chrom, __pyx_n_s_pos, __pyx_n_s_id_2, __pyx_n_s_ref, __pyx_n_s_c, __pyx_n_s_left, __pyx_n_s_faref_leftflank, __pyx_n_s_faref, __pyx_n_s_alt, __pyx_n_s_qual, __pyx_n_s_filter_2, __pyx_n_s_info_2, __pyx_n_s_blurp, __pyx_n_s_elts, __pyx_n_s_v, __pyx_n_s_format, __pyx_n_s_f, __pyx_n_s_newalts, __pyx_n_s_have_deletions, __pyx_n_s_a, __pyx_n_s_l, __pyx_n_s_addns, __pyx_n_s_i, __pyx_n_s_na, __pyx_n_s_s, __pyx_n_s_addn, __pyx_n_s_allele, __pyx_n_s_movable, __pyx_n_s_longest, __pyx_n_s_shortest, __pyx_n_s_samples_3, __pyx_n_s_sample, __pyx_n_s_dict_3, __pyx_n_s_values, __pyx_n_s_idx, __pyx_n_s_expected_4, __pyx_n_s_value, __pyx_n_s_d, __pyx_n_s_key, __pyx_n_s_allele, __pyx_n_s_allele, __pyx_n_s_allele, __pyx_n_s_allele, __pyx_n_s_allele); if (unlikely(!__pyx_tuple__89)) __PYX_ERR(0, 671, __pyx_L1_error)
39247 __Pyx_GOTREF(__pyx_tuple__89);
39248 __Pyx_GIVEREF(__pyx_tuple__89);
39249 __pyx_codeobj__90 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 48, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__89, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_parse_data, 671, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__90)) __PYX_ERR(0, 671, __pyx_L1_error)
39250
39251 /* "pysam/libcvcf.pyx":883
39252 *
39253 *
39254 * def write_data(self, stream, data): # <<<<<<<<<<<<<<
39255 * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
39256 * for k in required:
39257 */
39258 __pyx_tuple__91 = PyTuple_Pack(10, __pyx_n_s_self, __pyx_n_s_stream, __pyx_n_s_data, __pyx_n_s_required_2, __pyx_n_s_k, __pyx_n_s_alt, __pyx_n_s_filter_2, __pyx_n_s_qual, __pyx_n_s_output_2, __pyx_n_s_s); if (unlikely(!__pyx_tuple__91)) __PYX_ERR(0, 883, __pyx_L1_error)
39259 __Pyx_GOTREF(__pyx_tuple__91);
39260 __Pyx_GIVEREF(__pyx_tuple__91);
39261 __pyx_codeobj__92 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 10, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__91, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_write_data, 883, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__92)) __PYX_ERR(0, 883, __pyx_L1_error)
39262
39263 /* "pysam/libcvcf.pyx":915
39264 * stream.write( "\t".join(output) + "\n" )
39265 *
39266 * def _parse_header(self, stream): # <<<<<<<<<<<<<<
39267 * self._lineno = 0
39268 * for line in stream:
39269 */
39270 __pyx_tuple__93 = PyTuple_Pack(3, __pyx_n_s_self, __pyx_n_s_stream, __pyx_n_s_line); if (unlikely(!__pyx_tuple__93)) __PYX_ERR(0, 915, __pyx_L1_error)
39271 __Pyx_GOTREF(__pyx_tuple__93);
39272 __Pyx_GIVEREF(__pyx_tuple__93);
39273 __pyx_codeobj__94 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 3, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__93, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_parse_header_2, 915, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__94)) __PYX_ERR(0, 915, __pyx_L1_error)
39274
39275 /* "pysam/libcvcf.pyx":929
39276 * return line
39277 *
39278 * def _parse(self, line, stream): # <<<<<<<<<<<<<<
39279 * # deal with files with header only
39280 * if line.startswith("##"): return
39281 */
39282 __pyx_tuple__95 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_line, __pyx_n_s_stream, __pyx_n_s_d); if (unlikely(!__pyx_tuple__95)) __PYX_ERR(0, 929, __pyx_L1_error)
39283 __Pyx_GOTREF(__pyx_tuple__95);
39284 __Pyx_GIVEREF(__pyx_tuple__95);
39285 __pyx_codeobj__29 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS|CO_GENERATOR, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__95, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_parse, 929, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__29)) __PYX_ERR(0, 929, __pyx_L1_error)
39286
39287 /* "pysam/libcvcf.pyx":947
39288 * ######################################################################################################
39289 *
39290 * def getsamples(self): # <<<<<<<<<<<<<<
39291 * """ List of samples in VCF file """
39292 * return self._samples
39293 */
39294 __pyx_codeobj__96 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__45, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_getsamples, 947, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__96)) __PYX_ERR(0, 947, __pyx_L1_error)
39295
39296 /* "pysam/libcvcf.pyx":951
39297 * return self._samples
39298 *
39299 * def setsamples(self,samples): # <<<<<<<<<<<<<<
39300 * """ List of samples in VCF file """
39301 * self._samples = samples
39302 */
39303 __pyx_tuple__97 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_samples_3); if (unlikely(!__pyx_tuple__97)) __PYX_ERR(0, 951, __pyx_L1_error)
39304 __Pyx_GOTREF(__pyx_tuple__97);
39305 __Pyx_GIVEREF(__pyx_tuple__97);
39306 __pyx_codeobj__98 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__97, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_setsamples, 951, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__98)) __PYX_ERR(0, 951, __pyx_L1_error)
39307
39308 /* "pysam/libcvcf.pyx":955
39309 * self._samples = samples
39310 *
39311 * def getheader(self): # <<<<<<<<<<<<<<
39312 * """ List of header key-value pairs (strings) """
39313 * return self._header
39314 */
39315 __pyx_codeobj__99 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__45, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_getheader, 955, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__99)) __PYX_ERR(0, 955, __pyx_L1_error)
39316
39317 /* "pysam/libcvcf.pyx":959
39318 * return self._header
39319 *
39320 * def setheader(self,header): # <<<<<<<<<<<<<<
39321 * """ List of header key-value pairs (strings) """
39322 * self._header = header
39323 */
39324 __pyx_tuple__100 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_header_2); if (unlikely(!__pyx_tuple__100)) __PYX_ERR(0, 959, __pyx_L1_error)
39325 __Pyx_GOTREF(__pyx_tuple__100);
39326 __Pyx_GIVEREF(__pyx_tuple__100);
39327 __pyx_codeobj__101 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__100, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_setheader, 959, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__101)) __PYX_ERR(0, 959, __pyx_L1_error)
39328
39329 /* "pysam/libcvcf.pyx":963
39330 * self._header = header
39331 *
39332 * def getinfo(self): # <<<<<<<<<<<<<<
39333 * """ Dictionary of ##INFO tags, as VCF.FORMAT values """
39334 * return self._info
39335 */
39336 __pyx_codeobj__102 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__45, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_getinfo, 963, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__102)) __PYX_ERR(0, 963, __pyx_L1_error)
39337
39338 /* "pysam/libcvcf.pyx":967
39339 * return self._info
39340 *
39341 * def setinfo(self,info): # <<<<<<<<<<<<<<
39342 * """ Dictionary of ##INFO tags, as VCF.FORMAT values """
39343 * self._info = info
39344 */
39345 __pyx_tuple__103 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_info_2); if (unlikely(!__pyx_tuple__103)) __PYX_ERR(0, 967, __pyx_L1_error)
39346 __Pyx_GOTREF(__pyx_tuple__103);
39347 __Pyx_GIVEREF(__pyx_tuple__103);
39348 __pyx_codeobj__104 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__103, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_setinfo, 967, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__104)) __PYX_ERR(0, 967, __pyx_L1_error)
39349
39350 /* "pysam/libcvcf.pyx":971
39351 * self._info = info
39352 *
39353 * def getformat(self): # <<<<<<<<<<<<<<
39354 * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
39355 * return self._format
39356 */
39357 __pyx_codeobj__105 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__45, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_getformat, 971, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__105)) __PYX_ERR(0, 971, __pyx_L1_error)
39358
39359 /* "pysam/libcvcf.pyx":975
39360 * return self._format
39361 *
39362 * def setformat(self,format): # <<<<<<<<<<<<<<
39363 * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
39364 * self._format = format
39365 */
39366 __pyx_tuple__106 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_format); if (unlikely(!__pyx_tuple__106)) __PYX_ERR(0, 975, __pyx_L1_error)
39367 __Pyx_GOTREF(__pyx_tuple__106);
39368 __Pyx_GIVEREF(__pyx_tuple__106);
39369 __pyx_codeobj__107 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__106, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_setformat, 975, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__107)) __PYX_ERR(0, 975, __pyx_L1_error)
39370
39371 /* "pysam/libcvcf.pyx":979
39372 * self._format = format
39373 *
39374 * def getfilter(self): # <<<<<<<<<<<<<<
39375 * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
39376 * return self._filter
39377 */
39378 __pyx_codeobj__108 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__45, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_getfilter, 979, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__108)) __PYX_ERR(0, 979, __pyx_L1_error)
39379
39380 /* "pysam/libcvcf.pyx":983
39381 * return self._filter
39382 *
39383 * def setfilter(self,filter): # <<<<<<<<<<<<<<
39384 * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
39385 * self._filter = filter
39386 */
39387 __pyx_tuple__109 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_filter_2); if (unlikely(!__pyx_tuple__109)) __PYX_ERR(0, 983, __pyx_L1_error)
39388 __Pyx_GOTREF(__pyx_tuple__109);
39389 __Pyx_GIVEREF(__pyx_tuple__109);
39390 __pyx_codeobj__110 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__109, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_setfilter, 983, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__110)) __PYX_ERR(0, 983, __pyx_L1_error)
39391
39392 /* "pysam/libcvcf.pyx":987
39393 * self._filter = filter
39394 *
39395 * def setversion(self, version): # <<<<<<<<<<<<<<
39396 * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")
39397 * self._version = version
39398 */
39399 __pyx_tuple__111 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_version_2); if (unlikely(!__pyx_tuple__111)) __PYX_ERR(0, 987, __pyx_L1_error)
39400 __Pyx_GOTREF(__pyx_tuple__111);
39401 __Pyx_GIVEREF(__pyx_tuple__111);
39402 __pyx_codeobj__112 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__111, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_setversion, 987, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__112)) __PYX_ERR(0, 987, __pyx_L1_error)
39403
39404 /* "pysam/libcvcf.pyx":991
39405 * self._version = version
39406 *
39407 * def setregions(self, regions): # <<<<<<<<<<<<<<
39408 * self._regions = regions
39409 *
39410 */
39411 __pyx_tuple__113 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_regions); if (unlikely(!__pyx_tuple__113)) __PYX_ERR(0, 991, __pyx_L1_error)
39412 __Pyx_GOTREF(__pyx_tuple__113);
39413 __Pyx_GIVEREF(__pyx_tuple__113);
39414 __pyx_codeobj__114 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__113, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_setregions, 991, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__114)) __PYX_ERR(0, 991, __pyx_L1_error)
39415
39416 /* "pysam/libcvcf.pyx":994
39417 * self._regions = regions
39418 *
39419 * def setreference(self, ref): # <<<<<<<<<<<<<<
39420 * """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
39421 * self._reference = ref
39422 */
39423 __pyx_tuple__115 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_ref); if (unlikely(!__pyx_tuple__115)) __PYX_ERR(0, 994, __pyx_L1_error)
39424 __Pyx_GOTREF(__pyx_tuple__115);
39425 __Pyx_GIVEREF(__pyx_tuple__115);
39426 __pyx_codeobj__116 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__115, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_setreference, 994, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__116)) __PYX_ERR(0, 994, __pyx_L1_error)
39427
39428 /* "pysam/libcvcf.pyx":998
39429 * self._reference = ref
39430 *
39431 * def ignoreerror(self, errorstring): # <<<<<<<<<<<<<<
39432 * try: self._ignored_errors.add(self.__dict__[errorstring])
39433 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
39434 */
39435 __pyx_tuple__117 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_errorstring); if (unlikely(!__pyx_tuple__117)) __PYX_ERR(0, 998, __pyx_L1_error)
39436 __Pyx_GOTREF(__pyx_tuple__117);
39437 __Pyx_GIVEREF(__pyx_tuple__117);
39438 __pyx_codeobj__118 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__117, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_ignoreerror, 998, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__118)) __PYX_ERR(0, 998, __pyx_L1_error)
39439
39440 /* "pysam/libcvcf.pyx":1002
39441 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
39442 *
39443 * def warnerror(self, errorstring): # <<<<<<<<<<<<<<
39444 * try: self._warn_errors.add(self.__dict__[errorstring])
39445 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
39446 */
39447 __pyx_codeobj__119 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__117, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_warnerror, 1002, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__119)) __PYX_ERR(0, 1002, __pyx_L1_error)
39448
39449 /* "pysam/libcvcf.pyx":1006
39450 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
39451 *
39452 * def parse(self, stream): # <<<<<<<<<<<<<<
39453 * """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
39454 * last_line = self._parse_header(stream)
39455 */
39456 __pyx_tuple__120 = PyTuple_Pack(3, __pyx_n_s_self, __pyx_n_s_stream, __pyx_n_s_last_line); if (unlikely(!__pyx_tuple__120)) __PYX_ERR(0, 1006, __pyx_L1_error)
39457 __Pyx_GOTREF(__pyx_tuple__120);
39458 __Pyx_GIVEREF(__pyx_tuple__120);
39459 __pyx_codeobj__121 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 3, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__120, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_parse_2, 1006, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__121)) __PYX_ERR(0, 1006, __pyx_L1_error)
39460
39461 /* "pysam/libcvcf.pyx":1013
39462 * return self._parse(last_line, stream)
39463 *
39464 * def write(self, stream, datagenerator): # <<<<<<<<<<<<<<
39465 * """ Writes a VCF file to a stream, using a data generator (or list) """
39466 * self.write_header(stream)
39467 */
39468 __pyx_tuple__122 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_stream, __pyx_n_s_datagenerator, __pyx_n_s_data); if (unlikely(!__pyx_tuple__122)) __PYX_ERR(0, 1013, __pyx_L1_error)
39469 __Pyx_GOTREF(__pyx_tuple__122);
39470 __Pyx_GIVEREF(__pyx_tuple__122);
39471 __pyx_codeobj__123 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__122, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_write, 1013, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__123)) __PYX_ERR(0, 1013, __pyx_L1_error)
39472
39473 /* "pysam/libcvcf.pyx":1019
39474 * for data in datagenerator: self.write_data(stream,data)
39475 *
39476 * def writeheader(self, stream): # <<<<<<<<<<<<<<
39477 * """ Writes a VCF header """
39478 * self.write_header(stream)
39479 */
39480 __pyx_codeobj__124 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__79, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_writeheader, 1019, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__124)) __PYX_ERR(0, 1019, __pyx_L1_error)
39481
39482 /* "pysam/libcvcf.pyx":1024
39483 * self.write_heading(stream)
39484 *
39485 * def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): # <<<<<<<<<<<<<<
39486 * """ Utility function: compares two calls for equality """
39487 * # a variant should always be assigned to a unique position, one base before
39488 */
39489 __pyx_tuple__125 = PyTuple_Pack(7, __pyx_n_s_self, __pyx_n_s_pos1, __pyx_n_s_ref1, __pyx_n_s_alt1, __pyx_n_s_pos2, __pyx_n_s_ref2, __pyx_n_s_alt2); if (unlikely(!__pyx_tuple__125)) __PYX_ERR(0, 1024, __pyx_L1_error)
39490 __Pyx_GOTREF(__pyx_tuple__125);
39491 __Pyx_GIVEREF(__pyx_tuple__125);
39492 __pyx_codeobj__126 = (PyObject*)__Pyx_PyCode_New(7, 0, 0, 7, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__125, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_compare_calls, 1024, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__126)) __PYX_ERR(0, 1024, __pyx_L1_error)
39493
39494 /* "pysam/libcvcf.pyx":1046
39495 * ###########################################################################################################
39496 *
39497 * def connect(self, filename, encoding="ascii"): # <<<<<<<<<<<<<<
39498 * '''connect to tabix file.'''
39499 * self.encoding=encoding
39500 */
39501 __pyx_tuple__127 = PyTuple_Pack(3, __pyx_n_s_self, __pyx_n_s_filename, __pyx_n_s_encoding); if (unlikely(!__pyx_tuple__127)) __PYX_ERR(0, 1046, __pyx_L1_error)
39502 __Pyx_GOTREF(__pyx_tuple__127);
39503 __Pyx_GIVEREF(__pyx_tuple__127);
39504 __pyx_codeobj__128 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 3, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__127, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_connect, 1046, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__128)) __PYX_ERR(0, 1046, __pyx_L1_error)
39505 __pyx_tuple__129 = PyTuple_Pack(1, ((PyObject*)__pyx_n_u_ascii)); if (unlikely(!__pyx_tuple__129)) __PYX_ERR(0, 1046, __pyx_L1_error)
39506 __Pyx_GOTREF(__pyx_tuple__129);
39507 __Pyx_GIVEREF(__pyx_tuple__129);
39508
39509 /* "pysam/libcvcf.pyx":1052
39510 * self._parse_header(self.tabixfile.header)
39511 *
39512 * def __del__(self): # <<<<<<<<<<<<<<
39513 * self.close()
39514 * self.tabixfile = None
39515 */
39516 __pyx_codeobj__130 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__45, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_del, 1052, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__130)) __PYX_ERR(0, 1052, __pyx_L1_error)
39517
39518 /* "pysam/libcvcf.pyx":1056
39519 * self.tabixfile = None
39520 *
39521 * def close(self): # <<<<<<<<<<<<<<
39522 * if self.tabixfile:
39523 * self.tabixfile.close()
39524 */
39525 __pyx_codeobj__131 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__45, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_close, 1056, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__131)) __PYX_ERR(0, 1056, __pyx_L1_error)
39526
39527 /* "pysam/libcvcf.pyx":1061
39528 * self.tabixfile = None
39529 *
39530 * def fetch(self, # <<<<<<<<<<<<<<
39531 * reference=None,
39532 * start=None,
39533 */
39534 __pyx_tuple__132 = PyTuple_Pack(5, __pyx_n_s_self, __pyx_n_s_reference, __pyx_n_s_start, __pyx_n_s_end, __pyx_n_s_region); if (unlikely(!__pyx_tuple__132)) __PYX_ERR(0, 1061, __pyx_L1_error)
39535 __Pyx_GOTREF(__pyx_tuple__132);
39536 __Pyx_GIVEREF(__pyx_tuple__132);
39537 __pyx_codeobj__133 = (PyObject*)__Pyx_PyCode_New(5, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__132, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_fetch, 1061, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__133)) __PYX_ERR(0, 1061, __pyx_L1_error)
39538 __pyx_tuple__134 = PyTuple_Pack(4, Py_None, Py_None, Py_None, Py_None); if (unlikely(!__pyx_tuple__134)) __PYX_ERR(0, 1061, __pyx_L1_error)
39539 __Pyx_GOTREF(__pyx_tuple__134);
39540 __Pyx_GIVEREF(__pyx_tuple__134);
39541
39542 /* "pysam/libcvcf.pyx":1075
39543 * parser = asVCFRecord(self))
39544 *
39545 * def validate(self, record): # <<<<<<<<<<<<<<
39546 * '''validate vcf record.
39547 *
39548 */
39549 __pyx_tuple__135 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_record); if (unlikely(!__pyx_tuple__135)) __PYX_ERR(0, 1075, __pyx_L1_error)
39550 __Pyx_GOTREF(__pyx_tuple__135);
39551 __Pyx_GIVEREF(__pyx_tuple__135);
39552 __pyx_codeobj__136 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__135, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcvcf_pyx, __pyx_n_s_validate, 1075, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__136)) __PYX_ERR(0, 1075, __pyx_L1_error)
39553
39554 /* "(tree fragment)":1
39555 * def __pyx_unpickle_asVCFRecord(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
39556 * cdef object __pyx_PickleError
39557 * cdef object __pyx_result
39558 */
39559 __pyx_tuple__137 = PyTuple_Pack(5, __pyx_n_s_pyx_type, __pyx_n_s_pyx_checksum, __pyx_n_s_pyx_state, __pyx_n_s_pyx_PickleError, __pyx_n_s_pyx_result); if (unlikely(!__pyx_tuple__137)) __PYX_ERR(1, 1, __pyx_L1_error)
39560 __Pyx_GOTREF(__pyx_tuple__137);
39561 __Pyx_GIVEREF(__pyx_tuple__137);
39562 __pyx_codeobj__138 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__137, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_asVCFRecord, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__138)) __PYX_ERR(1, 1, __pyx_L1_error)
39563 __Pyx_RefNannyFinishContext();
39564 return 0;
39565 __pyx_L1_error:;
39566 __Pyx_RefNannyFinishContext();
39567 return -1;
39568 }
39569 /* #### Code section: init_constants ### */
39570
39571 static CYTHON_SMALL_CODE int __Pyx_InitConstants(void) {
39572 if (__Pyx_CreateStringTabAndInitStrings() < 0) __PYX_ERR(0, 1, __pyx_L1_error);
39573 __pyx_float_0_0 = PyFloat_FromDouble(0.0); if (unlikely(!__pyx_float_0_0)) __PYX_ERR(0, 1, __pyx_L1_error)
39574 __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) __PYX_ERR(0, 1, __pyx_L1_error)
39575 __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) __PYX_ERR(0, 1, __pyx_L1_error)
39576 __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) __PYX_ERR(0, 1, __pyx_L1_error)
39577 __pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) __PYX_ERR(0, 1, __pyx_L1_error)
39578 __pyx_int_4 = PyInt_FromLong(4); if (unlikely(!__pyx_int_4)) __PYX_ERR(0, 1, __pyx_L1_error)
39579 __pyx_int_5 = PyInt_FromLong(5); if (unlikely(!__pyx_int_5)) __PYX_ERR(0, 1, __pyx_L1_error)
39580 __pyx_int_6 = PyInt_FromLong(6); if (unlikely(!__pyx_int_6)) __PYX_ERR(0, 1, __pyx_L1_error)
39581 __pyx_int_7 = PyInt_FromLong(7); if (unlikely(!__pyx_int_7)) __PYX_ERR(0, 1, __pyx_L1_error)
39582 __pyx_int_8 = PyInt_FromLong(8); if (unlikely(!__pyx_int_8)) __PYX_ERR(0, 1, __pyx_L1_error)
39583 __pyx_int_9 = PyInt_FromLong(9); if (unlikely(!__pyx_int_9)) __PYX_ERR(0, 1, __pyx_L1_error)
39584 __pyx_int_10 = PyInt_FromLong(10); if (unlikely(!__pyx_int_10)) __PYX_ERR(0, 1, __pyx_L1_error)
39585 __pyx_int_11 = PyInt_FromLong(11); if (unlikely(!__pyx_int_11)) __PYX_ERR(0, 1, __pyx_L1_error)
39586 __pyx_int_12 = PyInt_FromLong(12); if (unlikely(!__pyx_int_12)) __PYX_ERR(0, 1, __pyx_L1_error)
39587 __pyx_int_13 = PyInt_FromLong(13); if (unlikely(!__pyx_int_13)) __PYX_ERR(0, 1, __pyx_L1_error)
39588 __pyx_int_14 = PyInt_FromLong(14); if (unlikely(!__pyx_int_14)) __PYX_ERR(0, 1, __pyx_L1_error)
39589 __pyx_int_15 = PyInt_FromLong(15); if (unlikely(!__pyx_int_15)) __PYX_ERR(0, 1, __pyx_L1_error)
39590 __pyx_int_16 = PyInt_FromLong(16); if (unlikely(!__pyx_int_16)) __PYX_ERR(0, 1, __pyx_L1_error)
39591 __pyx_int_17 = PyInt_FromLong(17); if (unlikely(!__pyx_int_17)) __PYX_ERR(0, 1, __pyx_L1_error)
39592 __pyx_int_18 = PyInt_FromLong(18); if (unlikely(!__pyx_int_18)) __PYX_ERR(0, 1, __pyx_L1_error)
39593 __pyx_int_19 = PyInt_FromLong(19); if (unlikely(!__pyx_int_19)) __PYX_ERR(0, 1, __pyx_L1_error)
39594 __pyx_int_20 = PyInt_FromLong(20); if (unlikely(!__pyx_int_20)) __PYX_ERR(0, 1, __pyx_L1_error)
39595 __pyx_int_21 = PyInt_FromLong(21); if (unlikely(!__pyx_int_21)) __PYX_ERR(0, 1, __pyx_L1_error)
39596 __pyx_int_22 = PyInt_FromLong(22); if (unlikely(!__pyx_int_22)) __PYX_ERR(0, 1, __pyx_L1_error)
39597 __pyx_int_23 = PyInt_FromLong(23); if (unlikely(!__pyx_int_23)) __PYX_ERR(0, 1, __pyx_L1_error)
39598 __pyx_int_24 = PyInt_FromLong(24); if (unlikely(!__pyx_int_24)) __PYX_ERR(0, 1, __pyx_L1_error)
39599 __pyx_int_25 = PyInt_FromLong(25); if (unlikely(!__pyx_int_25)) __PYX_ERR(0, 1, __pyx_L1_error)
39600 __pyx_int_26 = PyInt_FromLong(26); if (unlikely(!__pyx_int_26)) __PYX_ERR(0, 1, __pyx_L1_error)
39601 __pyx_int_27 = PyInt_FromLong(27); if (unlikely(!__pyx_int_27)) __PYX_ERR(0, 1, __pyx_L1_error)
39602 __pyx_int_28 = PyInt_FromLong(28); if (unlikely(!__pyx_int_28)) __PYX_ERR(0, 1, __pyx_L1_error)
39603 __pyx_int_29 = PyInt_FromLong(29); if (unlikely(!__pyx_int_29)) __PYX_ERR(0, 1, __pyx_L1_error)
39604 __pyx_int_30 = PyInt_FromLong(30); if (unlikely(!__pyx_int_30)) __PYX_ERR(0, 1, __pyx_L1_error)
39605 __pyx_int_31 = PyInt_FromLong(31); if (unlikely(!__pyx_int_31)) __PYX_ERR(0, 1, __pyx_L1_error)
39606 __pyx_int_32 = PyInt_FromLong(32); if (unlikely(!__pyx_int_32)) __PYX_ERR(0, 1, __pyx_L1_error)
39607 __pyx_int_33 = PyInt_FromLong(33); if (unlikely(!__pyx_int_33)) __PYX_ERR(0, 1, __pyx_L1_error)
39608 __pyx_int_40 = PyInt_FromLong(40); if (unlikely(!__pyx_int_40)) __PYX_ERR(0, 1, __pyx_L1_error)
39609 __pyx_int_100 = PyInt_FromLong(100); if (unlikely(!__pyx_int_100)) __PYX_ERR(0, 1, __pyx_L1_error)
39610 __pyx_int_29527880 = PyInt_FromLong(29527880L); if (unlikely(!__pyx_int_29527880)) __PYX_ERR(0, 1, __pyx_L1_error)
39611 __pyx_int_214161357 = PyInt_FromLong(214161357L); if (unlikely(!__pyx_int_214161357)) __PYX_ERR(0, 1, __pyx_L1_error)
39612 __pyx_int_239654613 = PyInt_FromLong(239654613L); if (unlikely(!__pyx_int_239654613)) __PYX_ERR(0, 1, __pyx_L1_error)
39613 __pyx_int_3000000000 = PyInt_FromString((char *)"3000000000", 0, 0); if (unlikely(!__pyx_int_3000000000)) __PYX_ERR(0, 1, __pyx_L1_error)
39614 __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) __PYX_ERR(0, 1, __pyx_L1_error)
39615 return 0;
39616 __pyx_L1_error:;
39617 return -1;
39618 }
39619 /* #### Code section: init_globals ### */
39620
39621 static CYTHON_SMALL_CODE int __Pyx_InitGlobals(void) {
39622 /* AssertionsEnabled.init */
39623 if (likely(__Pyx_init_assertions_enabled() == 0)); else
39624
39625 if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1, __pyx_L1_error)
39626
39627 return 0;
39628 __pyx_L1_error:;
39629 return -1;
39630 }
39631 /* #### Code section: init_module ### */
39632
39633 static CYTHON_SMALL_CODE int __Pyx_modinit_global_init_code(void); /*proto*/
39634 static CYTHON_SMALL_CODE int __Pyx_modinit_variable_export_code(void); /*proto*/
39635 static CYTHON_SMALL_CODE int __Pyx_modinit_function_export_code(void); /*proto*/
39636 static CYTHON_SMALL_CODE int __Pyx_modinit_type_init_code(void); /*proto*/
39637 static CYTHON_SMALL_CODE int __Pyx_modinit_type_import_code(void); /*proto*/
39638 static CYTHON_SMALL_CODE int __Pyx_modinit_variable_import_code(void); /*proto*/
39639 static CYTHON_SMALL_CODE int __Pyx_modinit_function_import_code(void); /*proto*/
39640
39641 static int __Pyx_modinit_global_init_code(void) {
39642 __Pyx_RefNannyDeclarations
39643 __Pyx_RefNannySetupContext("__Pyx_modinit_global_init_code", 0);
39644 /*--- Global init code ---*/
39645 __Pyx_RefNannyFinishContext();
39646 return 0;
39647 }
39648
39649 static int __Pyx_modinit_variable_export_code(void) {
39650 __Pyx_RefNannyDeclarations
39651 __Pyx_RefNannySetupContext("__Pyx_modinit_variable_export_code", 0);
39652 /*--- Variable export code ---*/
39653 __Pyx_RefNannyFinishContext();
39654 return 0;
39655 }
39656
39657 static int __Pyx_modinit_function_export_code(void) {
39658 __Pyx_RefNannyDeclarations
39659 __Pyx_RefNannySetupContext("__Pyx_modinit_function_export_code", 0);
39660 /*--- Function export code ---*/
39661 __Pyx_RefNannyFinishContext();
39662 return 0;
39663 }
39664
39665 static int __Pyx_modinit_type_init_code(void) {
39666 __Pyx_RefNannyDeclarations
39667 PyObject *__pyx_t_1 = NULL;
39668 PyObject *__pyx_t_2 = NULL;
39669 PyObject *__pyx_t_3 = NULL;
39670 int __pyx_lineno = 0;
39671 const char *__pyx_filename = NULL;
39672 int __pyx_clineno = 0;
39673 __Pyx_RefNannySetupContext("__Pyx_modinit_type_init_code", 0);
39674 /*--- Type init code ---*/
39675 __pyx_t_1 = PyImport_ImportModule("pysam.libctabixproxies"); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1, __pyx_L1_error)
39676 __Pyx_GOTREF(__pyx_t_1);
39677 __pyx_ptype_5pysam_16libctabixproxies_TupleProxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "TupleProxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_TupleProxy) __PYX_ERR(0, 1, __pyx_L1_error)
39678 __pyx_vtabptr_5pysam_16libctabixproxies_TupleProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_TupleProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_TupleProxy)) __PYX_ERR(0, 1, __pyx_L1_error)
39679 __pyx_vtabptr_5pysam_7libcvcf_VCFRecord = &__pyx_vtable_5pysam_7libcvcf_VCFRecord;
39680 __pyx_vtable_5pysam_7libcvcf_VCFRecord.__pyx_base = *__pyx_vtabptr_5pysam_16libctabixproxies_TupleProxy;
39681 __pyx_vtable_5pysam_7libcvcf_VCFRecord.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t))__pyx_f_5pysam_7libcvcf_9VCFRecord_update;
39682 #if CYTHON_USE_TYPE_SPECS
39683 __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_16libctabixproxies_TupleProxy); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 104, __pyx_L1_error)
39684 __Pyx_GOTREF(__pyx_t_2);
39685 __pyx_ptype_5pysam_7libcvcf_VCFRecord = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_7libcvcf_VCFRecord_spec, __pyx_t_2);
39686 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
39687 if (unlikely(!__pyx_ptype_5pysam_7libcvcf_VCFRecord)) __PYX_ERR(0, 104, __pyx_L1_error)
39688 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_7libcvcf_VCFRecord_spec, __pyx_ptype_5pysam_7libcvcf_VCFRecord) < 0) __PYX_ERR(0, 104, __pyx_L1_error)
39689 #else
39690 __pyx_ptype_5pysam_7libcvcf_VCFRecord = &__pyx_type_5pysam_7libcvcf_VCFRecord;
39691 #endif
39692 #if !CYTHON_COMPILING_IN_LIMITED_API
39693 __pyx_ptype_5pysam_7libcvcf_VCFRecord->tp_base = __pyx_ptype_5pysam_16libctabixproxies_TupleProxy;
39694 #endif
39695 #if !CYTHON_USE_TYPE_SPECS
39696 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_7libcvcf_VCFRecord) < 0) __PYX_ERR(0, 104, __pyx_L1_error)
39697 #endif
39698 #if PY_MAJOR_VERSION < 3
39699 __pyx_ptype_5pysam_7libcvcf_VCFRecord->tp_print = 0;
39700 #endif
39701 #if !CYTHON_COMPILING_IN_LIMITED_API
39702 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_7libcvcf_VCFRecord->tp_dictoffset && __pyx_ptype_5pysam_7libcvcf_VCFRecord->tp_getattro == PyObject_GenericGetAttr)) {
39703 __pyx_ptype_5pysam_7libcvcf_VCFRecord->tp_getattro = __Pyx_PyObject_GenericGetAttr;
39704 }
39705 #endif
39706 if (__Pyx_SetVtable(__pyx_ptype_5pysam_7libcvcf_VCFRecord, __pyx_vtabptr_5pysam_7libcvcf_VCFRecord) < 0) __PYX_ERR(0, 104, __pyx_L1_error)
39707 #if !CYTHON_COMPILING_IN_LIMITED_API
39708 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_7libcvcf_VCFRecord) < 0) __PYX_ERR(0, 104, __pyx_L1_error)
39709 #endif
39710 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_VCFRecord, (PyObject *) __pyx_ptype_5pysam_7libcvcf_VCFRecord) < 0) __PYX_ERR(0, 104, __pyx_L1_error)
39711 #if !CYTHON_COMPILING_IN_LIMITED_API
39712 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_7libcvcf_VCFRecord) < 0) __PYX_ERR(0, 104, __pyx_L1_error)
39713 #endif
39714 __pyx_t_2 = PyImport_ImportModule("pysam.libctabix"); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1, __pyx_L1_error)
39715 __Pyx_GOTREF(__pyx_t_2);
39716 __pyx_ptype_5pysam_9libctabix_Parser = __Pyx_ImportType_3_0_11(__pyx_t_2, "pysam.libctabix", "Parser", sizeof(struct __pyx_obj_5pysam_9libctabix_Parser), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_Parser),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_Parser) __PYX_ERR(0, 1, __pyx_L1_error)
39717 __pyx_vtabptr_5pysam_9libctabix_Parser = (struct __pyx_vtabstruct_5pysam_9libctabix_Parser*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_Parser); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_Parser)) __PYX_ERR(0, 1, __pyx_L1_error)
39718 __pyx_vtabptr_5pysam_7libcvcf_asVCFRecord = &__pyx_vtable_5pysam_7libcvcf_asVCFRecord;
39719 __pyx_vtable_5pysam_7libcvcf_asVCFRecord.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_Parser;
39720 __pyx_vtable_5pysam_7libcvcf_asVCFRecord.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_7libcvcf_11asVCFRecord_parse;
39721 #if CYTHON_USE_TYPE_SPECS
39722 __pyx_t_3 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_Parser); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 241, __pyx_L1_error)
39723 __Pyx_GOTREF(__pyx_t_3);
39724 __pyx_ptype_5pysam_7libcvcf_asVCFRecord = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_7libcvcf_asVCFRecord_spec, __pyx_t_3);
39725 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
39726 if (unlikely(!__pyx_ptype_5pysam_7libcvcf_asVCFRecord)) __PYX_ERR(0, 241, __pyx_L1_error)
39727 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_7libcvcf_asVCFRecord_spec, __pyx_ptype_5pysam_7libcvcf_asVCFRecord) < 0) __PYX_ERR(0, 241, __pyx_L1_error)
39728 #else
39729 __pyx_ptype_5pysam_7libcvcf_asVCFRecord = &__pyx_type_5pysam_7libcvcf_asVCFRecord;
39730 #endif
39731 #if !CYTHON_COMPILING_IN_LIMITED_API
39732 __pyx_ptype_5pysam_7libcvcf_asVCFRecord->tp_base = __pyx_ptype_5pysam_9libctabix_Parser;
39733 #endif
39734 #if !CYTHON_USE_TYPE_SPECS
39735 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_7libcvcf_asVCFRecord) < 0) __PYX_ERR(0, 241, __pyx_L1_error)
39736 #endif
39737 #if PY_MAJOR_VERSION < 3
39738 __pyx_ptype_5pysam_7libcvcf_asVCFRecord->tp_print = 0;
39739 #endif
39740 #if !CYTHON_COMPILING_IN_LIMITED_API
39741 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_7libcvcf_asVCFRecord->tp_dictoffset && __pyx_ptype_5pysam_7libcvcf_asVCFRecord->tp_getattro == PyObject_GenericGetAttr)) {
39742 __pyx_ptype_5pysam_7libcvcf_asVCFRecord->tp_getattro = __Pyx_PyObject_GenericGetAttr;
39743 }
39744 #endif
39745 if (__Pyx_SetVtable(__pyx_ptype_5pysam_7libcvcf_asVCFRecord, __pyx_vtabptr_5pysam_7libcvcf_asVCFRecord) < 0) __PYX_ERR(0, 241, __pyx_L1_error)
39746 #if !CYTHON_COMPILING_IN_LIMITED_API
39747 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_7libcvcf_asVCFRecord) < 0) __PYX_ERR(0, 241, __pyx_L1_error)
39748 #endif
39749 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_asVCFRecord, (PyObject *) __pyx_ptype_5pysam_7libcvcf_asVCFRecord) < 0) __PYX_ERR(0, 241, __pyx_L1_error)
39750 #if !CYTHON_COMPILING_IN_LIMITED_API
39751 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_7libcvcf_asVCFRecord) < 0) __PYX_ERR(0, 241, __pyx_L1_error)
39752 #endif
39753 #if CYTHON_USE_TYPE_SPECS
39754 __pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_7libcvcf___pyx_scope_struct___parse_spec, NULL); if (unlikely(!__pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse)) __PYX_ERR(0, 929, __pyx_L1_error)
39755 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_7libcvcf___pyx_scope_struct___parse_spec, __pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse) < 0) __PYX_ERR(0, 929, __pyx_L1_error)
39756 #else
39757 __pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse = &__pyx_type_5pysam_7libcvcf___pyx_scope_struct___parse;
39758 #endif
39759 #if !CYTHON_COMPILING_IN_LIMITED_API
39760 #endif
39761 #if !CYTHON_USE_TYPE_SPECS
39762 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse) < 0) __PYX_ERR(0, 929, __pyx_L1_error)
39763 #endif
39764 #if PY_MAJOR_VERSION < 3
39765 __pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse->tp_print = 0;
39766 #endif
39767 #if !CYTHON_COMPILING_IN_LIMITED_API
39768 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse->tp_dictoffset && __pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse->tp_getattro == PyObject_GenericGetAttr)) {
39769 __pyx_ptype_5pysam_7libcvcf___pyx_scope_struct___parse->tp_getattro = __Pyx_PyObject_GenericGetAttrNoDict;
39770 }
39771 #endif
39772 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
39773 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
39774 __Pyx_RefNannyFinishContext();
39775 return 0;
39776 __pyx_L1_error:;
39777 __Pyx_XDECREF(__pyx_t_1);
39778 __Pyx_XDECREF(__pyx_t_2);
39779 __Pyx_XDECREF(__pyx_t_3);
39780 __Pyx_RefNannyFinishContext();
39781 return -1;
39782 }
39783
39784 static int __Pyx_modinit_type_import_code(void) {
39785 __Pyx_RefNannyDeclarations
39786 PyObject *__pyx_t_1 = NULL;
39787 int __pyx_lineno = 0;
39788 const char *__pyx_filename = NULL;
39789 int __pyx_clineno = 0;
39790 __Pyx_RefNannySetupContext("__Pyx_modinit_type_import_code", 0);
39791 /*--- Type import code ---*/
39792 __pyx_t_1 = PyImport_ImportModule("pysam.libchtslib"); if (unlikely(!__pyx_t_1)) __PYX_ERR(4, 2706, __pyx_L1_error)
39793 __Pyx_GOTREF(__pyx_t_1);
39794 __pyx_ptype_5pysam_10libchtslib_HTSFile = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libchtslib", "HTSFile", sizeof(struct __pyx_obj_5pysam_10libchtslib_HTSFile), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_10libchtslib_HTSFile),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_10libchtslib_HTSFile) __PYX_ERR(4, 2706, __pyx_L1_error)
39795 __pyx_vtabptr_5pysam_10libchtslib_HTSFile = (struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile*)__Pyx_GetVtable(__pyx_ptype_5pysam_10libchtslib_HTSFile); if (unlikely(!__pyx_vtabptr_5pysam_10libchtslib_HTSFile)) __PYX_ERR(4, 2706, __pyx_L1_error)
39796 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
39797 __pyx_t_1 = PyImport_ImportModule("pysam.libctabix"); if (unlikely(!__pyx_t_1)) __PYX_ERR(5, 48, __pyx_L1_error)
39798 __Pyx_GOTREF(__pyx_t_1);
39799 __pyx_ptype_5pysam_9libctabix_tabix_file_iterator = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "tabix_file_iterator", sizeof(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_tabix_file_iterator) __PYX_ERR(5, 48, __pyx_L1_error)
39800 __pyx_vtabptr_5pysam_9libctabix_tabix_file_iterator = (struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_tabix_file_iterator); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_tabix_file_iterator)) __PYX_ERR(5, 48, __pyx_L1_error)
39801 __pyx_ptype_5pysam_9libctabix_TabixFile = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "TabixFile", sizeof(struct __pyx_obj_5pysam_9libctabix_TabixFile), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_TabixFile),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_TabixFile) __PYX_ERR(5, 61, __pyx_L1_error)
39802 __pyx_vtabptr_5pysam_9libctabix_TabixFile = (struct __pyx_vtabstruct_5pysam_9libctabix_TabixFile*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_TabixFile); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_TabixFile)) __PYX_ERR(5, 61, __pyx_L1_error)
39803 __pyx_ptype_5pysam_9libctabix_asTuple = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "asTuple", sizeof(struct __pyx_obj_5pysam_9libctabix_asTuple), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_asTuple),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_asTuple) __PYX_ERR(5, 77, __pyx_L1_error)
39804 __pyx_vtabptr_5pysam_9libctabix_asTuple = (struct __pyx_vtabstruct_5pysam_9libctabix_asTuple*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_asTuple); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_asTuple)) __PYX_ERR(5, 77, __pyx_L1_error)
39805 __pyx_ptype_5pysam_9libctabix_asGTF = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "asGTF", sizeof(struct __pyx_obj_5pysam_9libctabix_asGTF), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_asGTF),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_asGTF) __PYX_ERR(5, 81, __pyx_L1_error)
39806 __pyx_vtabptr_5pysam_9libctabix_asGTF = (struct __pyx_vtabstruct_5pysam_9libctabix_asGTF*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_asGTF); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_asGTF)) __PYX_ERR(5, 81, __pyx_L1_error)
39807 __pyx_ptype_5pysam_9libctabix_asGFF3 = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "asGFF3", sizeof(struct __pyx_obj_5pysam_9libctabix_asGFF3), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_asGFF3),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_asGFF3) __PYX_ERR(5, 85, __pyx_L1_error)
39808 __pyx_vtabptr_5pysam_9libctabix_asGFF3 = (struct __pyx_vtabstruct_5pysam_9libctabix_asGFF3*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_asGFF3); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_asGFF3)) __PYX_ERR(5, 85, __pyx_L1_error)
39809 __pyx_ptype_5pysam_9libctabix_asBed = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "asBed", sizeof(struct __pyx_obj_5pysam_9libctabix_asBed), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_asBed),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_asBed) __PYX_ERR(5, 89, __pyx_L1_error)
39810 __pyx_vtabptr_5pysam_9libctabix_asBed = (struct __pyx_vtabstruct_5pysam_9libctabix_asBed*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_asBed); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_asBed)) __PYX_ERR(5, 89, __pyx_L1_error)
39811 __pyx_ptype_5pysam_9libctabix_asVCF = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "asVCF", sizeof(struct __pyx_obj_5pysam_9libctabix_asVCF), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_asVCF),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_asVCF) __PYX_ERR(5, 93, __pyx_L1_error)
39812 __pyx_vtabptr_5pysam_9libctabix_asVCF = (struct __pyx_vtabstruct_5pysam_9libctabix_asVCF*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_asVCF); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_asVCF)) __PYX_ERR(5, 93, __pyx_L1_error)
39813 __pyx_ptype_5pysam_9libctabix_TabixIterator = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "TabixIterator", sizeof(struct __pyx_obj_5pysam_9libctabix_TabixIterator), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_TabixIterator),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_TabixIterator) __PYX_ERR(5, 97, __pyx_L1_error)
39814 __pyx_vtabptr_5pysam_9libctabix_TabixIterator = (struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_TabixIterator); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_TabixIterator)) __PYX_ERR(5, 97, __pyx_L1_error)
39815 __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "TabixIteratorParsed", sizeof(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed) __PYX_ERR(5, 105, __pyx_L1_error)
39816 __pyx_vtabptr_5pysam_9libctabix_TabixIteratorParsed = (struct __pyx_vtabstruct_5pysam_9libctabix_TabixIteratorParsed*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_TabixIteratorParsed)) __PYX_ERR(5, 105, __pyx_L1_error)
39817 __pyx_ptype_5pysam_9libctabix_GZIterator = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "GZIterator", sizeof(struct __pyx_obj_5pysam_9libctabix_GZIterator), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_GZIterator),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_GZIterator) __PYX_ERR(5, 109, __pyx_L1_error)
39818 __pyx_vtabptr_5pysam_9libctabix_GZIterator = (struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_GZIterator); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_GZIterator)) __PYX_ERR(5, 109, __pyx_L1_error)
39819 __pyx_ptype_5pysam_9libctabix_GZIteratorHead = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "GZIteratorHead", sizeof(struct __pyx_obj_5pysam_9libctabix_GZIteratorHead), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_GZIteratorHead),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_GZIteratorHead) __PYX_ERR(5, 118, __pyx_L1_error)
39820 __pyx_vtabptr_5pysam_9libctabix_GZIteratorHead = (struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorHead*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_GZIteratorHead); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_GZIteratorHead)) __PYX_ERR(5, 118, __pyx_L1_error)
39821 __pyx_ptype_5pysam_9libctabix_GZIteratorParsed = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "GZIteratorParsed", sizeof(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_GZIteratorParsed) __PYX_ERR(5, 122, __pyx_L1_error)
39822 __pyx_vtabptr_5pysam_9libctabix_GZIteratorParsed = (struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorParsed*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_GZIteratorParsed); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_GZIteratorParsed)) __PYX_ERR(5, 122, __pyx_L1_error)
39823 __pyx_ptype_5pysam_9libctabix_Tabixfile = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabix", "Tabixfile", sizeof(struct __pyx_obj_5pysam_9libctabix_Tabixfile), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_9libctabix_Tabixfile),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_9libctabix_Tabixfile) __PYX_ERR(5, 127, __pyx_L1_error)
39824 __pyx_vtabptr_5pysam_9libctabix_Tabixfile = (struct __pyx_vtabstruct_5pysam_9libctabix_Tabixfile*)__Pyx_GetVtable(__pyx_ptype_5pysam_9libctabix_Tabixfile); if (unlikely(!__pyx_vtabptr_5pysam_9libctabix_Tabixfile)) __PYX_ERR(5, 127, __pyx_L1_error)
39825 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
39826 __pyx_t_1 = PyImport_ImportModule("pysam.libctabixproxies"); if (unlikely(!__pyx_t_1)) __PYX_ERR(6, 27, __pyx_L1_error)
39827 __Pyx_GOTREF(__pyx_t_1);
39828 __pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "TupleProxyIterator", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxyIterator), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxyIterator),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator) __PYX_ERR(6, 27, __pyx_L1_error)
39829 __pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "NamedTupleProxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy) __PYX_ERR(6, 32, __pyx_L1_error)
39830 __pyx_vtabptr_5pysam_16libctabixproxies_NamedTupleProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_NamedTupleProxy)) __PYX_ERR(6, 32, __pyx_L1_error)
39831 __pyx_ptype_5pysam_16libctabixproxies_GTFProxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "GTFProxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_GTFProxy) __PYX_ERR(6, 36, __pyx_L1_error)
39832 __pyx_vtabptr_5pysam_16libctabixproxies_GTFProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_GTFProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_GTFProxy)) __PYX_ERR(6, 36, __pyx_L1_error)
39833 __pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "GFF3Proxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy) __PYX_ERR(6, 42, __pyx_L1_error)
39834 __pyx_vtabptr_5pysam_16libctabixproxies_GFF3Proxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_GFF3Proxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_GFF3Proxy)) __PYX_ERR(6, 42, __pyx_L1_error)
39835 __pyx_ptype_5pysam_16libctabixproxies_BedProxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "BedProxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_BedProxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_BedProxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_BedProxy) __PYX_ERR(6, 46, __pyx_L1_error)
39836 __pyx_vtabptr_5pysam_16libctabixproxies_BedProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_BedProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_BedProxy)) __PYX_ERR(6, 46, __pyx_L1_error)
39837 __pyx_ptype_5pysam_16libctabixproxies_VCFProxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "VCFProxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_VCFProxy) __PYX_ERR(6, 58, __pyx_L1_error)
39838 __pyx_vtabptr_5pysam_16libctabixproxies_VCFProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_VCFProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_VCFProxy)) __PYX_ERR(6, 58, __pyx_L1_error)
39839 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
39840 __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(7, 9, __pyx_L1_error)
39841 __Pyx_GOTREF(__pyx_t_1);
39842 __pyx_ptype_7cpython_4type_type = __Pyx_ImportType_3_0_11(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "type",
39843 #if defined(PYPY_VERSION_NUM) && PYPY_VERSION_NUM < 0x050B0000
39844 sizeof(PyTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyTypeObject),
39845 #elif CYTHON_COMPILING_IN_LIMITED_API
39846 sizeof(PyTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyTypeObject),
39847 #else
39848 sizeof(PyHeapTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyHeapTypeObject),
39849 #endif
39850 __Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_4type_type) __PYX_ERR(7, 9, __pyx_L1_error)
39851 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
39852 __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(8, 8, __pyx_L1_error)
39853 __Pyx_GOTREF(__pyx_t_1);
39854 __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType_3_0_11(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyBoolObject),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_4bool_bool) __PYX_ERR(8, 8, __pyx_L1_error)
39855 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
39856 __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(9, 15, __pyx_L1_error)
39857 __Pyx_GOTREF(__pyx_t_1);
39858 __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType_3_0_11(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyComplexObject),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_7complex_complex) __PYX_ERR(9, 15, __pyx_L1_error)
39859 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
39860 __pyx_t_1 = PyImport_ImportModule("array"); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 69, __pyx_L1_error)
39861 __Pyx_GOTREF(__pyx_t_1);
39862 __pyx_ptype_7cpython_5array_array = __Pyx_ImportType_3_0_11(__pyx_t_1, "array", "array", sizeof(arrayobject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(arrayobject),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_5array_array) __PYX_ERR(3, 69, __pyx_L1_error)
39863 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
39864 __Pyx_RefNannyFinishContext();
39865 return 0;
39866 __pyx_L1_error:;
39867 __Pyx_XDECREF(__pyx_t_1);
39868 __Pyx_RefNannyFinishContext();
39869 return -1;
39870 }
39871
39872 static int __Pyx_modinit_variable_import_code(void) {
39873 __Pyx_RefNannyDeclarations
39874 __Pyx_RefNannySetupContext("__Pyx_modinit_variable_import_code", 0);
39875 /*--- Variable import code ---*/
39876 __Pyx_RefNannyFinishContext();
39877 return 0;
39878 }
39879
39880 static int __Pyx_modinit_function_import_code(void) {
39881 __Pyx_RefNannyDeclarations
39882 PyObject *__pyx_t_1 = NULL;
39883 int __pyx_lineno = 0;
39884 const char *__pyx_filename = NULL;
39885 int __pyx_clineno = 0;
39886 __Pyx_RefNannySetupContext("__Pyx_modinit_function_import_code", 0);
39887 /*--- Function import code ---*/
39888 __pyx_t_1 = PyImport_ImportModule("pysam.libcutils"); if (!__pyx_t_1) __PYX_ERR(0, 1, __pyx_L1_error)
39889 __Pyx_GOTREF(__pyx_t_1);
39890 if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "force_str", (void (**)(void))&__pyx_f_5pysam_9libcutils_force_str, "PyObject *(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_str *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
39891 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
39892 __Pyx_RefNannyFinishContext();
39893 return 0;
39894 __pyx_L1_error:;
39895 __Pyx_XDECREF(__pyx_t_1);
39896 __Pyx_RefNannyFinishContext();
39897 return -1;
39898 }
39899
39900
39901 #if PY_MAJOR_VERSION >= 3
39902 #if CYTHON_PEP489_MULTI_PHASE_INIT
39903 static PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def); /*proto*/
39904 static int __pyx_pymod_exec_libcvcf(PyObject* module); /*proto*/
39905 static PyModuleDef_Slot __pyx_moduledef_slots[] = {
39906 {Py_mod_create, (void*)__pyx_pymod_create},
39907 {Py_mod_exec, (void*)__pyx_pymod_exec_libcvcf},
39908 {0, NULL}
39909 };
39910 #endif
39911
39912 #ifdef __cplusplus
39913 namespace {
39914 struct PyModuleDef __pyx_moduledef =
39915 #else
39916 static struct PyModuleDef __pyx_moduledef =
39917 #endif
39918 {
39919 PyModuleDef_HEAD_INIT,
39920 "libcvcf",
39921 0, /* m_doc */
39922 #if CYTHON_PEP489_MULTI_PHASE_INIT
39923 0, /* m_size */
39924 #elif CYTHON_USE_MODULE_STATE
39925 sizeof(__pyx_mstate), /* m_size */
39926 #else
39927 -1, /* m_size */
39928 #endif
39929 __pyx_methods /* m_methods */,
39930 #if CYTHON_PEP489_MULTI_PHASE_INIT
39931 __pyx_moduledef_slots, /* m_slots */
39932 #else
39933 NULL, /* m_reload */
39934 #endif
39935 #if CYTHON_USE_MODULE_STATE
39936 __pyx_m_traverse, /* m_traverse */
39937 __pyx_m_clear, /* m_clear */
39938 NULL /* m_free */
39939 #else
39940 NULL, /* m_traverse */
39941 NULL, /* m_clear */
39942 NULL /* m_free */
39943 #endif
39944 };
39945 #ifdef __cplusplus
39946 } /* anonymous namespace */
39947 #endif
39948 #endif
39949
39950 #ifndef CYTHON_NO_PYINIT_EXPORT
39951 #define __Pyx_PyMODINIT_FUNC PyMODINIT_FUNC
39952 #elif PY_MAJOR_VERSION < 3
39953 #ifdef __cplusplus
39954 #define __Pyx_PyMODINIT_FUNC extern "C" void
39955 #else
39956 #define __Pyx_PyMODINIT_FUNC void
39957 #endif
39958 #else
39959 #ifdef __cplusplus
39960 #define __Pyx_PyMODINIT_FUNC extern "C" PyObject *
39961 #else
39962 #define __Pyx_PyMODINIT_FUNC PyObject *
39963 #endif
39964 #endif
39965
39966
39967 #if PY_MAJOR_VERSION < 3
39968 __Pyx_PyMODINIT_FUNC initlibcvcf(void) CYTHON_SMALL_CODE; /*proto*/
39969 __Pyx_PyMODINIT_FUNC initlibcvcf(void)
39970 #else
39971 __Pyx_PyMODINIT_FUNC PyInit_libcvcf(void) CYTHON_SMALL_CODE; /*proto*/
39972 __Pyx_PyMODINIT_FUNC PyInit_libcvcf(void)
39973 #if CYTHON_PEP489_MULTI_PHASE_INIT
39974 {
39975 return PyModuleDef_Init(&__pyx_moduledef);
39976 }
39977 static CYTHON_SMALL_CODE int __Pyx_check_single_interpreter(void) {
39978 #if PY_VERSION_HEX >= 0x030700A1
39979 static PY_INT64_T main_interpreter_id = -1;
39980 PY_INT64_T current_id = PyInterpreterState_GetID(PyThreadState_Get()->interp);
39981 if (main_interpreter_id == -1) {
39982 main_interpreter_id = current_id;
39983 return (unlikely(current_id == -1)) ? -1 : 0;
39984 } else if (unlikely(main_interpreter_id != current_id))
39985 #else
39986 static PyInterpreterState *main_interpreter = NULL;
39987 PyInterpreterState *current_interpreter = PyThreadState_Get()->interp;
39988 if (!main_interpreter) {
39989 main_interpreter = current_interpreter;
39990 } else if (unlikely(main_interpreter != current_interpreter))
39991 #endif
39992 {
39993 PyErr_SetString(
39994 PyExc_ImportError,
39995 "Interpreter change detected - this module can only be loaded into one interpreter per process.");
39996 return -1;
39997 }
39998 return 0;
39999 }
40000 #if CYTHON_COMPILING_IN_LIMITED_API
40001 static CYTHON_SMALL_CODE int __Pyx_copy_spec_to_module(PyObject *spec, PyObject *module, const char* from_name, const char* to_name, int allow_none)
40002 #else
40003 static CYTHON_SMALL_CODE int __Pyx_copy_spec_to_module(PyObject *spec, PyObject *moddict, const char* from_name, const char* to_name, int allow_none)
40004 #endif
40005 {
40006 PyObject *value = PyObject_GetAttrString(spec, from_name);
40007 int result = 0;
40008 if (likely(value)) {
40009 if (allow_none || value != Py_None) {
40010 #if CYTHON_COMPILING_IN_LIMITED_API
40011 result = PyModule_AddObject(module, to_name, value);
40012 #else
40013 result = PyDict_SetItemString(moddict, to_name, value);
40014 #endif
40015 }
40016 Py_DECREF(value);
40017 } else if (PyErr_ExceptionMatches(PyExc_AttributeError)) {
40018 PyErr_Clear();
40019 } else {
40020 result = -1;
40021 }
40022 return result;
40023 }
40024 static CYTHON_SMALL_CODE PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def) {
40025 PyObject *module = NULL, *moddict, *modname;
40026 CYTHON_UNUSED_VAR(def);
40027 if (__Pyx_check_single_interpreter())
40028 return NULL;
40029 if (__pyx_m)
40030 return __Pyx_NewRef(__pyx_m);
40031 modname = PyObject_GetAttrString(spec, "name");
40032 if (unlikely(!modname)) goto bad;
40033 module = PyModule_NewObject(modname);
40034 Py_DECREF(modname);
40035 if (unlikely(!module)) goto bad;
40036 #if CYTHON_COMPILING_IN_LIMITED_API
40037 moddict = module;
40038 #else
40039 moddict = PyModule_GetDict(module);
40040 if (unlikely(!moddict)) goto bad;
40041 #endif
40042 if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "loader", "__loader__", 1) < 0)) goto bad;
40043 if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "origin", "__file__", 1) < 0)) goto bad;
40044 if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "parent", "__package__", 1) < 0)) goto bad;
40045 if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "submodule_search_locations", "__path__", 0) < 0)) goto bad;
40046 return module;
40047 bad:
40048 Py_XDECREF(module);
40049 return NULL;
40050 }
40051
40052
40053 static CYTHON_SMALL_CODE int __pyx_pymod_exec_libcvcf(PyObject *__pyx_pyinit_module)
40054 #endif
40055 #endif
40056 {
40057 int stringtab_initialized = 0;
40058 #if CYTHON_USE_MODULE_STATE
40059 int pystate_addmodule_run = 0;
40060 #endif
40061 PyObject *__pyx_t_1 = NULL;
40062 PyObject *__pyx_t_2 = NULL;
40063 PyObject *__pyx_t_3 = NULL;
40064 PyObject *__pyx_t_4 = NULL;
40065 PyObject *__pyx_t_5 = NULL;
40066 int __pyx_lineno = 0;
40067 const char *__pyx_filename = NULL;
40068 int __pyx_clineno = 0;
40069 __Pyx_RefNannyDeclarations
40070 #if CYTHON_PEP489_MULTI_PHASE_INIT
40071 if (__pyx_m) {
40072 if (__pyx_m == __pyx_pyinit_module) return 0;
40073 PyErr_SetString(PyExc_RuntimeError, "Module 'libcvcf' has already been imported. Re-initialisation is not supported.");
40074 return -1;
40075 }
40076 #elif PY_MAJOR_VERSION >= 3
40077 if (__pyx_m) return __Pyx_NewRef(__pyx_m);
40078 #endif
40079 /*--- Module creation code ---*/
40080 #if CYTHON_PEP489_MULTI_PHASE_INIT
40081 __pyx_m = __pyx_pyinit_module;
40082 Py_INCREF(__pyx_m);
40083 #else
40084 #if PY_MAJOR_VERSION < 3
40085 __pyx_m = Py_InitModule4("libcvcf", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
40086 if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error)
40087 #elif CYTHON_USE_MODULE_STATE
40088 __pyx_t_1 = PyModule_Create(&__pyx_moduledef); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1, __pyx_L1_error)
40089 {
40090 int add_module_result = PyState_AddModule(__pyx_t_1, &__pyx_moduledef);
40091 __pyx_t_1 = 0; /* transfer ownership from __pyx_t_1 to "libcvcf" pseudovariable */
40092 if (unlikely((add_module_result < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
40093 pystate_addmodule_run = 1;
40094 }
40095 #else
40096 __pyx_m = PyModule_Create(&__pyx_moduledef);
40097 if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error)
40098 #endif
40099 #endif
40100 CYTHON_UNUSED_VAR(__pyx_t_1);
40101 __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) __PYX_ERR(0, 1, __pyx_L1_error)
40102 Py_INCREF(__pyx_d);
40103 __pyx_b = __Pyx_PyImport_AddModuleRef(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) __PYX_ERR(0, 1, __pyx_L1_error)
40104 __pyx_cython_runtime = __Pyx_PyImport_AddModuleRef((const char *) "cython_runtime"); if (unlikely(!__pyx_cython_runtime)) __PYX_ERR(0, 1, __pyx_L1_error)
40105 if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40106 #if CYTHON_REFNANNY
40107 __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
40108 if (!__Pyx_RefNanny) {
40109 PyErr_Clear();
40110 __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny");
40111 if (!__Pyx_RefNanny)
40112 Py_FatalError("failed to import 'refnanny' module");
40113 }
40114 #endif
40115 __Pyx_RefNannySetupContext("__Pyx_PyMODINIT_FUNC PyInit_libcvcf(void)", 0);
40116 if (__Pyx_check_binary_version(__PYX_LIMITED_VERSION_HEX, __Pyx_get_runtime_version(), CYTHON_COMPILING_IN_LIMITED_API) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40117 #ifdef __Pxy_PyFrame_Initialize_Offsets
40118 __Pxy_PyFrame_Initialize_Offsets();
40119 #endif
40120 __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) __PYX_ERR(0, 1, __pyx_L1_error)
40121 __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) __PYX_ERR(0, 1, __pyx_L1_error)
40122 __pyx_empty_unicode = PyUnicode_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_unicode)) __PYX_ERR(0, 1, __pyx_L1_error)
40123 #ifdef __Pyx_CyFunction_USED
40124 if (__pyx_CyFunction_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40125 #endif
40126 #ifdef __Pyx_FusedFunction_USED
40127 if (__pyx_FusedFunction_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40128 #endif
40129 #ifdef __Pyx_Coroutine_USED
40130 if (__pyx_Coroutine_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40131 #endif
40132 #ifdef __Pyx_Generator_USED
40133 if (__pyx_Generator_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40134 #endif
40135 #ifdef __Pyx_AsyncGen_USED
40136 if (__pyx_AsyncGen_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40137 #endif
40138 #ifdef __Pyx_StopAsyncIteration_USED
40139 if (__pyx_StopAsyncIteration_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40140 #endif
40141 /*--- Library function declarations ---*/
40142 /*--- Threads initialization code ---*/
40143 #if defined(WITH_THREAD) && PY_VERSION_HEX < 0x030700F0 && defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
40144 PyEval_InitThreads();
40145 #endif
40146 /*--- Initialize various global constants etc. ---*/
40147 if (__Pyx_InitConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40148 stringtab_initialized = 1;
40149 if (__Pyx_InitGlobals() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40150 #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
40151 if (__Pyx_init_sys_getdefaultencoding_params() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40152 #endif
40153 if (__pyx_module_is_main_pysam__libcvcf) {
40154 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40155 }
40156 #if PY_MAJOR_VERSION >= 3
40157 {
40158 PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error)
40159 if (!PyDict_GetItemString(modules, "pysam.libcvcf")) {
40160 if (unlikely((PyDict_SetItemString(modules, "pysam.libcvcf", __pyx_m) < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
40161 }
40162 }
40163 #endif
40164 /*--- Builtin init code ---*/
40165 if (__Pyx_InitCachedBuiltins() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40166 /*--- Constants init code ---*/
40167 if (__Pyx_InitCachedConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40168 /*--- Global type/function init code ---*/
40169 (void)__Pyx_modinit_global_init_code();
40170 (void)__Pyx_modinit_variable_export_code();
40171 (void)__Pyx_modinit_function_export_code();
40172 if (unlikely((__Pyx_modinit_type_init_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
40173 if (unlikely((__Pyx_modinit_type_import_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
40174 (void)__Pyx_modinit_variable_import_code();
40175 if (unlikely((__Pyx_modinit_function_import_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
40176 /*--- Execution code ---*/
40177 #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
40178 if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
40179 #endif
40180
40181 /* "pysam/libcvcf.pyx":49
40182 * #
40183 *
40184 * from collections import namedtuple, defaultdict # <<<<<<<<<<<<<<
40185 * from operator import itemgetter
40186 * import sys, re, copy, bisect
40187 */
40188 __pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 49, __pyx_L1_error)
40189 __Pyx_GOTREF(__pyx_t_2);
40190 __Pyx_INCREF(__pyx_n_s_namedtuple);
40191 __Pyx_GIVEREF(__pyx_n_s_namedtuple);
40192 if (__Pyx_PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_namedtuple)) __PYX_ERR(0, 49, __pyx_L1_error);
40193 __Pyx_INCREF(__pyx_n_s_defaultdict);
40194 __Pyx_GIVEREF(__pyx_n_s_defaultdict);
40195 if (__Pyx_PyList_SET_ITEM(__pyx_t_2, 1, __pyx_n_s_defaultdict)) __PYX_ERR(0, 49, __pyx_L1_error);
40196 __pyx_t_3 = __Pyx_Import(__pyx_n_s_collections, __pyx_t_2, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 49, __pyx_L1_error)
40197 __Pyx_GOTREF(__pyx_t_3);
40198 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40199 __pyx_t_2 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_namedtuple); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 49, __pyx_L1_error)
40200 __Pyx_GOTREF(__pyx_t_2);
40201 if (PyDict_SetItem(__pyx_d, __pyx_n_s_namedtuple, __pyx_t_2) < 0) __PYX_ERR(0, 49, __pyx_L1_error)
40202 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40203 __pyx_t_2 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_defaultdict); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 49, __pyx_L1_error)
40204 __Pyx_GOTREF(__pyx_t_2);
40205 if (PyDict_SetItem(__pyx_d, __pyx_n_s_defaultdict, __pyx_t_2) < 0) __PYX_ERR(0, 49, __pyx_L1_error)
40206 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40207 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
40208
40209 /* "pysam/libcvcf.pyx":50
40210 *
40211 * from collections import namedtuple, defaultdict
40212 * from operator import itemgetter # <<<<<<<<<<<<<<
40213 * import sys, re, copy, bisect
40214 *
40215 */
40216 __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 50, __pyx_L1_error)
40217 __Pyx_GOTREF(__pyx_t_3);
40218 __Pyx_INCREF(__pyx_n_s_itemgetter);
40219 __Pyx_GIVEREF(__pyx_n_s_itemgetter);
40220 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 0, __pyx_n_s_itemgetter)) __PYX_ERR(0, 50, __pyx_L1_error);
40221 __pyx_t_2 = __Pyx_Import(__pyx_n_s_operator, __pyx_t_3, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 50, __pyx_L1_error)
40222 __Pyx_GOTREF(__pyx_t_2);
40223 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
40224 __pyx_t_3 = __Pyx_ImportFrom(__pyx_t_2, __pyx_n_s_itemgetter); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 50, __pyx_L1_error)
40225 __Pyx_GOTREF(__pyx_t_3);
40226 if (PyDict_SetItem(__pyx_d, __pyx_n_s_itemgetter, __pyx_t_3) < 0) __PYX_ERR(0, 50, __pyx_L1_error)
40227 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
40228 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40229
40230 /* "pysam/libcvcf.pyx":51
40231 * from collections import namedtuple, defaultdict
40232 * from operator import itemgetter
40233 * import sys, re, copy, bisect # <<<<<<<<<<<<<<
40234 *
40235 * from libc.stdlib cimport atoi
40236 */
40237 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_sys, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 51, __pyx_L1_error)
40238 __Pyx_GOTREF(__pyx_t_2);
40239 if (PyDict_SetItem(__pyx_d, __pyx_n_s_sys, __pyx_t_2) < 0) __PYX_ERR(0, 51, __pyx_L1_error)
40240 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40241 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_re, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 51, __pyx_L1_error)
40242 __Pyx_GOTREF(__pyx_t_2);
40243 if (PyDict_SetItem(__pyx_d, __pyx_n_s_re, __pyx_t_2) < 0) __PYX_ERR(0, 51, __pyx_L1_error)
40244 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40245 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_copy_2, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 51, __pyx_L1_error)
40246 __Pyx_GOTREF(__pyx_t_2);
40247 if (PyDict_SetItem(__pyx_d, __pyx_n_s_copy_2, __pyx_t_2) < 0) __PYX_ERR(0, 51, __pyx_L1_error)
40248 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40249 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_bisect, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 51, __pyx_L1_error)
40250 __Pyx_GOTREF(__pyx_t_2);
40251 if (PyDict_SetItem(__pyx_d, __pyx_n_s_bisect, __pyx_t_2) < 0) __PYX_ERR(0, 51, __pyx_L1_error)
40252 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40253
40254 /* "pysam/libcvcf.pyx":62
40255 * from pysam.libcutils cimport force_str
40256 *
40257 * import pysam # <<<<<<<<<<<<<<
40258 *
40259 * gtsRegEx = re.compile("[|/\\\\]")
40260 */
40261 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_pysam, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 62, __pyx_L1_error)
40262 __Pyx_GOTREF(__pyx_t_2);
40263 if (PyDict_SetItem(__pyx_d, __pyx_n_s_pysam, __pyx_t_2) < 0) __PYX_ERR(0, 62, __pyx_L1_error)
40264 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40265
40266 /* "pysam/libcvcf.pyx":64
40267 * import pysam
40268 *
40269 * gtsRegEx = re.compile("[|/\\\\]") # <<<<<<<<<<<<<<
40270 * alleleRegEx = re.compile('^[ACGTN]+$')
40271 *
40272 */
40273 __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_re); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 64, __pyx_L1_error)
40274 __Pyx_GOTREF(__pyx_t_2);
40275 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_compile); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 64, __pyx_L1_error)
40276 __Pyx_GOTREF(__pyx_t_3);
40277 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40278 __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__35, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 64, __pyx_L1_error)
40279 __Pyx_GOTREF(__pyx_t_2);
40280 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
40281 if (PyDict_SetItem(__pyx_d, __pyx_n_s_gtsRegEx, __pyx_t_2) < 0) __PYX_ERR(0, 64, __pyx_L1_error)
40282 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40283
40284 /* "pysam/libcvcf.pyx":65
40285 *
40286 * gtsRegEx = re.compile("[|/\\\\]")
40287 * alleleRegEx = re.compile('^[ACGTN]+$') # <<<<<<<<<<<<<<
40288 *
40289 * # Utility function. Uses 0-based coordinates
40290 */
40291 __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_re); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 65, __pyx_L1_error)
40292 __Pyx_GOTREF(__pyx_t_2);
40293 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_compile); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 65, __pyx_L1_error)
40294 __Pyx_GOTREF(__pyx_t_3);
40295 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40296 __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__36, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 65, __pyx_L1_error)
40297 __Pyx_GOTREF(__pyx_t_2);
40298 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
40299 if (PyDict_SetItem(__pyx_d, __pyx_n_s_alleleRegEx, __pyx_t_2) < 0) __PYX_ERR(0, 65, __pyx_L1_error)
40300 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40301
40302 /* "pysam/libcvcf.pyx":68
40303 *
40304 * # Utility function. Uses 0-based coordinates
40305 * def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<<
40306 * # obtain sequence from .fa file, without truncation
40307 * if end<=start: return ""
40308 */
40309 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_1get_sequence, 0, __pyx_n_s_get_sequence, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__38)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 68, __pyx_L1_error)
40310 __Pyx_GOTREF(__pyx_t_2);
40311 if (PyDict_SetItem(__pyx_d, __pyx_n_s_get_sequence, __pyx_t_2) < 0) __PYX_ERR(0, 68, __pyx_L1_error)
40312 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40313
40314 /* "pysam/libcvcf.pyx":78
40315 *
40316 * # Utility function. Parses a region string
40317 * def parse_regions( string ): # <<<<<<<<<<<<<<
40318 * result = []
40319 * for r in string.split(','):
40320 */
40321 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3parse_regions, 0, __pyx_n_s_parse_regions, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__40)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 78, __pyx_L1_error)
40322 __Pyx_GOTREF(__pyx_t_2);
40323 if (PyDict_SetItem(__pyx_d, __pyx_n_s_parse_regions, __pyx_t_2) < 0) __PYX_ERR(0, 78, __pyx_L1_error)
40324 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40325
40326 /* "pysam/libcvcf.pyx":96
40327 *
40328 *
40329 * FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue') # <<<<<<<<<<<<<<
40330 *
40331 * ###########################################################################################################
40332 */
40333 __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_namedtuple); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 96, __pyx_L1_error)
40334 __Pyx_GOTREF(__pyx_t_2);
40335 __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__41, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 96, __pyx_L1_error)
40336 __Pyx_GOTREF(__pyx_t_3);
40337 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
40338 if (PyDict_SetItem(__pyx_d, __pyx_n_s_FORMAT, __pyx_t_3) < 0) __PYX_ERR(0, 96, __pyx_L1_error)
40339 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
40340
40341 /* "pysam/libcvcf.pyx":134
40342 * self.encoding = vcf.encoding
40343 *
40344 * def error(self, line, error, opt=None): # <<<<<<<<<<<<<<
40345 * '''raise error.'''
40346 * # pass to vcf file for error handling
40347 */
40348 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_9VCFRecord_5error, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_VCFRecord_error, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__43)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 134, __pyx_L1_error)
40349 __Pyx_GOTREF(__pyx_t_3);
40350 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_tuple__44);
40351 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_7libcvcf_VCFRecord, __pyx_n_s_error, __pyx_t_3) < 0) __PYX_ERR(0, 134, __pyx_L1_error)
40352 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
40353 PyType_Modified(__pyx_ptype_5pysam_7libcvcf_VCFRecord);
40354
40355 /* "(tree fragment)":1
40356 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
40357 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
40358 * def __setstate_cython__(self, __pyx_state):
40359 */
40360 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_9VCFRecord_11__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_VCFRecord___reduce_cython, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__46)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error)
40361 __Pyx_GOTREF(__pyx_t_3);
40362 if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
40363 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
40364
40365 /* "(tree fragment)":3
40366 * def __reduce_cython__(self):
40367 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
40368 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
40369 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
40370 */
40371 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_9VCFRecord_13__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_VCFRecord___setstate_cython, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__48)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 3, __pyx_L1_error)
40372 __Pyx_GOTREF(__pyx_t_3);
40373 if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_3) < 0) __PYX_ERR(1, 3, __pyx_L1_error)
40374 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
40375
40376 /* "(tree fragment)":1
40377 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
40378 * cdef tuple state
40379 * cdef object _dict
40380 */
40381 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_11asVCFRecord_3__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asVCFRecord___reduce_cython, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__50)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error)
40382 __Pyx_GOTREF(__pyx_t_3);
40383 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_7libcvcf_asVCFRecord, __pyx_n_s_reduce_cython, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
40384 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
40385 PyType_Modified(__pyx_ptype_5pysam_7libcvcf_asVCFRecord);
40386
40387 /* "(tree fragment)":16
40388 * else:
40389 * return __pyx_unpickle_asVCFRecord, (type(self), 0xe48d6d5, state)
40390 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
40391 * __pyx_unpickle_asVCFRecord__set_state(self, __pyx_state)
40392 */
40393 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_11asVCFRecord_5__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asVCFRecord___setstate_cython, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__51)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 16, __pyx_L1_error)
40394 __Pyx_GOTREF(__pyx_t_3);
40395 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_7libcvcf_asVCFRecord, __pyx_n_s_setstate_cython, __pyx_t_3) < 0) __PYX_ERR(1, 16, __pyx_L1_error)
40396 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
40397 PyType_Modified(__pyx_ptype_5pysam_7libcvcf_asVCFRecord);
40398
40399 /* "pysam/libcvcf.pyx":253
40400 * return r
40401 *
40402 * class VCF(object): # <<<<<<<<<<<<<<
40403 *
40404 * # types
40405 */
40406 __pyx_t_3 = __Pyx_PEP560_update_bases(__pyx_tuple__53); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 253, __pyx_L1_error)
40407 __Pyx_GOTREF(__pyx_t_3);
40408 __pyx_t_2 = __Pyx_CalculateMetaclass(NULL, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 253, __pyx_L1_error)
40409 __Pyx_GOTREF(__pyx_t_2);
40410 __pyx_t_4 = __Pyx_Py3MetaclassPrepare(__pyx_t_2, __pyx_t_3, __pyx_n_s_VCF, __pyx_n_s_VCF, (PyObject *) NULL, __pyx_n_s_pysam_libcvcf, (PyObject *) NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 253, __pyx_L1_error)
40411 __Pyx_GOTREF(__pyx_t_4);
40412 if (__pyx_t_3 != __pyx_tuple__53) {
40413 if (unlikely((PyDict_SetItemString(__pyx_t_4, "__orig_bases__", __pyx_tuple__53) < 0))) __PYX_ERR(0, 253, __pyx_L1_error)
40414 }
40415
40416 /* "pysam/libcvcf.pyx":256
40417 *
40418 * # types
40419 * NT_UNKNOWN = 0 # <<<<<<<<<<<<<<
40420 * NT_NUMBER = 1
40421 * NT_ALLELES = 2
40422 */
40423 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_NT_UNKNOWN, __pyx_int_0) < 0) __PYX_ERR(0, 256, __pyx_L1_error)
40424
40425 /* "pysam/libcvcf.pyx":257
40426 * # types
40427 * NT_UNKNOWN = 0
40428 * NT_NUMBER = 1 # <<<<<<<<<<<<<<
40429 * NT_ALLELES = 2
40430 * NT_NR_ALLELES = 3
40431 */
40432 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_NT_NUMBER, __pyx_int_1) < 0) __PYX_ERR(0, 257, __pyx_L1_error)
40433
40434 /* "pysam/libcvcf.pyx":258
40435 * NT_UNKNOWN = 0
40436 * NT_NUMBER = 1
40437 * NT_ALLELES = 2 # <<<<<<<<<<<<<<
40438 * NT_NR_ALLELES = 3
40439 * NT_GENOTYPES = 4
40440 */
40441 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_NT_ALLELES, __pyx_int_2) < 0) __PYX_ERR(0, 258, __pyx_L1_error)
40442
40443 /* "pysam/libcvcf.pyx":259
40444 * NT_NUMBER = 1
40445 * NT_ALLELES = 2
40446 * NT_NR_ALLELES = 3 # <<<<<<<<<<<<<<
40447 * NT_GENOTYPES = 4
40448 * NT_PHASED_GENOTYPES = 5
40449 */
40450 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_NT_NR_ALLELES, __pyx_int_3) < 0) __PYX_ERR(0, 259, __pyx_L1_error)
40451
40452 /* "pysam/libcvcf.pyx":260
40453 * NT_ALLELES = 2
40454 * NT_NR_ALLELES = 3
40455 * NT_GENOTYPES = 4 # <<<<<<<<<<<<<<
40456 * NT_PHASED_GENOTYPES = 5
40457 *
40458 */
40459 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_NT_GENOTYPES, __pyx_int_4) < 0) __PYX_ERR(0, 260, __pyx_L1_error)
40460
40461 /* "pysam/libcvcf.pyx":261
40462 * NT_NR_ALLELES = 3
40463 * NT_GENOTYPES = 4
40464 * NT_PHASED_GENOTYPES = 5 # <<<<<<<<<<<<<<
40465 *
40466 * _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier",
40467 */
40468 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_NT_PHASED_GENOTYPES, __pyx_int_5) < 0) __PYX_ERR(0, 261, __pyx_L1_error)
40469
40470 /* "pysam/libcvcf.pyx":263
40471 * NT_PHASED_GENOTYPES = 5
40472 *
40473 * _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier", # <<<<<<<<<<<<<<
40474 * 1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string",
40475 * 2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s",
40476 */
40477 __pyx_t_5 = __Pyx_PyDict_NewPresized(34); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 263, __pyx_L1_error)
40478 __Pyx_GOTREF(__pyx_t_5);
40479 if (PyDict_SetItem(__pyx_t_5, __pyx_int_0, __pyx_kp_u_UNKNOWN_FORMAT_STRING_Unknown_fi) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40480 if (PyDict_SetItem(__pyx_t_5, __pyx_int_1, __pyx_kp_u_BADLY_FORMATTED_FORMAT_STRING_Fo) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40481 if (PyDict_SetItem(__pyx_t_5, __pyx_int_2, __pyx_kp_u_BADLY_FORMATTED_HEADING_Did_not) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40482 if (PyDict_SetItem(__pyx_t_5, __pyx_int_3, __pyx_kp_u_BAD_NUMBER_OF_COLUMNS_Wrong_numb) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40483 if (PyDict_SetItem(__pyx_t_5, __pyx_int_4, __pyx_kp_u_POS_NOT_NUMERICAL_Position_colum) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40484 if (PyDict_SetItem(__pyx_t_5, __pyx_int_5, __pyx_kp_u_UNKNOWN_CHAR_IN_REF_Unknown_char) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40485 if (PyDict_SetItem(__pyx_t_5, __pyx_int_6, __pyx_kp_u_V33_BAD_REF_Reference_should_be) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40486 if (PyDict_SetItem(__pyx_t_5, __pyx_int_7, __pyx_kp_u_V33_BAD_ALLELE_Cannot_interpret) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40487 if (PyDict_SetItem(__pyx_t_5, __pyx_int_8, __pyx_kp_u_POS_NOT_POSITIVE_Position_field) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40488 if (PyDict_SetItem(__pyx_t_5, __pyx_int_9, __pyx_kp_u_QUAL_NOT_NUMERICAL_Quality_field) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40489 if (PyDict_SetItem(__pyx_t_5, __pyx_int_10, __pyx_kp_u_ERROR_INFO_STRING_Error_while_pa) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40490 if (PyDict_SetItem(__pyx_t_5, __pyx_int_11, __pyx_kp_u_ERROR_UNKNOWN_KEY_Unknown_key_s) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40491 if (PyDict_SetItem(__pyx_t_5, __pyx_int_12, __pyx_kp_u_ERROR_FORMAT_NOT_NUMERICAL_Expec) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40492 if (PyDict_SetItem(__pyx_t_5, __pyx_int_13, __pyx_kp_u_ERROR_FORMAT_NOT_CHAR_Eexpected) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40493 if (PyDict_SetItem(__pyx_t_5, __pyx_int_14, __pyx_kp_u_FILTER_NOT_DEFINED_Identifier_s) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40494 if (PyDict_SetItem(__pyx_t_5, __pyx_int_15, __pyx_kp_u_FORMAT_NOT_DEFINED_Identifier_s) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40495 if (PyDict_SetItem(__pyx_t_5, __pyx_int_16, __pyx_kp_u_BAD_NUMBER_OF_VALUES_Found_too_m) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40496 if (PyDict_SetItem(__pyx_t_5, __pyx_int_17, __pyx_kp_u_BAD_NUMBER_OF_PARAMETERS_Found_u) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40497 if (PyDict_SetItem(__pyx_t_5, __pyx_int_18, __pyx_kp_u_BAD_GENOTYPE_Cannot_parse_genoty) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40498 if (PyDict_SetItem(__pyx_t_5, __pyx_int_19, __pyx_kp_u_V40_BAD_ALLELE_Bad_allele_found) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40499 if (PyDict_SetItem(__pyx_t_5, __pyx_int_20, __pyx_kp_u_MISSING_REF_Reference_allele_mis) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40500 if (PyDict_SetItem(__pyx_t_5, __pyx_int_21, __pyx_kp_u_V33_UNMATCHED_DELETION_Deleted_s) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40501 if (PyDict_SetItem(__pyx_t_5, __pyx_int_22, __pyx_kp_u_V40_MISSING_ANGLE_BRACKETS_Forma) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40502 if (PyDict_SetItem(__pyx_t_5, __pyx_int_23, __pyx_kp_u_FORMAT_MISSING_QUOTES_Descriptio) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40503 if (PyDict_SetItem(__pyx_t_5, __pyx_int_24, __pyx_kp_u_V40_FORMAT_MUST_HAVE_NAMED_FIELD_2) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40504 if (PyDict_SetItem(__pyx_t_5, __pyx_int_25, __pyx_kp_u_HEADING_NOT_SEPARATED_BY_TABS_He) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40505 if (PyDict_SetItem(__pyx_t_5, __pyx_int_26, __pyx_kp_u_WRONG_REF_Wrong_reference_s) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40506 if (PyDict_SetItem(__pyx_t_5, __pyx_int_27, __pyx_kp_u_ERROR_TRAILING_DATA_Numerical_fi) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40507 if (PyDict_SetItem(__pyx_t_5, __pyx_int_28, __pyx_kp_u_BAD_CHR_TAG_Error_calculating_ch) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40508 if (PyDict_SetItem(__pyx_t_5, __pyx_int_29, __pyx_kp_u_ZERO_LENGTH_ALLELE_Found_zero_le) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40509 if (PyDict_SetItem(__pyx_t_5, __pyx_int_30, __pyx_kp_u_MISSING_INDEL_ALLELE_REF_BASE_In) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40510 if (PyDict_SetItem(__pyx_t_5, __pyx_int_31, __pyx_kp_u_ZERO_FOR_NON_FLAG_FIELD_number_s) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40511 if (PyDict_SetItem(__pyx_t_5, __pyx_int_32, __pyx_kp_u_ERROR_FORMAT_NOT_INTEGER_Expecte) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40512 if (PyDict_SetItem(__pyx_t_5, __pyx_int_33, __pyx_kp_u_ERROR_FLAG_HAS_VALUE_Flag_fields) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40513 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_errors, __pyx_t_5) < 0) __PYX_ERR(0, 263, __pyx_L1_error)
40514 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40515
40516 /* "pysam/libcvcf.pyx":300
40517 *
40518 * # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields
40519 * _header = [] # <<<<<<<<<<<<<<
40520 *
40521 * # version number; 33=v3.3; 40=v4.0
40522 */
40523 __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 300, __pyx_L1_error)
40524 __Pyx_GOTREF(__pyx_t_5);
40525 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_header, __pyx_t_5) < 0) __PYX_ERR(0, 300, __pyx_L1_error)
40526 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40527
40528 /* "pysam/libcvcf.pyx":303
40529 *
40530 * # version number; 33=v3.3; 40=v4.0
40531 * _version = 40 # <<<<<<<<<<<<<<
40532 *
40533 * # info, filter and format data
40534 */
40535 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_version, __pyx_int_40) < 0) __PYX_ERR(0, 303, __pyx_L1_error)
40536
40537 /* "pysam/libcvcf.pyx":306
40538 *
40539 * # info, filter and format data
40540 * _info = {} # <<<<<<<<<<<<<<
40541 * _filter = {}
40542 * _format = {}
40543 */
40544 __pyx_t_5 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 306, __pyx_L1_error)
40545 __Pyx_GOTREF(__pyx_t_5);
40546 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_info, __pyx_t_5) < 0) __PYX_ERR(0, 306, __pyx_L1_error)
40547 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40548
40549 /* "pysam/libcvcf.pyx":307
40550 * # info, filter and format data
40551 * _info = {}
40552 * _filter = {} # <<<<<<<<<<<<<<
40553 * _format = {}
40554 *
40555 */
40556 __pyx_t_5 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 307, __pyx_L1_error)
40557 __Pyx_GOTREF(__pyx_t_5);
40558 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_filter, __pyx_t_5) < 0) __PYX_ERR(0, 307, __pyx_L1_error)
40559 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40560
40561 /* "pysam/libcvcf.pyx":308
40562 * _info = {}
40563 * _filter = {}
40564 * _format = {} # <<<<<<<<<<<<<<
40565 *
40566 * # header; and required columns
40567 */
40568 __pyx_t_5 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 308, __pyx_L1_error)
40569 __Pyx_GOTREF(__pyx_t_5);
40570 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_format_2, __pyx_t_5) < 0) __PYX_ERR(0, 308, __pyx_L1_error)
40571 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40572
40573 /* "pysam/libcvcf.pyx":311
40574 *
40575 * # header; and required columns
40576 * _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"] # <<<<<<<<<<<<<<
40577 * _samples = []
40578 *
40579 */
40580 __pyx_t_5 = PyList_New(9); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 311, __pyx_L1_error)
40581 __Pyx_GOTREF(__pyx_t_5);
40582 __Pyx_INCREF(__pyx_n_u_CHROM);
40583 __Pyx_GIVEREF(__pyx_n_u_CHROM);
40584 if (__Pyx_PyList_SET_ITEM(__pyx_t_5, 0, __pyx_n_u_CHROM)) __PYX_ERR(0, 311, __pyx_L1_error);
40585 __Pyx_INCREF(__pyx_n_u_POS);
40586 __Pyx_GIVEREF(__pyx_n_u_POS);
40587 if (__Pyx_PyList_SET_ITEM(__pyx_t_5, 1, __pyx_n_u_POS)) __PYX_ERR(0, 311, __pyx_L1_error);
40588 __Pyx_INCREF(__pyx_n_u_ID_2);
40589 __Pyx_GIVEREF(__pyx_n_u_ID_2);
40590 if (__Pyx_PyList_SET_ITEM(__pyx_t_5, 2, __pyx_n_u_ID_2)) __PYX_ERR(0, 311, __pyx_L1_error);
40591 __Pyx_INCREF(__pyx_n_u_REF);
40592 __Pyx_GIVEREF(__pyx_n_u_REF);
40593 if (__Pyx_PyList_SET_ITEM(__pyx_t_5, 3, __pyx_n_u_REF)) __PYX_ERR(0, 311, __pyx_L1_error);
40594 __Pyx_INCREF(__pyx_n_u_ALT);
40595 __Pyx_GIVEREF(__pyx_n_u_ALT);
40596 if (__Pyx_PyList_SET_ITEM(__pyx_t_5, 4, __pyx_n_u_ALT)) __PYX_ERR(0, 311, __pyx_L1_error);
40597 __Pyx_INCREF(__pyx_n_u_QUAL);
40598 __Pyx_GIVEREF(__pyx_n_u_QUAL);
40599 if (__Pyx_PyList_SET_ITEM(__pyx_t_5, 5, __pyx_n_u_QUAL)) __PYX_ERR(0, 311, __pyx_L1_error);
40600 __Pyx_INCREF(__pyx_n_u_FILTER);
40601 __Pyx_GIVEREF(__pyx_n_u_FILTER);
40602 if (__Pyx_PyList_SET_ITEM(__pyx_t_5, 6, __pyx_n_u_FILTER)) __PYX_ERR(0, 311, __pyx_L1_error);
40603 __Pyx_INCREF(__pyx_n_u_INFO);
40604 __Pyx_GIVEREF(__pyx_n_u_INFO);
40605 if (__Pyx_PyList_SET_ITEM(__pyx_t_5, 7, __pyx_n_u_INFO)) __PYX_ERR(0, 311, __pyx_L1_error);
40606 __Pyx_INCREF(__pyx_n_u_FORMAT);
40607 __Pyx_GIVEREF(__pyx_n_u_FORMAT);
40608 if (__Pyx_PyList_SET_ITEM(__pyx_t_5, 8, __pyx_n_u_FORMAT)) __PYX_ERR(0, 311, __pyx_L1_error);
40609 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_required, __pyx_t_5) < 0) __PYX_ERR(0, 311, __pyx_L1_error)
40610 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40611
40612 /* "pysam/libcvcf.pyx":312
40613 * # header; and required columns
40614 * _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
40615 * _samples = [] # <<<<<<<<<<<<<<
40616 *
40617 * # control behaviour
40618 */
40619 __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 312, __pyx_L1_error)
40620 __Pyx_GOTREF(__pyx_t_5);
40621 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_samples, __pyx_t_5) < 0) __PYX_ERR(0, 312, __pyx_L1_error)
40622 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40623
40624 /* "pysam/libcvcf.pyx":315
40625 *
40626 * # control behaviour
40627 * _ignored_errors = set([11,31]) # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD # <<<<<<<<<<<<<<
40628 * _warn_errors = set([])
40629 * _leftalign = False
40630 */
40631 __pyx_t_5 = PySet_New(0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 315, __pyx_L1_error)
40632 __Pyx_GOTREF(__pyx_t_5);
40633 if (PySet_Add(__pyx_t_5, __pyx_int_11) < 0) __PYX_ERR(0, 315, __pyx_L1_error)
40634 if (PySet_Add(__pyx_t_5, __pyx_int_31) < 0) __PYX_ERR(0, 315, __pyx_L1_error)
40635 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_ignored_errors, __pyx_t_5) < 0) __PYX_ERR(0, 315, __pyx_L1_error)
40636 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40637
40638 /* "pysam/libcvcf.pyx":316
40639 * # control behaviour
40640 * _ignored_errors = set([11,31]) # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD
40641 * _warn_errors = set([]) # <<<<<<<<<<<<<<
40642 * _leftalign = False
40643 *
40644 */
40645 __pyx_t_5 = PySet_New(0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 316, __pyx_L1_error)
40646 __Pyx_GOTREF(__pyx_t_5);
40647 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_warn_errors, __pyx_t_5) < 0) __PYX_ERR(0, 316, __pyx_L1_error)
40648 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40649
40650 /* "pysam/libcvcf.pyx":317
40651 * _ignored_errors = set([11,31]) # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD
40652 * _warn_errors = set([])
40653 * _leftalign = False # <<<<<<<<<<<<<<
40654 *
40655 * # reference sequence
40656 */
40657 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_leftalign_2, Py_False) < 0) __PYX_ERR(0, 317, __pyx_L1_error)
40658
40659 /* "pysam/libcvcf.pyx":320
40660 *
40661 * # reference sequence
40662 * _reference = None # <<<<<<<<<<<<<<
40663 *
40664 * # regions to include; None includes everything
40665 */
40666 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_reference_2, Py_None) < 0) __PYX_ERR(0, 320, __pyx_L1_error)
40667
40668 /* "pysam/libcvcf.pyx":323
40669 *
40670 * # regions to include; None includes everything
40671 * _regions = None # <<<<<<<<<<<<<<
40672 *
40673 * # statefull stuff
40674 */
40675 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_regions_2, Py_None) < 0) __PYX_ERR(0, 323, __pyx_L1_error)
40676
40677 /* "pysam/libcvcf.pyx":326
40678 *
40679 * # statefull stuff
40680 * _lineno = -1 # <<<<<<<<<<<<<<
40681 * _line = None
40682 * _lines = None
40683 */
40684 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_lineno, __pyx_int_neg_1) < 0) __PYX_ERR(0, 326, __pyx_L1_error)
40685
40686 /* "pysam/libcvcf.pyx":327
40687 * # statefull stuff
40688 * _lineno = -1
40689 * _line = None # <<<<<<<<<<<<<<
40690 * _lines = None
40691 *
40692 */
40693 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_line_2, Py_None) < 0) __PYX_ERR(0, 327, __pyx_L1_error)
40694
40695 /* "pysam/libcvcf.pyx":328
40696 * _lineno = -1
40697 * _line = None
40698 * _lines = None # <<<<<<<<<<<<<<
40699 *
40700 * def __init__(self, _copy=None, reference=None, regions=None,
40701 */
40702 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_lines_2, Py_None) < 0) __PYX_ERR(0, 328, __pyx_L1_error)
40703
40704 /* "pysam/libcvcf.pyx":330
40705 * _lines = None
40706 *
40707 * def __init__(self, _copy=None, reference=None, regions=None, # <<<<<<<<<<<<<<
40708 * lines=None, leftalign=False):
40709 * # make error identifiers accessible by name
40710 */
40711 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_1__init__, 0, __pyx_n_s_VCF___init, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__55)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 330, __pyx_L1_error)
40712 __Pyx_GOTREF(__pyx_t_5);
40713 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_5, __pyx_tuple__56);
40714 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_init, __pyx_t_5) < 0) __PYX_ERR(0, 330, __pyx_L1_error)
40715 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40716
40717 /* "pysam/libcvcf.pyx":355
40718 * self.tabixfile = None
40719 *
40720 * def error(self,line,error,opt=None): # <<<<<<<<<<<<<<
40721 * if error in self._ignored_errors: return
40722 * errorlabel, errorstring = self._errors[error].split(':')
40723 */
40724 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_3error, 0, __pyx_n_s_VCF_error, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__58)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 355, __pyx_L1_error)
40725 __Pyx_GOTREF(__pyx_t_5);
40726 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_5, __pyx_tuple__44);
40727 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_error, __pyx_t_5) < 0) __PYX_ERR(0, 355, __pyx_L1_error)
40728 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40729
40730 /* "pysam/libcvcf.pyx":364
40731 * raise ValueError(errorstring)
40732 *
40733 * def parse_format(self,line,format,filter=False): # <<<<<<<<<<<<<<
40734 * if self._version == 40:
40735 * if not format.startswith('<'):
40736 */
40737 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_5parse_format, 0, __pyx_n_s_VCF_parse_format, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__60)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 364, __pyx_L1_error)
40738 __Pyx_GOTREF(__pyx_t_5);
40739 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_5, __pyx_tuple__61);
40740 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_parse_format, __pyx_t_5) < 0) __PYX_ERR(0, 364, __pyx_L1_error)
40741 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40742
40743 /* "pysam/libcvcf.pyx":436
40744 * return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
40745 *
40746 * def format_format( self, fmt, filter=False ): # <<<<<<<<<<<<<<
40747 * values = [('ID',fmt.id)]
40748 * if fmt.number != None and not filter:
40749 */
40750 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_7format_format, 0, __pyx_n_s_VCF_format_format, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__63)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 436, __pyx_L1_error)
40751 __Pyx_GOTREF(__pyx_t_5);
40752 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_5, __pyx_tuple__61);
40753 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_format_format, __pyx_t_5) < 0) __PYX_ERR(0, 436, __pyx_L1_error)
40754 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40755
40756 /* "pysam/libcvcf.pyx":456
40757 * return format
40758 *
40759 * def get_expected(self, format, formatdict, alt): # <<<<<<<<<<<<<<
40760 * fmt = formatdict[format]
40761 * if fmt.numbertype == self.NT_UNKNOWN: return -1
40762 */
40763 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_9get_expected, 0, __pyx_n_s_VCF_get_expected, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__65)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 456, __pyx_L1_error)
40764 __Pyx_GOTREF(__pyx_t_5);
40765 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_get_expected, __pyx_t_5) < 0) __PYX_ERR(0, 456, __pyx_L1_error)
40766 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40767
40768 /* "pysam/libcvcf.pyx":467
40769 *
40770 *
40771 * def _add_definition(self, formatdict, key, data, line ): # <<<<<<<<<<<<<<
40772 * if key in formatdict: return
40773 * self.error(line,self.ERROR_UNKNOWN_KEY,key)
40774 */
40775 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_11_add_definition, 0, __pyx_n_s_VCF__add_definition, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__67)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 467, __pyx_L1_error)
40776 __Pyx_GOTREF(__pyx_t_5);
40777 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_add_definition, __pyx_t_5) < 0) __PYX_ERR(0, 467, __pyx_L1_error)
40778 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40779
40780 /* "pysam/libcvcf.pyx":484
40781 *
40782 * # todo: trim trailing missing values
40783 * def format_formatdata( self, data, format, key=True, value=True, separator=":" ): # <<<<<<<<<<<<<<
40784 * output, sdata = [], []
40785 * if type(data) == type([]): # for FORMAT field, make data with dummy values
40786 */
40787 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_13format_formatdata, 0, __pyx_n_s_VCF_format_formatdata, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__69)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 484, __pyx_L1_error)
40788 __Pyx_GOTREF(__pyx_t_5);
40789 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_5, __pyx_tuple__70);
40790 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_format_formatdata, __pyx_t_5) < 0) __PYX_ERR(0, 484, __pyx_L1_error)
40791 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40792
40793 /* "pysam/libcvcf.pyx":518
40794 *
40795 *
40796 * def enter_default_format(self): # <<<<<<<<<<<<<<
40797 * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
40798 * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
40799 */
40800 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_15enter_default_format, 0, __pyx_n_s_VCF_enter_default_format, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__72)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 518, __pyx_L1_error)
40801 __Pyx_GOTREF(__pyx_t_5);
40802 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_enter_default_format, __pyx_t_5) < 0) __PYX_ERR(0, 518, __pyx_L1_error)
40803 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40804
40805 /* "pysam/libcvcf.pyx":537
40806 * self._format[f.id] = f
40807 *
40808 * def parse_header(self, line): # <<<<<<<<<<<<<<
40809 *
40810 * assert line.startswith('##')
40811 */
40812 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_17parse_header, 0, __pyx_n_s_VCF_parse_header, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__74)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 537, __pyx_L1_error)
40813 __Pyx_GOTREF(__pyx_t_5);
40814 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_parse_header, __pyx_t_5) < 0) __PYX_ERR(0, 537, __pyx_L1_error)
40815 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40816
40817 /* "pysam/libcvcf.pyx":570
40818 *
40819 *
40820 * def write_header( self, stream ): # <<<<<<<<<<<<<<
40821 * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
40822 * for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
40823 */
40824 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_19write_header, 0, __pyx_n_s_VCF_write_header, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__76)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 570, __pyx_L1_error)
40825 __Pyx_GOTREF(__pyx_t_5);
40826 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_write_header, __pyx_t_5) < 0) __PYX_ERR(0, 570, __pyx_L1_error)
40827 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40828
40829 /* "pysam/libcvcf.pyx":577
40830 *
40831 *
40832 * def parse_heading( self, line ): # <<<<<<<<<<<<<<
40833 * assert line.startswith('#')
40834 * assert not line.startswith('##')
40835 */
40836 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_21parse_heading, 0, __pyx_n_s_VCF_parse_heading, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__78)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 577, __pyx_L1_error)
40837 __Pyx_GOTREF(__pyx_t_5);
40838 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_parse_heading, __pyx_t_5) < 0) __PYX_ERR(0, 577, __pyx_L1_error)
40839 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40840
40841 /* "pysam/libcvcf.pyx":605
40842 * self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] )
40843 *
40844 * def write_heading( self, stream ): # <<<<<<<<<<<<<<
40845 * stream.write("#" + "\t".join(self._required + self._samples) + "\n")
40846 *
40847 */
40848 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_23write_heading, 0, __pyx_n_s_VCF_write_heading, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__80)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 605, __pyx_L1_error)
40849 __Pyx_GOTREF(__pyx_t_5);
40850 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_write_heading, __pyx_t_5) < 0) __PYX_ERR(0, 605, __pyx_L1_error)
40851 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40852
40853 /* "pysam/libcvcf.pyx":608
40854 * stream.write("#" + "\t".join(self._required + self._samples) + "\n")
40855 *
40856 * def convertGT(self, GTstring): # <<<<<<<<<<<<<<
40857 * if GTstring == ".": return ["."]
40858 * try:
40859 */
40860 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_25convertGT, 0, __pyx_n_s_VCF_convertGT, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__82)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 608, __pyx_L1_error)
40861 __Pyx_GOTREF(__pyx_t_5);
40862 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_convertGT, __pyx_t_5) < 0) __PYX_ERR(0, 608, __pyx_L1_error)
40863 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40864
40865 /* "pysam/libcvcf.pyx":620
40866 * return [".","|","."]
40867 *
40868 * def convertGTback(self, GTdata): # <<<<<<<<<<<<<<
40869 * return ''.join(map(str,GTdata))
40870 *
40871 */
40872 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_27convertGTback, 0, __pyx_n_s_VCF_convertGTback, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__84)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 620, __pyx_L1_error)
40873 __Pyx_GOTREF(__pyx_t_5);
40874 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_convertGTback, __pyx_t_5) < 0) __PYX_ERR(0, 620, __pyx_L1_error)
40875 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40876
40877 /* "pysam/libcvcf.pyx":623
40878 * return ''.join(map(str,GTdata))
40879 *
40880 * def parse_formatdata( self, key, value, formatdict, line ): # <<<<<<<<<<<<<<
40881 * # To do: check that the right number of values is present
40882 * f = formatdict.get(key,None)
40883 */
40884 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_29parse_formatdata, 0, __pyx_n_s_VCF_parse_formatdata, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__86)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 623, __pyx_L1_error)
40885 __Pyx_GOTREF(__pyx_t_5);
40886 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_parse_formatdata, __pyx_t_5) < 0) __PYX_ERR(0, 623, __pyx_L1_error)
40887 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40888
40889 /* "pysam/libcvcf.pyx":665
40890 * self.error(line,self.ERROR_INFO_STRING)
40891 *
40892 * def inregion(self, chrom, pos): # <<<<<<<<<<<<<<
40893 * if not self._regions: return True
40894 * for r in self._regions:
40895 */
40896 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_31inregion, 0, __pyx_n_s_VCF_inregion, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__88)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 665, __pyx_L1_error)
40897 __Pyx_GOTREF(__pyx_t_5);
40898 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_inregion, __pyx_t_5) < 0) __PYX_ERR(0, 665, __pyx_L1_error)
40899 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40900
40901 /* "pysam/libcvcf.pyx":671
40902 * return False
40903 *
40904 * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<<
40905 * cols = line.split('\t')
40906 * if len(cols) != len(self._samples)+9:
40907 */
40908 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_33parse_data, 0, __pyx_n_s_VCF_parse_data, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__90)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 671, __pyx_L1_error)
40909 __Pyx_GOTREF(__pyx_t_5);
40910 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_5, __pyx_tuple__61);
40911 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_parse_data, __pyx_t_5) < 0) __PYX_ERR(0, 671, __pyx_L1_error)
40912 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40913
40914 /* "pysam/libcvcf.pyx":883
40915 *
40916 *
40917 * def write_data(self, stream, data): # <<<<<<<<<<<<<<
40918 * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
40919 * for k in required:
40920 */
40921 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_35write_data, 0, __pyx_n_s_VCF_write_data, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__92)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 883, __pyx_L1_error)
40922 __Pyx_GOTREF(__pyx_t_5);
40923 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_write_data, __pyx_t_5) < 0) __PYX_ERR(0, 883, __pyx_L1_error)
40924 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40925
40926 /* "pysam/libcvcf.pyx":915
40927 * stream.write( "\t".join(output) + "\n" )
40928 *
40929 * def _parse_header(self, stream): # <<<<<<<<<<<<<<
40930 * self._lineno = 0
40931 * for line in stream:
40932 */
40933 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_37_parse_header, 0, __pyx_n_s_VCF__parse_header, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__94)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 915, __pyx_L1_error)
40934 __Pyx_GOTREF(__pyx_t_5);
40935 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_parse_header_2, __pyx_t_5) < 0) __PYX_ERR(0, 915, __pyx_L1_error)
40936 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40937
40938 /* "pysam/libcvcf.pyx":929
40939 * return line
40940 *
40941 * def _parse(self, line, stream): # <<<<<<<<<<<<<<
40942 * # deal with files with header only
40943 * if line.startswith("##"): return
40944 */
40945 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_39_parse, 0, __pyx_n_s_VCF__parse, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__29)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 929, __pyx_L1_error)
40946 __Pyx_GOTREF(__pyx_t_5);
40947 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_parse, __pyx_t_5) < 0) __PYX_ERR(0, 929, __pyx_L1_error)
40948 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40949
40950 /* "pysam/libcvcf.pyx":947
40951 * ######################################################################################################
40952 *
40953 * def getsamples(self): # <<<<<<<<<<<<<<
40954 * """ List of samples in VCF file """
40955 * return self._samples
40956 */
40957 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_42getsamples, 0, __pyx_n_s_VCF_getsamples, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__96)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 947, __pyx_L1_error)
40958 __Pyx_GOTREF(__pyx_t_5);
40959 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_getsamples, __pyx_t_5) < 0) __PYX_ERR(0, 947, __pyx_L1_error)
40960 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40961
40962 /* "pysam/libcvcf.pyx":951
40963 * return self._samples
40964 *
40965 * def setsamples(self,samples): # <<<<<<<<<<<<<<
40966 * """ List of samples in VCF file """
40967 * self._samples = samples
40968 */
40969 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_44setsamples, 0, __pyx_n_s_VCF_setsamples, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__98)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 951, __pyx_L1_error)
40970 __Pyx_GOTREF(__pyx_t_5);
40971 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_setsamples, __pyx_t_5) < 0) __PYX_ERR(0, 951, __pyx_L1_error)
40972 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40973
40974 /* "pysam/libcvcf.pyx":955
40975 * self._samples = samples
40976 *
40977 * def getheader(self): # <<<<<<<<<<<<<<
40978 * """ List of header key-value pairs (strings) """
40979 * return self._header
40980 */
40981 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_46getheader, 0, __pyx_n_s_VCF_getheader, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__99)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 955, __pyx_L1_error)
40982 __Pyx_GOTREF(__pyx_t_5);
40983 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_getheader, __pyx_t_5) < 0) __PYX_ERR(0, 955, __pyx_L1_error)
40984 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40985
40986 /* "pysam/libcvcf.pyx":959
40987 * return self._header
40988 *
40989 * def setheader(self,header): # <<<<<<<<<<<<<<
40990 * """ List of header key-value pairs (strings) """
40991 * self._header = header
40992 */
40993 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_48setheader, 0, __pyx_n_s_VCF_setheader, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__101)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 959, __pyx_L1_error)
40994 __Pyx_GOTREF(__pyx_t_5);
40995 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_setheader, __pyx_t_5) < 0) __PYX_ERR(0, 959, __pyx_L1_error)
40996 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
40997
40998 /* "pysam/libcvcf.pyx":963
40999 * self._header = header
41000 *
41001 * def getinfo(self): # <<<<<<<<<<<<<<
41002 * """ Dictionary of ##INFO tags, as VCF.FORMAT values """
41003 * return self._info
41004 */
41005 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_50getinfo, 0, __pyx_n_s_VCF_getinfo, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__102)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 963, __pyx_L1_error)
41006 __Pyx_GOTREF(__pyx_t_5);
41007 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_getinfo, __pyx_t_5) < 0) __PYX_ERR(0, 963, __pyx_L1_error)
41008 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41009
41010 /* "pysam/libcvcf.pyx":967
41011 * return self._info
41012 *
41013 * def setinfo(self,info): # <<<<<<<<<<<<<<
41014 * """ Dictionary of ##INFO tags, as VCF.FORMAT values """
41015 * self._info = info
41016 */
41017 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_52setinfo, 0, __pyx_n_s_VCF_setinfo, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__104)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 967, __pyx_L1_error)
41018 __Pyx_GOTREF(__pyx_t_5);
41019 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_setinfo, __pyx_t_5) < 0) __PYX_ERR(0, 967, __pyx_L1_error)
41020 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41021
41022 /* "pysam/libcvcf.pyx":971
41023 * self._info = info
41024 *
41025 * def getformat(self): # <<<<<<<<<<<<<<
41026 * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
41027 * return self._format
41028 */
41029 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_54getformat, 0, __pyx_n_s_VCF_getformat, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__105)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 971, __pyx_L1_error)
41030 __Pyx_GOTREF(__pyx_t_5);
41031 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_getformat, __pyx_t_5) < 0) __PYX_ERR(0, 971, __pyx_L1_error)
41032 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41033
41034 /* "pysam/libcvcf.pyx":975
41035 * return self._format
41036 *
41037 * def setformat(self,format): # <<<<<<<<<<<<<<
41038 * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
41039 * self._format = format
41040 */
41041 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_56setformat, 0, __pyx_n_s_VCF_setformat, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__107)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 975, __pyx_L1_error)
41042 __Pyx_GOTREF(__pyx_t_5);
41043 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_setformat, __pyx_t_5) < 0) __PYX_ERR(0, 975, __pyx_L1_error)
41044 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41045
41046 /* "pysam/libcvcf.pyx":979
41047 * self._format = format
41048 *
41049 * def getfilter(self): # <<<<<<<<<<<<<<
41050 * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
41051 * return self._filter
41052 */
41053 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_58getfilter, 0, __pyx_n_s_VCF_getfilter, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__108)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 979, __pyx_L1_error)
41054 __Pyx_GOTREF(__pyx_t_5);
41055 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_getfilter, __pyx_t_5) < 0) __PYX_ERR(0, 979, __pyx_L1_error)
41056 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41057
41058 /* "pysam/libcvcf.pyx":983
41059 * return self._filter
41060 *
41061 * def setfilter(self,filter): # <<<<<<<<<<<<<<
41062 * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
41063 * self._filter = filter
41064 */
41065 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_60setfilter, 0, __pyx_n_s_VCF_setfilter, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__110)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 983, __pyx_L1_error)
41066 __Pyx_GOTREF(__pyx_t_5);
41067 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_setfilter, __pyx_t_5) < 0) __PYX_ERR(0, 983, __pyx_L1_error)
41068 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41069
41070 /* "pysam/libcvcf.pyx":987
41071 * self._filter = filter
41072 *
41073 * def setversion(self, version): # <<<<<<<<<<<<<<
41074 * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")
41075 * self._version = version
41076 */
41077 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_62setversion, 0, __pyx_n_s_VCF_setversion, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__112)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 987, __pyx_L1_error)
41078 __Pyx_GOTREF(__pyx_t_5);
41079 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_setversion, __pyx_t_5) < 0) __PYX_ERR(0, 987, __pyx_L1_error)
41080 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41081
41082 /* "pysam/libcvcf.pyx":991
41083 * self._version = version
41084 *
41085 * def setregions(self, regions): # <<<<<<<<<<<<<<
41086 * self._regions = regions
41087 *
41088 */
41089 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_64setregions, 0, __pyx_n_s_VCF_setregions, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__114)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 991, __pyx_L1_error)
41090 __Pyx_GOTREF(__pyx_t_5);
41091 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_setregions, __pyx_t_5) < 0) __PYX_ERR(0, 991, __pyx_L1_error)
41092 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41093
41094 /* "pysam/libcvcf.pyx":994
41095 * self._regions = regions
41096 *
41097 * def setreference(self, ref): # <<<<<<<<<<<<<<
41098 * """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
41099 * self._reference = ref
41100 */
41101 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_66setreference, 0, __pyx_n_s_VCF_setreference, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__116)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 994, __pyx_L1_error)
41102 __Pyx_GOTREF(__pyx_t_5);
41103 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_setreference, __pyx_t_5) < 0) __PYX_ERR(0, 994, __pyx_L1_error)
41104 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41105
41106 /* "pysam/libcvcf.pyx":998
41107 * self._reference = ref
41108 *
41109 * def ignoreerror(self, errorstring): # <<<<<<<<<<<<<<
41110 * try: self._ignored_errors.add(self.__dict__[errorstring])
41111 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
41112 */
41113 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_68ignoreerror, 0, __pyx_n_s_VCF_ignoreerror, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__118)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 998, __pyx_L1_error)
41114 __Pyx_GOTREF(__pyx_t_5);
41115 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_ignoreerror, __pyx_t_5) < 0) __PYX_ERR(0, 998, __pyx_L1_error)
41116 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41117
41118 /* "pysam/libcvcf.pyx":1002
41119 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
41120 *
41121 * def warnerror(self, errorstring): # <<<<<<<<<<<<<<
41122 * try: self._warn_errors.add(self.__dict__[errorstring])
41123 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
41124 */
41125 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_70warnerror, 0, __pyx_n_s_VCF_warnerror, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__119)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1002, __pyx_L1_error)
41126 __Pyx_GOTREF(__pyx_t_5);
41127 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_warnerror, __pyx_t_5) < 0) __PYX_ERR(0, 1002, __pyx_L1_error)
41128 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41129
41130 /* "pysam/libcvcf.pyx":1006
41131 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
41132 *
41133 * def parse(self, stream): # <<<<<<<<<<<<<<
41134 * """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
41135 * last_line = self._parse_header(stream)
41136 */
41137 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_72parse, 0, __pyx_n_s_VCF_parse, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__121)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1006, __pyx_L1_error)
41138 __Pyx_GOTREF(__pyx_t_5);
41139 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_parse_2, __pyx_t_5) < 0) __PYX_ERR(0, 1006, __pyx_L1_error)
41140 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41141
41142 /* "pysam/libcvcf.pyx":1013
41143 * return self._parse(last_line, stream)
41144 *
41145 * def write(self, stream, datagenerator): # <<<<<<<<<<<<<<
41146 * """ Writes a VCF file to a stream, using a data generator (or list) """
41147 * self.write_header(stream)
41148 */
41149 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_74write, 0, __pyx_n_s_VCF_write, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__123)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1013, __pyx_L1_error)
41150 __Pyx_GOTREF(__pyx_t_5);
41151 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_write, __pyx_t_5) < 0) __PYX_ERR(0, 1013, __pyx_L1_error)
41152 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41153
41154 /* "pysam/libcvcf.pyx":1019
41155 * for data in datagenerator: self.write_data(stream,data)
41156 *
41157 * def writeheader(self, stream): # <<<<<<<<<<<<<<
41158 * """ Writes a VCF header """
41159 * self.write_header(stream)
41160 */
41161 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_76writeheader, 0, __pyx_n_s_VCF_writeheader, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__124)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1019, __pyx_L1_error)
41162 __Pyx_GOTREF(__pyx_t_5);
41163 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_writeheader, __pyx_t_5) < 0) __PYX_ERR(0, 1019, __pyx_L1_error)
41164 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41165
41166 /* "pysam/libcvcf.pyx":1024
41167 * self.write_heading(stream)
41168 *
41169 * def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): # <<<<<<<<<<<<<<
41170 * """ Utility function: compares two calls for equality """
41171 * # a variant should always be assigned to a unique position, one base before
41172 */
41173 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_78compare_calls, 0, __pyx_n_s_VCF_compare_calls, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__126)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1024, __pyx_L1_error)
41174 __Pyx_GOTREF(__pyx_t_5);
41175 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_compare_calls, __pyx_t_5) < 0) __PYX_ERR(0, 1024, __pyx_L1_error)
41176 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41177
41178 /* "pysam/libcvcf.pyx":1046
41179 * ###########################################################################################################
41180 *
41181 * def connect(self, filename, encoding="ascii"): # <<<<<<<<<<<<<<
41182 * '''connect to tabix file.'''
41183 * self.encoding=encoding
41184 */
41185 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_80connect, 0, __pyx_n_s_VCF_connect, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__128)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1046, __pyx_L1_error)
41186 __Pyx_GOTREF(__pyx_t_5);
41187 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_5, __pyx_tuple__129);
41188 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_connect, __pyx_t_5) < 0) __PYX_ERR(0, 1046, __pyx_L1_error)
41189 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41190
41191 /* "pysam/libcvcf.pyx":1052
41192 * self._parse_header(self.tabixfile.header)
41193 *
41194 * def __del__(self): # <<<<<<<<<<<<<<
41195 * self.close()
41196 * self.tabixfile = None
41197 */
41198 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_82__del__, 0, __pyx_n_s_VCF___del, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__130)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1052, __pyx_L1_error)
41199 __Pyx_GOTREF(__pyx_t_5);
41200 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_del, __pyx_t_5) < 0) __PYX_ERR(0, 1052, __pyx_L1_error)
41201 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41202
41203 /* "pysam/libcvcf.pyx":1056
41204 * self.tabixfile = None
41205 *
41206 * def close(self): # <<<<<<<<<<<<<<
41207 * if self.tabixfile:
41208 * self.tabixfile.close()
41209 */
41210 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_84close, 0, __pyx_n_s_VCF_close, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__131)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1056, __pyx_L1_error)
41211 __Pyx_GOTREF(__pyx_t_5);
41212 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_close, __pyx_t_5) < 0) __PYX_ERR(0, 1056, __pyx_L1_error)
41213 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41214
41215 /* "pysam/libcvcf.pyx":1061
41216 * self.tabixfile = None
41217 *
41218 * def fetch(self, # <<<<<<<<<<<<<<
41219 * reference=None,
41220 * start=None,
41221 */
41222 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_86fetch, 0, __pyx_n_s_VCF_fetch, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__133)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1061, __pyx_L1_error)
41223 __Pyx_GOTREF(__pyx_t_5);
41224 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_5, __pyx_tuple__134);
41225 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_fetch, __pyx_t_5) < 0) __PYX_ERR(0, 1061, __pyx_L1_error)
41226 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41227
41228 /* "pysam/libcvcf.pyx":1075
41229 * parser = asVCFRecord(self))
41230 *
41231 * def validate(self, record): # <<<<<<<<<<<<<<
41232 * '''validate vcf record.
41233 *
41234 */
41235 __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_3VCF_88validate, 0, __pyx_n_s_VCF_validate, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__136)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1075, __pyx_L1_error)
41236 __Pyx_GOTREF(__pyx_t_5);
41237 if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_validate, __pyx_t_5) < 0) __PYX_ERR(0, 1075, __pyx_L1_error)
41238 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41239
41240 /* "pysam/libcvcf.pyx":253
41241 * return r
41242 *
41243 * class VCF(object): # <<<<<<<<<<<<<<
41244 *
41245 * # types
41246 */
41247 __pyx_t_5 = __Pyx_Py3ClassCreate(__pyx_t_2, __pyx_n_s_VCF, __pyx_t_3, __pyx_t_4, NULL, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 253, __pyx_L1_error)
41248 __Pyx_GOTREF(__pyx_t_5);
41249 if (PyDict_SetItem(__pyx_d, __pyx_n_s_VCF, __pyx_t_5) < 0) __PYX_ERR(0, 253, __pyx_L1_error)
41250 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
41251 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
41252 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
41253 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
41254
41255 /* "pysam/libcvcf.pyx":1202
41256 * pos -= 1
41257 *
41258 * __all__ = [ # <<<<<<<<<<<<<<
41259 * "VCF", "VCFRecord", ]
41260 */
41261 __pyx_t_3 = PyList_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1202, __pyx_L1_error)
41262 __Pyx_GOTREF(__pyx_t_3);
41263 __Pyx_INCREF(__pyx_n_u_VCF);
41264 __Pyx_GIVEREF(__pyx_n_u_VCF);
41265 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 0, __pyx_n_u_VCF)) __PYX_ERR(0, 1202, __pyx_L1_error);
41266 __Pyx_INCREF(__pyx_n_u_VCFRecord);
41267 __Pyx_GIVEREF(__pyx_n_u_VCFRecord);
41268 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 1, __pyx_n_u_VCFRecord)) __PYX_ERR(0, 1202, __pyx_L1_error);
41269 if (PyDict_SetItem(__pyx_d, __pyx_n_s_all, __pyx_t_3) < 0) __PYX_ERR(0, 1202, __pyx_L1_error)
41270 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
41271
41272 /* "(tree fragment)":1
41273 * def __pyx_unpickle_asVCFRecord(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
41274 * cdef object __pyx_PickleError
41275 * cdef object __pyx_result
41276 */
41277 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_7libcvcf_5__pyx_unpickle_asVCFRecord, 0, __pyx_n_s_pyx_unpickle_asVCFRecord, NULL, __pyx_n_s_pysam_libcvcf, __pyx_d, ((PyObject *)__pyx_codeobj__138)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error)
41278 __Pyx_GOTREF(__pyx_t_3);
41279 if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_asVCFRecord, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
41280 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
41281
41282 /* "pysam/libcvcf.pyx":1
41283 * # cython: embedsignature=True # <<<<<<<<<<<<<<
41284 * #
41285 * # Code to read, write and edit VCF files
41286 */
41287 __pyx_t_3 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1, __pyx_L1_error)
41288 __Pyx_GOTREF(__pyx_t_3);
41289 if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_3) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
41290 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
41291
41292 /*--- Wrapped vars code ---*/
41293
41294 goto __pyx_L0;
41295 __pyx_L1_error:;
41296 __Pyx_XDECREF(__pyx_t_2);
41297 __Pyx_XDECREF(__pyx_t_3);
41298 __Pyx_XDECREF(__pyx_t_4);
41299 __Pyx_XDECREF(__pyx_t_5);
41300 if (__pyx_m) {
41301 if (__pyx_d && stringtab_initialized) {
41302 __Pyx_AddTraceback("init pysam.libcvcf", __pyx_clineno, __pyx_lineno, __pyx_filename);
41303 }
41304 #if !CYTHON_USE_MODULE_STATE
41305 Py_CLEAR(__pyx_m);
41306 #else
41307 Py_DECREF(__pyx_m);
41308 if (pystate_addmodule_run) {
41309 PyObject *tp, *value, *tb;
41310 PyErr_Fetch(&tp, &value, &tb);
41311 PyState_RemoveModule(&__pyx_moduledef);
41312 PyErr_Restore(tp, value, tb);
41313 }
41314 #endif
41315 } else if (!PyErr_Occurred()) {
41316 PyErr_SetString(PyExc_ImportError, "init pysam.libcvcf");
41317 }
41318 __pyx_L0:;
41319 __Pyx_RefNannyFinishContext();
41320 #if CYTHON_PEP489_MULTI_PHASE_INIT
41321 return (__pyx_m != NULL) ? 0 : -1;
41322 #elif PY_MAJOR_VERSION >= 3
41323 return __pyx_m;
41324 #else
41325 return;
41326 #endif
41327 }
41328 /* #### Code section: cleanup_globals ### */
41329 /* #### Code section: cleanup_module ### */
41330 /* #### Code section: main_method ### */
41331 /* #### Code section: utility_code_pragmas ### */
41332 #ifdef _MSC_VER
41333 #pragma warning( push )
41334 /* Warning 4127: conditional expression is constant
41335 * Cython uses constant conditional expressions to allow in inline functions to be optimized at
41336 * compile-time, so this warning is not useful
41337 */
41338 #pragma warning( disable : 4127 )
41339 #endif
41340
41341
41342
41343 /* #### Code section: utility_code_def ### */
41344
41345 /* --- Runtime support code --- */
41346 /* Refnanny */
41347 #if CYTHON_REFNANNY
41348 static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
41349 PyObject *m = NULL, *p = NULL;
41350 void *r = NULL;
41351 m = PyImport_ImportModule(modname);
41352 if (!m) goto end;
41353 p = PyObject_GetAttrString(m, "RefNannyAPI");
41354 if (!p) goto end;
41355 r = PyLong_AsVoidPtr(p);
41356 end:
41357 Py_XDECREF(p);
41358 Py_XDECREF(m);
41359 return (__Pyx_RefNannyAPIStruct *)r;
41360 }
41361 #endif
41362
41363 /* PyErrExceptionMatches */
41364 #if CYTHON_FAST_THREAD_STATE
41365 static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) {
41366 Py_ssize_t i, n;
41367 n = PyTuple_GET_SIZE(tuple);
41368 #if PY_MAJOR_VERSION >= 3
41369 for (i=0; i<n; i++) {
41370 if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1;
41371 }
41372 #endif
41373 for (i=0; i<n; i++) {
41374 if (__Pyx_PyErr_GivenExceptionMatches(exc_type, PyTuple_GET_ITEM(tuple, i))) return 1;
41375 }
41376 return 0;
41377 }
41378 static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) {
41379 int result;
41380 PyObject *exc_type;
41381 #if PY_VERSION_HEX >= 0x030C00A6
41382 PyObject *current_exception = tstate->current_exception;
41383 if (unlikely(!current_exception)) return 0;
41384 exc_type = (PyObject*) Py_TYPE(current_exception);
41385 if (exc_type == err) return 1;
41386 #else
41387 exc_type = tstate->curexc_type;
41388 if (exc_type == err) return 1;
41389 if (unlikely(!exc_type)) return 0;
41390 #endif
41391 #if CYTHON_AVOID_BORROWED_REFS
41392 Py_INCREF(exc_type);
41393 #endif
41394 if (unlikely(PyTuple_Check(err))) {
41395 result = __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err);
41396 } else {
41397 result = __Pyx_PyErr_GivenExceptionMatches(exc_type, err);
41398 }
41399 #if CYTHON_AVOID_BORROWED_REFS
41400 Py_DECREF(exc_type);
41401 #endif
41402 return result;
41403 }
41404 #endif
41405
41406 /* PyErrFetchRestore */
41407 #if CYTHON_FAST_THREAD_STATE
41408 static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
41409 #if PY_VERSION_HEX >= 0x030C00A6
41410 PyObject *tmp_value;
41411 assert(type == NULL || (value != NULL && type == (PyObject*) Py_TYPE(value)));
41412 if (value) {
41413 #if CYTHON_COMPILING_IN_CPYTHON
41414 if (unlikely(((PyBaseExceptionObject*) value)->traceback != tb))
41415 #endif
41416 PyException_SetTraceback(value, tb);
41417 }
41418 tmp_value = tstate->current_exception;
41419 tstate->current_exception = value;
41420 Py_XDECREF(tmp_value);
41421 Py_XDECREF(type);
41422 Py_XDECREF(tb);
41423 #else
41424 PyObject *tmp_type, *tmp_value, *tmp_tb;
41425 tmp_type = tstate->curexc_type;
41426 tmp_value = tstate->curexc_value;
41427 tmp_tb = tstate->curexc_traceback;
41428 tstate->curexc_type = type;
41429 tstate->curexc_value = value;
41430 tstate->curexc_traceback = tb;
41431 Py_XDECREF(tmp_type);
41432 Py_XDECREF(tmp_value);
41433 Py_XDECREF(tmp_tb);
41434 #endif
41435 }
41436 static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
41437 #if PY_VERSION_HEX >= 0x030C00A6
41438 PyObject* exc_value;
41439 exc_value = tstate->current_exception;
41440 tstate->current_exception = 0;
41441 *value = exc_value;
41442 *type = NULL;
41443 *tb = NULL;
41444 if (exc_value) {
41445 *type = (PyObject*) Py_TYPE(exc_value);
41446 Py_INCREF(*type);
41447 #if CYTHON_COMPILING_IN_CPYTHON
41448 *tb = ((PyBaseExceptionObject*) exc_value)->traceback;
41449 Py_XINCREF(*tb);
41450 #else
41451 *tb = PyException_GetTraceback(exc_value);
41452 #endif
41453 }
41454 #else
41455 *type = tstate->curexc_type;
41456 *value = tstate->curexc_value;
41457 *tb = tstate->curexc_traceback;
41458 tstate->curexc_type = 0;
41459 tstate->curexc_value = 0;
41460 tstate->curexc_traceback = 0;
41461 #endif
41462 }
41463 #endif
41464
41465 /* PyObjectGetAttrStr */
41466 #if CYTHON_USE_TYPE_SLOTS
41467 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
41468 PyTypeObject* tp = Py_TYPE(obj);
41469 if (likely(tp->tp_getattro))
41470 return tp->tp_getattro(obj, attr_name);
41471 #if PY_MAJOR_VERSION < 3
41472 if (likely(tp->tp_getattr))
41473 return tp->tp_getattr(obj, PyString_AS_STRING(attr_name));
41474 #endif
41475 return PyObject_GetAttr(obj, attr_name);
41476 }
41477 #endif
41478
41479 /* PyObjectGetAttrStrNoError */
41480 #if __PYX_LIMITED_VERSION_HEX < 0x030d00A1
41481 static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) {
41482 __Pyx_PyThreadState_declare
41483 __Pyx_PyThreadState_assign
41484 if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError)))
41485 __Pyx_PyErr_Clear();
41486 }
41487 #endif
41488 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) {
41489 PyObject *result;
41490 #if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1
41491 (void) PyObject_GetOptionalAttr(obj, attr_name, &result);
41492 return result;
41493 #else
41494 #if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1
41495 PyTypeObject* tp = Py_TYPE(obj);
41496 if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) {
41497 return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1);
41498 }
41499 #endif
41500 result = __Pyx_PyObject_GetAttrStr(obj, attr_name);
41501 if (unlikely(!result)) {
41502 __Pyx_PyObject_GetAttrStr_ClearAttributeError();
41503 }
41504 return result;
41505 #endif
41506 }
41507
41508 /* GetBuiltinName */
41509 static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
41510 PyObject* result = __Pyx_PyObject_GetAttrStrNoError(__pyx_b, name);
41511 if (unlikely(!result) && !PyErr_Occurred()) {
41512 PyErr_Format(PyExc_NameError,
41513 #if PY_MAJOR_VERSION >= 3
41514 "name '%U' is not defined", name);
41515 #else
41516 "name '%.200s' is not defined", PyString_AS_STRING(name));
41517 #endif
41518 }
41519 return result;
41520 }
41521
41522 /* TupleAndListFromArray */
41523 #if CYTHON_COMPILING_IN_CPYTHON
41524 static CYTHON_INLINE void __Pyx_copy_object_array(PyObject *const *CYTHON_RESTRICT src, PyObject** CYTHON_RESTRICT dest, Py_ssize_t length) {
41525 PyObject *v;
41526 Py_ssize_t i;
41527 for (i = 0; i < length; i++) {
41528 v = dest[i] = src[i];
41529 Py_INCREF(v);
41530 }
41531 }
41532 static CYTHON_INLINE PyObject *
41533 __Pyx_PyTuple_FromArray(PyObject *const *src, Py_ssize_t n)
41534 {
41535 PyObject *res;
41536 if (n <= 0) {
41537 Py_INCREF(__pyx_empty_tuple);
41538 return __pyx_empty_tuple;
41539 }
41540 res = PyTuple_New(n);
41541 if (unlikely(res == NULL)) return NULL;
41542 __Pyx_copy_object_array(src, ((PyTupleObject*)res)->ob_item, n);
41543 return res;
41544 }
41545 static CYTHON_INLINE PyObject *
41546 __Pyx_PyList_FromArray(PyObject *const *src, Py_ssize_t n)
41547 {
41548 PyObject *res;
41549 if (n <= 0) {
41550 return PyList_New(0);
41551 }
41552 res = PyList_New(n);
41553 if (unlikely(res == NULL)) return NULL;
41554 __Pyx_copy_object_array(src, ((PyListObject*)res)->ob_item, n);
41555 return res;
41556 }
41557 #endif
41558
41559 /* BytesEquals */
41560 static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
41561 #if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API
41562 return PyObject_RichCompareBool(s1, s2, equals);
41563 #else
41564 if (s1 == s2) {
41565 return (equals == Py_EQ);
41566 } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
41567 const char *ps1, *ps2;
41568 Py_ssize_t length = PyBytes_GET_SIZE(s1);
41569 if (length != PyBytes_GET_SIZE(s2))
41570 return (equals == Py_NE);
41571 ps1 = PyBytes_AS_STRING(s1);
41572 ps2 = PyBytes_AS_STRING(s2);
41573 if (ps1[0] != ps2[0]) {
41574 return (equals == Py_NE);
41575 } else if (length == 1) {
41576 return (equals == Py_EQ);
41577 } else {
41578 int result;
41579 #if CYTHON_USE_UNICODE_INTERNALS && (PY_VERSION_HEX < 0x030B0000)
41580 Py_hash_t hash1, hash2;
41581 hash1 = ((PyBytesObject*)s1)->ob_shash;
41582 hash2 = ((PyBytesObject*)s2)->ob_shash;
41583 if (hash1 != hash2 && hash1 != -1 && hash2 != -1) {
41584 return (equals == Py_NE);
41585 }
41586 #endif
41587 result = memcmp(ps1, ps2, (size_t)length);
41588 return (equals == Py_EQ) ? (result == 0) : (result != 0);
41589 }
41590 } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
41591 return (equals == Py_NE);
41592 } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
41593 return (equals == Py_NE);
41594 } else {
41595 int result;
41596 PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
41597 if (!py_result)
41598 return -1;
41599 result = __Pyx_PyObject_IsTrue(py_result);
41600 Py_DECREF(py_result);
41601 return result;
41602 }
41603 #endif
41604 }
41605
41606 /* UnicodeEquals */
41607 static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
41608 #if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API
41609 return PyObject_RichCompareBool(s1, s2, equals);
41610 #else
41611 #if PY_MAJOR_VERSION < 3
41612 PyObject* owned_ref = NULL;
41613 #endif
41614 int s1_is_unicode, s2_is_unicode;
41615 if (s1 == s2) {
41616 goto return_eq;
41617 }
41618 s1_is_unicode = PyUnicode_CheckExact(s1);
41619 s2_is_unicode = PyUnicode_CheckExact(s2);
41620 #if PY_MAJOR_VERSION < 3
41621 if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) {
41622 owned_ref = PyUnicode_FromObject(s2);
41623 if (unlikely(!owned_ref))
41624 return -1;
41625 s2 = owned_ref;
41626 s2_is_unicode = 1;
41627 } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) {
41628 owned_ref = PyUnicode_FromObject(s1);
41629 if (unlikely(!owned_ref))
41630 return -1;
41631 s1 = owned_ref;
41632 s1_is_unicode = 1;
41633 } else if (((!s2_is_unicode) & (!s1_is_unicode))) {
41634 return __Pyx_PyBytes_Equals(s1, s2, equals);
41635 }
41636 #endif
41637 if (s1_is_unicode & s2_is_unicode) {
41638 Py_ssize_t length;
41639 int kind;
41640 void *data1, *data2;
41641 if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0))
41642 return -1;
41643 length = __Pyx_PyUnicode_GET_LENGTH(s1);
41644 if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) {
41645 goto return_ne;
41646 }
41647 #if CYTHON_USE_UNICODE_INTERNALS
41648 {
41649 Py_hash_t hash1, hash2;
41650 #if CYTHON_PEP393_ENABLED
41651 hash1 = ((PyASCIIObject*)s1)->hash;
41652 hash2 = ((PyASCIIObject*)s2)->hash;
41653 #else
41654 hash1 = ((PyUnicodeObject*)s1)->hash;
41655 hash2 = ((PyUnicodeObject*)s2)->hash;
41656 #endif
41657 if (hash1 != hash2 && hash1 != -1 && hash2 != -1) {
41658 goto return_ne;
41659 }
41660 }
41661 #endif
41662 kind = __Pyx_PyUnicode_KIND(s1);
41663 if (kind != __Pyx_PyUnicode_KIND(s2)) {
41664 goto return_ne;
41665 }
41666 data1 = __Pyx_PyUnicode_DATA(s1);
41667 data2 = __Pyx_PyUnicode_DATA(s2);
41668 if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) {
41669 goto return_ne;
41670 } else if (length == 1) {
41671 goto return_eq;
41672 } else {
41673 int result = memcmp(data1, data2, (size_t)(length * kind));
41674 #if PY_MAJOR_VERSION < 3
41675 Py_XDECREF(owned_ref);
41676 #endif
41677 return (equals == Py_EQ) ? (result == 0) : (result != 0);
41678 }
41679 } else if ((s1 == Py_None) & s2_is_unicode) {
41680 goto return_ne;
41681 } else if ((s2 == Py_None) & s1_is_unicode) {
41682 goto return_ne;
41683 } else {
41684 int result;
41685 PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
41686 #if PY_MAJOR_VERSION < 3
41687 Py_XDECREF(owned_ref);
41688 #endif
41689 if (!py_result)
41690 return -1;
41691 result = __Pyx_PyObject_IsTrue(py_result);
41692 Py_DECREF(py_result);
41693 return result;
41694 }
41695 return_eq:
41696 #if PY_MAJOR_VERSION < 3
41697 Py_XDECREF(owned_ref);
41698 #endif
41699 return (equals == Py_EQ);
41700 return_ne:
41701 #if PY_MAJOR_VERSION < 3
41702 Py_XDECREF(owned_ref);
41703 #endif
41704 return (equals == Py_NE);
41705 #endif
41706 }
41707
41708 /* fastcall */
41709 #if CYTHON_METH_FASTCALL
41710 static CYTHON_INLINE PyObject * __Pyx_GetKwValue_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues, PyObject *s)
41711 {
41712 Py_ssize_t i, n = PyTuple_GET_SIZE(kwnames);
41713 for (i = 0; i < n; i++)
41714 {
41715 if (s == PyTuple_GET_ITEM(kwnames, i)) return kwvalues[i];
41716 }
41717 for (i = 0; i < n; i++)
41718 {
41719 int eq = __Pyx_PyUnicode_Equals(s, PyTuple_GET_ITEM(kwnames, i), Py_EQ);
41720 if (unlikely(eq != 0)) {
41721 if (unlikely(eq < 0)) return NULL;
41722 return kwvalues[i];
41723 }
41724 }
41725 return NULL;
41726 }
41727 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000
41728 CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues) {
41729 Py_ssize_t i, nkwargs = PyTuple_GET_SIZE(kwnames);
41730 PyObject *dict;
41731 dict = PyDict_New();
41732 if (unlikely(!dict))
41733 return NULL;
41734 for (i=0; i<nkwargs; i++) {
41735 PyObject *key = PyTuple_GET_ITEM(kwnames, i);
41736 if (unlikely(PyDict_SetItem(dict, key, kwvalues[i]) < 0))
41737 goto bad;
41738 }
41739 return dict;
41740 bad:
41741 Py_DECREF(dict);
41742 return NULL;
41743 }
41744 #endif
41745 #endif
41746
41747 /* RaiseArgTupleInvalid */
41748 static void __Pyx_RaiseArgtupleInvalid(
41749 const char* func_name,
41750 int exact,
41751 Py_ssize_t num_min,
41752 Py_ssize_t num_max,
41753 Py_ssize_t num_found)
41754 {
41755 Py_ssize_t num_expected;
41756 const char *more_or_less;
41757 if (num_found < num_min) {
41758 num_expected = num_min;
41759 more_or_less = "at least";
41760 } else {
41761 num_expected = num_max;
41762 more_or_less = "at most";
41763 }
41764 if (exact) {
41765 more_or_less = "exactly";
41766 }
41767 PyErr_Format(PyExc_TypeError,
41768 "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
41769 func_name, more_or_less, num_expected,
41770 (num_expected == 1) ? "" : "s", num_found);
41771 }
41772
41773 /* RaiseDoubleKeywords */
41774 static void __Pyx_RaiseDoubleKeywordsError(
41775 const char* func_name,
41776 PyObject* kw_name)
41777 {
41778 PyErr_Format(PyExc_TypeError,
41779 #if PY_MAJOR_VERSION >= 3
41780 "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
41781 #else
41782 "%s() got multiple values for keyword argument '%s'", func_name,
41783 PyString_AsString(kw_name));
41784 #endif
41785 }
41786
41787 /* ParseKeywords */
41788 static int __Pyx_ParseOptionalKeywords(
41789 PyObject *kwds,
41790 PyObject *const *kwvalues,
41791 PyObject **argnames[],
41792 PyObject *kwds2,
41793 PyObject *values[],
41794 Py_ssize_t num_pos_args,
41795 const char* function_name)
41796 {
41797 PyObject *key = 0, *value = 0;
41798 Py_ssize_t pos = 0;
41799 PyObject*** name;
41800 PyObject*** first_kw_arg = argnames + num_pos_args;
41801 int kwds_is_tuple = CYTHON_METH_FASTCALL && likely(PyTuple_Check(kwds));
41802 while (1) {
41803 Py_XDECREF(key); key = NULL;
41804 Py_XDECREF(value); value = NULL;
41805 if (kwds_is_tuple) {
41806 Py_ssize_t size;
41807 #if CYTHON_ASSUME_SAFE_MACROS
41808 size = PyTuple_GET_SIZE(kwds);
41809 #else
41810 size = PyTuple_Size(kwds);
41811 if (size < 0) goto bad;
41812 #endif
41813 if (pos >= size) break;
41814 #if CYTHON_AVOID_BORROWED_REFS
41815 key = __Pyx_PySequence_ITEM(kwds, pos);
41816 if (!key) goto bad;
41817 #elif CYTHON_ASSUME_SAFE_MACROS
41818 key = PyTuple_GET_ITEM(kwds, pos);
41819 #else
41820 key = PyTuple_GetItem(kwds, pos);
41821 if (!key) goto bad;
41822 #endif
41823 value = kwvalues[pos];
41824 pos++;
41825 }
41826 else
41827 {
41828 if (!PyDict_Next(kwds, &pos, &key, &value)) break;
41829 #if CYTHON_AVOID_BORROWED_REFS
41830 Py_INCREF(key);
41831 #endif
41832 }
41833 name = first_kw_arg;
41834 while (*name && (**name != key)) name++;
41835 if (*name) {
41836 values[name-argnames] = value;
41837 #if CYTHON_AVOID_BORROWED_REFS
41838 Py_INCREF(value);
41839 Py_DECREF(key);
41840 #endif
41841 key = NULL;
41842 value = NULL;
41843 continue;
41844 }
41845 #if !CYTHON_AVOID_BORROWED_REFS
41846 Py_INCREF(key);
41847 #endif
41848 Py_INCREF(value);
41849 name = first_kw_arg;
41850 #if PY_MAJOR_VERSION < 3
41851 if (likely(PyString_Check(key))) {
41852 while (*name) {
41853 if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
41854 && _PyString_Eq(**name, key)) {
41855 values[name-argnames] = value;
41856 #if CYTHON_AVOID_BORROWED_REFS
41857 value = NULL;
41858 #endif
41859 break;
41860 }
41861 name++;
41862 }
41863 if (*name) continue;
41864 else {
41865 PyObject*** argname = argnames;
41866 while (argname != first_kw_arg) {
41867 if ((**argname == key) || (
41868 (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
41869 && _PyString_Eq(**argname, key))) {
41870 goto arg_passed_twice;
41871 }
41872 argname++;
41873 }
41874 }
41875 } else
41876 #endif
41877 if (likely(PyUnicode_Check(key))) {
41878 while (*name) {
41879 int cmp = (
41880 #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
41881 (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 :
41882 #endif
41883 PyUnicode_Compare(**name, key)
41884 );
41885 if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
41886 if (cmp == 0) {
41887 values[name-argnames] = value;
41888 #if CYTHON_AVOID_BORROWED_REFS
41889 value = NULL;
41890 #endif
41891 break;
41892 }
41893 name++;
41894 }
41895 if (*name) continue;
41896 else {
41897 PyObject*** argname = argnames;
41898 while (argname != first_kw_arg) {
41899 int cmp = (**argname == key) ? 0 :
41900 #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
41901 (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 :
41902 #endif
41903 PyUnicode_Compare(**argname, key);
41904 if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
41905 if (cmp == 0) goto arg_passed_twice;
41906 argname++;
41907 }
41908 }
41909 } else
41910 goto invalid_keyword_type;
41911 if (kwds2) {
41912 if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
41913 } else {
41914 goto invalid_keyword;
41915 }
41916 }
41917 Py_XDECREF(key);
41918 Py_XDECREF(value);
41919 return 0;
41920 arg_passed_twice:
41921 __Pyx_RaiseDoubleKeywordsError(function_name, key);
41922 goto bad;
41923 invalid_keyword_type:
41924 PyErr_Format(PyExc_TypeError,
41925 "%.200s() keywords must be strings", function_name);
41926 goto bad;
41927 invalid_keyword:
41928 #if PY_MAJOR_VERSION < 3
41929 PyErr_Format(PyExc_TypeError,
41930 "%.200s() got an unexpected keyword argument '%.200s'",
41931 function_name, PyString_AsString(key));
41932 #else
41933 PyErr_Format(PyExc_TypeError,
41934 "%s() got an unexpected keyword argument '%U'",
41935 function_name, key);
41936 #endif
41937 bad:
41938 Py_XDECREF(key);
41939 Py_XDECREF(value);
41940 return -1;
41941 }
41942
41943 /* PyDictVersioning */
41944 #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS
41945 static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) {
41946 PyObject *dict = Py_TYPE(obj)->tp_dict;
41947 return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0;
41948 }
41949 static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) {
41950 PyObject **dictptr = NULL;
41951 Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset;
41952 if (offset) {
41953 #if CYTHON_COMPILING_IN_CPYTHON
41954 dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj);
41955 #else
41956 dictptr = _PyObject_GetDictPtr(obj);
41957 #endif
41958 }
41959 return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0;
41960 }
41961 static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) {
41962 PyObject *dict = Py_TYPE(obj)->tp_dict;
41963 if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict)))
41964 return 0;
41965 return obj_dict_version == __Pyx_get_object_dict_version(obj);
41966 }
41967 #endif
41968
41969 /* GetModuleGlobalName */
41970 #if CYTHON_USE_DICT_VERSIONS
41971 static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value)
41972 #else
41973 static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name)
41974 #endif
41975 {
41976 PyObject *result;
41977 #if !CYTHON_AVOID_BORROWED_REFS
41978 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && PY_VERSION_HEX < 0x030d0000
41979 result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash);
41980 __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
41981 if (likely(result)) {
41982 return __Pyx_NewRef(result);
41983 } else if (unlikely(PyErr_Occurred())) {
41984 return NULL;
41985 }
41986 #elif CYTHON_COMPILING_IN_LIMITED_API
41987 if (unlikely(!__pyx_m)) {
41988 return NULL;
41989 }
41990 result = PyObject_GetAttr(__pyx_m, name);
41991 if (likely(result)) {
41992 return result;
41993 }
41994 #else
41995 result = PyDict_GetItem(__pyx_d, name);
41996 __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
41997 if (likely(result)) {
41998 return __Pyx_NewRef(result);
41999 }
42000 #endif
42001 #else
42002 result = PyObject_GetItem(__pyx_d, name);
42003 __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
42004 if (likely(result)) {
42005 return __Pyx_NewRef(result);
42006 }
42007 PyErr_Clear();
42008 #endif
42009 return __Pyx_GetBuiltinName(name);
42010 }
42011
42012 /* PyFunctionFastCall */
42013 #if CYTHON_FAST_PYCALL && !CYTHON_VECTORCALL
42014 static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na,
42015 PyObject *globals) {
42016 PyFrameObject *f;
42017 PyThreadState *tstate = __Pyx_PyThreadState_Current;
42018 PyObject **fastlocals;
42019 Py_ssize_t i;
42020 PyObject *result;
42021 assert(globals != NULL);
42022 /* XXX Perhaps we should create a specialized
42023 PyFrame_New() that doesn't take locals, but does
42024 take builtins without sanity checking them.
42025 */
42026 assert(tstate != NULL);
42027 f = PyFrame_New(tstate, co, globals, NULL);
42028 if (f == NULL) {
42029 return NULL;
42030 }
42031 fastlocals = __Pyx_PyFrame_GetLocalsplus(f);
42032 for (i = 0; i < na; i++) {
42033 Py_INCREF(*args);
42034 fastlocals[i] = *args++;
42035 }
42036 result = PyEval_EvalFrameEx(f,0);
42037 ++tstate->recursion_depth;
42038 Py_DECREF(f);
42039 --tstate->recursion_depth;
42040 return result;
42041 }
42042 static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) {
42043 PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func);
42044 PyObject *globals = PyFunction_GET_GLOBALS(func);
42045 PyObject *argdefs = PyFunction_GET_DEFAULTS(func);
42046 PyObject *closure;
42047 #if PY_MAJOR_VERSION >= 3
42048 PyObject *kwdefs;
42049 #endif
42050 PyObject *kwtuple, **k;
42051 PyObject **d;
42052 Py_ssize_t nd;
42053 Py_ssize_t nk;
42054 PyObject *result;
42055 assert(kwargs == NULL || PyDict_Check(kwargs));
42056 nk = kwargs ? PyDict_Size(kwargs) : 0;
42057 #if PY_MAJOR_VERSION < 3
42058 if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) {
42059 return NULL;
42060 }
42061 #else
42062 if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) {
42063 return NULL;
42064 }
42065 #endif
42066 if (
42067 #if PY_MAJOR_VERSION >= 3
42068 co->co_kwonlyargcount == 0 &&
42069 #endif
42070 likely(kwargs == NULL || nk == 0) &&
42071 co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) {
42072 if (argdefs == NULL && co->co_argcount == nargs) {
42073 result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals);
42074 goto done;
42075 }
42076 else if (nargs == 0 && argdefs != NULL
42077 && co->co_argcount == Py_SIZE(argdefs)) {
42078 /* function called with no arguments, but all parameters have
42079 a default value: use default values as arguments .*/
42080 args = &PyTuple_GET_ITEM(argdefs, 0);
42081 result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals);
42082 goto done;
42083 }
42084 }
42085 if (kwargs != NULL) {
42086 Py_ssize_t pos, i;
42087 kwtuple = PyTuple_New(2 * nk);
42088 if (kwtuple == NULL) {
42089 result = NULL;
42090 goto done;
42091 }
42092 k = &PyTuple_GET_ITEM(kwtuple, 0);
42093 pos = i = 0;
42094 while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) {
42095 Py_INCREF(k[i]);
42096 Py_INCREF(k[i+1]);
42097 i += 2;
42098 }
42099 nk = i / 2;
42100 }
42101 else {
42102 kwtuple = NULL;
42103 k = NULL;
42104 }
42105 closure = PyFunction_GET_CLOSURE(func);
42106 #if PY_MAJOR_VERSION >= 3
42107 kwdefs = PyFunction_GET_KW_DEFAULTS(func);
42108 #endif
42109 if (argdefs != NULL) {
42110 d = &PyTuple_GET_ITEM(argdefs, 0);
42111 nd = Py_SIZE(argdefs);
42112 }
42113 else {
42114 d = NULL;
42115 nd = 0;
42116 }
42117 #if PY_MAJOR_VERSION >= 3
42118 result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL,
42119 args, (int)nargs,
42120 k, (int)nk,
42121 d, (int)nd, kwdefs, closure);
42122 #else
42123 result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL,
42124 args, (int)nargs,
42125 k, (int)nk,
42126 d, (int)nd, closure);
42127 #endif
42128 Py_XDECREF(kwtuple);
42129 done:
42130 Py_LeaveRecursiveCall();
42131 return result;
42132 }
42133 #endif
42134
42135 /* PyObjectCall */
42136 #if CYTHON_COMPILING_IN_CPYTHON
42137 static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
42138 PyObject *result;
42139 ternaryfunc call = Py_TYPE(func)->tp_call;
42140 if (unlikely(!call))
42141 return PyObject_Call(func, arg, kw);
42142 #if PY_MAJOR_VERSION < 3
42143 if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
42144 return NULL;
42145 #else
42146 if (unlikely(Py_EnterRecursiveCall(" while calling a Python object")))
42147 return NULL;
42148 #endif
42149 result = (*call)(func, arg, kw);
42150 Py_LeaveRecursiveCall();
42151 if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
42152 PyErr_SetString(
42153 PyExc_SystemError,
42154 "NULL result without error in PyObject_Call");
42155 }
42156 return result;
42157 }
42158 #endif
42159
42160 /* PyObjectCallMethO */
42161 #if CYTHON_COMPILING_IN_CPYTHON
42162 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) {
42163 PyObject *self, *result;
42164 PyCFunction cfunc;
42165 cfunc = __Pyx_CyOrPyCFunction_GET_FUNCTION(func);
42166 self = __Pyx_CyOrPyCFunction_GET_SELF(func);
42167 #if PY_MAJOR_VERSION < 3
42168 if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
42169 return NULL;
42170 #else
42171 if (unlikely(Py_EnterRecursiveCall(" while calling a Python object")))
42172 return NULL;
42173 #endif
42174 result = cfunc(self, arg);
42175 Py_LeaveRecursiveCall();
42176 if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
42177 PyErr_SetString(
42178 PyExc_SystemError,
42179 "NULL result without error in PyObject_Call");
42180 }
42181 return result;
42182 }
42183 #endif
42184
42185 /* PyObjectFastCall */
42186 #if PY_VERSION_HEX < 0x03090000 || CYTHON_COMPILING_IN_LIMITED_API
42187 static PyObject* __Pyx_PyObject_FastCall_fallback(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs) {
42188 PyObject *argstuple;
42189 PyObject *result = 0;
42190 size_t i;
42191 argstuple = PyTuple_New((Py_ssize_t)nargs);
42192 if (unlikely(!argstuple)) return NULL;
42193 for (i = 0; i < nargs; i++) {
42194 Py_INCREF(args[i]);
42195 if (__Pyx_PyTuple_SET_ITEM(argstuple, (Py_ssize_t)i, args[i]) < 0) goto bad;
42196 }
42197 result = __Pyx_PyObject_Call(func, argstuple, kwargs);
42198 bad:
42199 Py_DECREF(argstuple);
42200 return result;
42201 }
42202 #endif
42203 static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t _nargs, PyObject *kwargs) {
42204 Py_ssize_t nargs = __Pyx_PyVectorcall_NARGS(_nargs);
42205 #if CYTHON_COMPILING_IN_CPYTHON
42206 if (nargs == 0 && kwargs == NULL) {
42207 if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_NOARGS))
42208 return __Pyx_PyObject_CallMethO(func, NULL);
42209 }
42210 else if (nargs == 1 && kwargs == NULL) {
42211 if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_O))
42212 return __Pyx_PyObject_CallMethO(func, args[0]);
42213 }
42214 #endif
42215 #if PY_VERSION_HEX < 0x030800B1
42216 #if CYTHON_FAST_PYCCALL
42217 if (PyCFunction_Check(func)) {
42218 if (kwargs) {
42219 return _PyCFunction_FastCallDict(func, args, nargs, kwargs);
42220 } else {
42221 return _PyCFunction_FastCallKeywords(func, args, nargs, NULL);
42222 }
42223 }
42224 #if PY_VERSION_HEX >= 0x030700A1
42225 if (!kwargs && __Pyx_IS_TYPE(func, &PyMethodDescr_Type)) {
42226 return _PyMethodDescr_FastCallKeywords(func, args, nargs, NULL);
42227 }
42228 #endif
42229 #endif
42230 #if CYTHON_FAST_PYCALL
42231 if (PyFunction_Check(func)) {
42232 return __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs);
42233 }
42234 #endif
42235 #endif
42236 if (kwargs == NULL) {
42237 #if CYTHON_VECTORCALL
42238 #if PY_VERSION_HEX < 0x03090000
42239 vectorcallfunc f = _PyVectorcall_Function(func);
42240 #else
42241 vectorcallfunc f = PyVectorcall_Function(func);
42242 #endif
42243 if (f) {
42244 return f(func, args, (size_t)nargs, NULL);
42245 }
42246 #elif defined(__Pyx_CyFunction_USED) && CYTHON_BACKPORT_VECTORCALL
42247 if (__Pyx_CyFunction_CheckExact(func)) {
42248 __pyx_vectorcallfunc f = __Pyx_CyFunction_func_vectorcall(func);
42249 if (f) return f(func, args, (size_t)nargs, NULL);
42250 }
42251 #endif
42252 }
42253 if (nargs == 0) {
42254 return __Pyx_PyObject_Call(func, __pyx_empty_tuple, kwargs);
42255 }
42256 #if PY_VERSION_HEX >= 0x03090000 && !CYTHON_COMPILING_IN_LIMITED_API
42257 return PyObject_VectorcallDict(func, args, (size_t)nargs, kwargs);
42258 #else
42259 return __Pyx_PyObject_FastCall_fallback(func, args, (size_t)nargs, kwargs);
42260 #endif
42261 }
42262
42263 /* GetItemInt */
42264 static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
42265 PyObject *r;
42266 if (unlikely(!j)) return NULL;
42267 r = PyObject_GetItem(o, j);
42268 Py_DECREF(j);
42269 return r;
42270 }
42271 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
42272 CYTHON_NCP_UNUSED int wraparound,
42273 CYTHON_NCP_UNUSED int boundscheck) {
42274 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
42275 Py_ssize_t wrapped_i = i;
42276 if (wraparound & unlikely(i < 0)) {
42277 wrapped_i += PyList_GET_SIZE(o);
42278 }
42279 if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) {
42280 PyObject *r = PyList_GET_ITEM(o, wrapped_i);
42281 Py_INCREF(r);
42282 return r;
42283 }
42284 return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
42285 #else
42286 return PySequence_GetItem(o, i);
42287 #endif
42288 }
42289 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
42290 CYTHON_NCP_UNUSED int wraparound,
42291 CYTHON_NCP_UNUSED int boundscheck) {
42292 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
42293 Py_ssize_t wrapped_i = i;
42294 if (wraparound & unlikely(i < 0)) {
42295 wrapped_i += PyTuple_GET_SIZE(o);
42296 }
42297 if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) {
42298 PyObject *r = PyTuple_GET_ITEM(o, wrapped_i);
42299 Py_INCREF(r);
42300 return r;
42301 }
42302 return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
42303 #else
42304 return PySequence_GetItem(o, i);
42305 #endif
42306 }
42307 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list,
42308 CYTHON_NCP_UNUSED int wraparound,
42309 CYTHON_NCP_UNUSED int boundscheck) {
42310 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS
42311 if (is_list || PyList_CheckExact(o)) {
42312 Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
42313 if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) {
42314 PyObject *r = PyList_GET_ITEM(o, n);
42315 Py_INCREF(r);
42316 return r;
42317 }
42318 }
42319 else if (PyTuple_CheckExact(o)) {
42320 Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
42321 if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) {
42322 PyObject *r = PyTuple_GET_ITEM(o, n);
42323 Py_INCREF(r);
42324 return r;
42325 }
42326 } else {
42327 PyMappingMethods *mm = Py_TYPE(o)->tp_as_mapping;
42328 PySequenceMethods *sm = Py_TYPE(o)->tp_as_sequence;
42329 if (mm && mm->mp_subscript) {
42330 PyObject *r, *key = PyInt_FromSsize_t(i);
42331 if (unlikely(!key)) return NULL;
42332 r = mm->mp_subscript(o, key);
42333 Py_DECREF(key);
42334 return r;
42335 }
42336 if (likely(sm && sm->sq_item)) {
42337 if (wraparound && unlikely(i < 0) && likely(sm->sq_length)) {
42338 Py_ssize_t l = sm->sq_length(o);
42339 if (likely(l >= 0)) {
42340 i += l;
42341 } else {
42342 if (!PyErr_ExceptionMatches(PyExc_OverflowError))
42343 return NULL;
42344 PyErr_Clear();
42345 }
42346 }
42347 return sm->sq_item(o, i);
42348 }
42349 }
42350 #else
42351 if (is_list || !PyMapping_Check(o)) {
42352 return PySequence_GetItem(o, i);
42353 }
42354 #endif
42355 return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
42356 }
42357
42358 /* PyObjectCallOneArg */
42359 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
42360 PyObject *args[2] = {NULL, arg};
42361 return __Pyx_PyObject_FastCall(func, args+1, 1 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET);
42362 }
42363
42364 /* PyIntBinop */
42365 #if !CYTHON_COMPILING_IN_PYPY
42366 static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check) {
42367 CYTHON_MAYBE_UNUSED_VAR(intval);
42368 CYTHON_MAYBE_UNUSED_VAR(inplace);
42369 CYTHON_UNUSED_VAR(zerodivision_check);
42370 #if PY_MAJOR_VERSION < 3
42371 if (likely(PyInt_CheckExact(op1))) {
42372 const long b = intval;
42373 long x;
42374 long a = PyInt_AS_LONG(op1);
42375
42376 x = (long)((unsigned long)a - (unsigned long)b);
42377 if (likely((x^a) >= 0 || (x^~b) >= 0))
42378 return PyInt_FromLong(x);
42379 return PyLong_Type.tp_as_number->nb_subtract(op1, op2);
42380 }
42381 #endif
42382 #if CYTHON_USE_PYLONG_INTERNALS
42383 if (likely(PyLong_CheckExact(op1))) {
42384 const long b = intval;
42385 long a, x;
42386 #ifdef HAVE_LONG_LONG
42387 const PY_LONG_LONG llb = intval;
42388 PY_LONG_LONG lla, llx;
42389 #endif
42390 if (unlikely(__Pyx_PyLong_IsZero(op1))) {
42391 return PyLong_FromLong(-intval);
42392 }
42393 if (likely(__Pyx_PyLong_IsCompact(op1))) {
42394 a = __Pyx_PyLong_CompactValue(op1);
42395 } else {
42396 const digit* digits = __Pyx_PyLong_Digits(op1);
42397 const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(op1);
42398 switch (size) {
42399 case -2:
42400 if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
42401 a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
42402 break;
42403 #ifdef HAVE_LONG_LONG
42404 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
42405 lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
42406 goto long_long;
42407 #endif
42408 }
42409 CYTHON_FALLTHROUGH;
42410 case 2:
42411 if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
42412 a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
42413 break;
42414 #ifdef HAVE_LONG_LONG
42415 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
42416 lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
42417 goto long_long;
42418 #endif
42419 }
42420 CYTHON_FALLTHROUGH;
42421 case -3:
42422 if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
42423 a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
42424 break;
42425 #ifdef HAVE_LONG_LONG
42426 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
42427 lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
42428 goto long_long;
42429 #endif
42430 }
42431 CYTHON_FALLTHROUGH;
42432 case 3:
42433 if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
42434 a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
42435 break;
42436 #ifdef HAVE_LONG_LONG
42437 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
42438 lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
42439 goto long_long;
42440 #endif
42441 }
42442 CYTHON_FALLTHROUGH;
42443 case -4:
42444 if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
42445 a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
42446 break;
42447 #ifdef HAVE_LONG_LONG
42448 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
42449 lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
42450 goto long_long;
42451 #endif
42452 }
42453 CYTHON_FALLTHROUGH;
42454 case 4:
42455 if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
42456 a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
42457 break;
42458 #ifdef HAVE_LONG_LONG
42459 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
42460 lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
42461 goto long_long;
42462 #endif
42463 }
42464 CYTHON_FALLTHROUGH;
42465 default: return PyLong_Type.tp_as_number->nb_subtract(op1, op2);
42466 }
42467 }
42468 x = a - b;
42469 return PyLong_FromLong(x);
42470 #ifdef HAVE_LONG_LONG
42471 long_long:
42472 llx = lla - llb;
42473 return PyLong_FromLongLong(llx);
42474 #endif
42475
42476
42477 }
42478 #endif
42479 if (PyFloat_CheckExact(op1)) {
42480 const long b = intval;
42481 #if CYTHON_COMPILING_IN_LIMITED_API
42482 double a = __pyx_PyFloat_AsDouble(op1);
42483 #else
42484 double a = PyFloat_AS_DOUBLE(op1);
42485 #endif
42486 double result;
42487
42488 PyFPE_START_PROTECT("subtract", return NULL)
42489 result = ((double)a) - (double)b;
42490 PyFPE_END_PROTECT(result)
42491 return PyFloat_FromDouble(result);
42492 }
42493 return (inplace ? PyNumber_InPlaceSubtract : PyNumber_Subtract)(op1, op2);
42494 }
42495 #endif
42496
42497 /* GetTopmostException */
42498 #if CYTHON_USE_EXC_INFO_STACK && CYTHON_FAST_THREAD_STATE
42499 static _PyErr_StackItem *
42500 __Pyx_PyErr_GetTopmostException(PyThreadState *tstate)
42501 {
42502 _PyErr_StackItem *exc_info = tstate->exc_info;
42503 while ((exc_info->exc_value == NULL || exc_info->exc_value == Py_None) &&
42504 exc_info->previous_item != NULL)
42505 {
42506 exc_info = exc_info->previous_item;
42507 }
42508 return exc_info;
42509 }
42510 #endif
42511
42512 /* SaveResetException */
42513 #if CYTHON_FAST_THREAD_STATE
42514 static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
42515 #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4
42516 _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate);
42517 PyObject *exc_value = exc_info->exc_value;
42518 if (exc_value == NULL || exc_value == Py_None) {
42519 *value = NULL;
42520 *type = NULL;
42521 *tb = NULL;
42522 } else {
42523 *value = exc_value;
42524 Py_INCREF(*value);
42525 *type = (PyObject*) Py_TYPE(exc_value);
42526 Py_INCREF(*type);
42527 *tb = PyException_GetTraceback(exc_value);
42528 }
42529 #elif CYTHON_USE_EXC_INFO_STACK
42530 _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate);
42531 *type = exc_info->exc_type;
42532 *value = exc_info->exc_value;
42533 *tb = exc_info->exc_traceback;
42534 Py_XINCREF(*type);
42535 Py_XINCREF(*value);
42536 Py_XINCREF(*tb);
42537 #else
42538 *type = tstate->exc_type;
42539 *value = tstate->exc_value;
42540 *tb = tstate->exc_traceback;
42541 Py_XINCREF(*type);
42542 Py_XINCREF(*value);
42543 Py_XINCREF(*tb);
42544 #endif
42545 }
42546 static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
42547 #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4
42548 _PyErr_StackItem *exc_info = tstate->exc_info;
42549 PyObject *tmp_value = exc_info->exc_value;
42550 exc_info->exc_value = value;
42551 Py_XDECREF(tmp_value);
42552 Py_XDECREF(type);
42553 Py_XDECREF(tb);
42554 #else
42555 PyObject *tmp_type, *tmp_value, *tmp_tb;
42556 #if CYTHON_USE_EXC_INFO_STACK
42557 _PyErr_StackItem *exc_info = tstate->exc_info;
42558 tmp_type = exc_info->exc_type;
42559 tmp_value = exc_info->exc_value;
42560 tmp_tb = exc_info->exc_traceback;
42561 exc_info->exc_type = type;
42562 exc_info->exc_value = value;
42563 exc_info->exc_traceback = tb;
42564 #else
42565 tmp_type = tstate->exc_type;
42566 tmp_value = tstate->exc_value;
42567 tmp_tb = tstate->exc_traceback;
42568 tstate->exc_type = type;
42569 tstate->exc_value = value;
42570 tstate->exc_traceback = tb;
42571 #endif
42572 Py_XDECREF(tmp_type);
42573 Py_XDECREF(tmp_value);
42574 Py_XDECREF(tmp_tb);
42575 #endif
42576 }
42577 #endif
42578
42579 /* GetException */
42580 #if CYTHON_FAST_THREAD_STATE
42581 static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb)
42582 #else
42583 static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
42584 #endif
42585 {
42586 PyObject *local_type = NULL, *local_value, *local_tb = NULL;
42587 #if CYTHON_FAST_THREAD_STATE
42588 PyObject *tmp_type, *tmp_value, *tmp_tb;
42589 #if PY_VERSION_HEX >= 0x030C00A6
42590 local_value = tstate->current_exception;
42591 tstate->current_exception = 0;
42592 if (likely(local_value)) {
42593 local_type = (PyObject*) Py_TYPE(local_value);
42594 Py_INCREF(local_type);
42595 local_tb = PyException_GetTraceback(local_value);
42596 }
42597 #else
42598 local_type = tstate->curexc_type;
42599 local_value = tstate->curexc_value;
42600 local_tb = tstate->curexc_traceback;
42601 tstate->curexc_type = 0;
42602 tstate->curexc_value = 0;
42603 tstate->curexc_traceback = 0;
42604 #endif
42605 #else
42606 PyErr_Fetch(&local_type, &local_value, &local_tb);
42607 #endif
42608 PyErr_NormalizeException(&local_type, &local_value, &local_tb);
42609 #if CYTHON_FAST_THREAD_STATE && PY_VERSION_HEX >= 0x030C00A6
42610 if (unlikely(tstate->current_exception))
42611 #elif CYTHON_FAST_THREAD_STATE
42612 if (unlikely(tstate->curexc_type))
42613 #else
42614 if (unlikely(PyErr_Occurred()))
42615 #endif
42616 goto bad;
42617 #if PY_MAJOR_VERSION >= 3
42618 if (local_tb) {
42619 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
42620 goto bad;
42621 }
42622 #endif
42623 Py_XINCREF(local_tb);
42624 Py_XINCREF(local_type);
42625 Py_XINCREF(local_value);
42626 *type = local_type;
42627 *value = local_value;
42628 *tb = local_tb;
42629 #if CYTHON_FAST_THREAD_STATE
42630 #if CYTHON_USE_EXC_INFO_STACK
42631 {
42632 _PyErr_StackItem *exc_info = tstate->exc_info;
42633 #if PY_VERSION_HEX >= 0x030B00a4
42634 tmp_value = exc_info->exc_value;
42635 exc_info->exc_value = local_value;
42636 tmp_type = NULL;
42637 tmp_tb = NULL;
42638 Py_XDECREF(local_type);
42639 Py_XDECREF(local_tb);
42640 #else
42641 tmp_type = exc_info->exc_type;
42642 tmp_value = exc_info->exc_value;
42643 tmp_tb = exc_info->exc_traceback;
42644 exc_info->exc_type = local_type;
42645 exc_info->exc_value = local_value;
42646 exc_info->exc_traceback = local_tb;
42647 #endif
42648 }
42649 #else
42650 tmp_type = tstate->exc_type;
42651 tmp_value = tstate->exc_value;
42652 tmp_tb = tstate->exc_traceback;
42653 tstate->exc_type = local_type;
42654 tstate->exc_value = local_value;
42655 tstate->exc_traceback = local_tb;
42656 #endif
42657 Py_XDECREF(tmp_type);
42658 Py_XDECREF(tmp_value);
42659 Py_XDECREF(tmp_tb);
42660 #else
42661 PyErr_SetExcInfo(local_type, local_value, local_tb);
42662 #endif
42663 return 0;
42664 bad:
42665 *type = 0;
42666 *value = 0;
42667 *tb = 0;
42668 Py_XDECREF(local_type);
42669 Py_XDECREF(local_value);
42670 Py_XDECREF(local_tb);
42671 return -1;
42672 }
42673
42674 /* RaiseException */
42675 #if PY_MAJOR_VERSION < 3
42676 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
42677 __Pyx_PyThreadState_declare
42678 CYTHON_UNUSED_VAR(cause);
42679 Py_XINCREF(type);
42680 if (!value || value == Py_None)
42681 value = NULL;
42682 else
42683 Py_INCREF(value);
42684 if (!tb || tb == Py_None)
42685 tb = NULL;
42686 else {
42687 Py_INCREF(tb);
42688 if (!PyTraceBack_Check(tb)) {
42689 PyErr_SetString(PyExc_TypeError,
42690 "raise: arg 3 must be a traceback or None");
42691 goto raise_error;
42692 }
42693 }
42694 if (PyType_Check(type)) {
42695 #if CYTHON_COMPILING_IN_PYPY
42696 if (!value) {
42697 Py_INCREF(Py_None);
42698 value = Py_None;
42699 }
42700 #endif
42701 PyErr_NormalizeException(&type, &value, &tb);
42702 } else {
42703 if (value) {
42704 PyErr_SetString(PyExc_TypeError,
42705 "instance exception may not have a separate value");
42706 goto raise_error;
42707 }
42708 value = type;
42709 type = (PyObject*) Py_TYPE(type);
42710 Py_INCREF(type);
42711 if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
42712 PyErr_SetString(PyExc_TypeError,
42713 "raise: exception class must be a subclass of BaseException");
42714 goto raise_error;
42715 }
42716 }
42717 __Pyx_PyThreadState_assign
42718 __Pyx_ErrRestore(type, value, tb);
42719 return;
42720 raise_error:
42721 Py_XDECREF(value);
42722 Py_XDECREF(type);
42723 Py_XDECREF(tb);
42724 return;
42725 }
42726 #else
42727 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
42728 PyObject* owned_instance = NULL;
42729 if (tb == Py_None) {
42730 tb = 0;
42731 } else if (tb && !PyTraceBack_Check(tb)) {
42732 PyErr_SetString(PyExc_TypeError,
42733 "raise: arg 3 must be a traceback or None");
42734 goto bad;
42735 }
42736 if (value == Py_None)
42737 value = 0;
42738 if (PyExceptionInstance_Check(type)) {
42739 if (value) {
42740 PyErr_SetString(PyExc_TypeError,
42741 "instance exception may not have a separate value");
42742 goto bad;
42743 }
42744 value = type;
42745 type = (PyObject*) Py_TYPE(value);
42746 } else if (PyExceptionClass_Check(type)) {
42747 PyObject *instance_class = NULL;
42748 if (value && PyExceptionInstance_Check(value)) {
42749 instance_class = (PyObject*) Py_TYPE(value);
42750 if (instance_class != type) {
42751 int is_subclass = PyObject_IsSubclass(instance_class, type);
42752 if (!is_subclass) {
42753 instance_class = NULL;
42754 } else if (unlikely(is_subclass == -1)) {
42755 goto bad;
42756 } else {
42757 type = instance_class;
42758 }
42759 }
42760 }
42761 if (!instance_class) {
42762 PyObject *args;
42763 if (!value)
42764 args = PyTuple_New(0);
42765 else if (PyTuple_Check(value)) {
42766 Py_INCREF(value);
42767 args = value;
42768 } else
42769 args = PyTuple_Pack(1, value);
42770 if (!args)
42771 goto bad;
42772 owned_instance = PyObject_Call(type, args, NULL);
42773 Py_DECREF(args);
42774 if (!owned_instance)
42775 goto bad;
42776 value = owned_instance;
42777 if (!PyExceptionInstance_Check(value)) {
42778 PyErr_Format(PyExc_TypeError,
42779 "calling %R should have returned an instance of "
42780 "BaseException, not %R",
42781 type, Py_TYPE(value));
42782 goto bad;
42783 }
42784 }
42785 } else {
42786 PyErr_SetString(PyExc_TypeError,
42787 "raise: exception class must be a subclass of BaseException");
42788 goto bad;
42789 }
42790 if (cause) {
42791 PyObject *fixed_cause;
42792 if (cause == Py_None) {
42793 fixed_cause = NULL;
42794 } else if (PyExceptionClass_Check(cause)) {
42795 fixed_cause = PyObject_CallObject(cause, NULL);
42796 if (fixed_cause == NULL)
42797 goto bad;
42798 } else if (PyExceptionInstance_Check(cause)) {
42799 fixed_cause = cause;
42800 Py_INCREF(fixed_cause);
42801 } else {
42802 PyErr_SetString(PyExc_TypeError,
42803 "exception causes must derive from "
42804 "BaseException");
42805 goto bad;
42806 }
42807 PyException_SetCause(value, fixed_cause);
42808 }
42809 PyErr_SetObject(type, value);
42810 if (tb) {
42811 #if PY_VERSION_HEX >= 0x030C00A6
42812 PyException_SetTraceback(value, tb);
42813 #elif CYTHON_FAST_THREAD_STATE
42814 PyThreadState *tstate = __Pyx_PyThreadState_Current;
42815 PyObject* tmp_tb = tstate->curexc_traceback;
42816 if (tb != tmp_tb) {
42817 Py_INCREF(tb);
42818 tstate->curexc_traceback = tb;
42819 Py_XDECREF(tmp_tb);
42820 }
42821 #else
42822 PyObject *tmp_type, *tmp_value, *tmp_tb;
42823 PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb);
42824 Py_INCREF(tb);
42825 PyErr_Restore(tmp_type, tmp_value, tb);
42826 Py_XDECREF(tmp_tb);
42827 #endif
42828 }
42829 bad:
42830 Py_XDECREF(owned_instance);
42831 return;
42832 }
42833 #endif
42834
42835 /* pybytes_as_double */
42836 static double __Pyx_SlowPyString_AsDouble(PyObject *obj) {
42837 PyObject *float_value;
42838 #if PY_MAJOR_VERSION >= 3
42839 float_value = PyFloat_FromString(obj);
42840 #else
42841 float_value = PyFloat_FromString(obj, 0);
42842 #endif
42843 if (likely(float_value)) {
42844 #if CYTHON_ASSUME_SAFE_MACROS
42845 double value = PyFloat_AS_DOUBLE(float_value);
42846 #else
42847 double value = PyFloat_AsDouble(float_value);
42848 #endif
42849 Py_DECREF(float_value);
42850 return value;
42851 }
42852 return (double)-1;
42853 }
42854 static const char* __Pyx__PyBytes_AsDouble_Copy(const char* start, char* buffer, Py_ssize_t length) {
42855 int last_was_punctuation = 1;
42856 Py_ssize_t i;
42857 for (i=0; i < length; i++) {
42858 char chr = start[i];
42859 int is_punctuation = (chr == '_') | (chr == '.') | (chr == 'e') | (chr == 'E');
42860 *buffer = chr;
42861 buffer += (chr != '_');
42862 if (unlikely(last_was_punctuation & is_punctuation)) goto parse_failure;
42863 last_was_punctuation = is_punctuation;
42864 }
42865 if (unlikely(last_was_punctuation)) goto parse_failure;
42866 *buffer = '\0';
42867 return buffer;
42868 parse_failure:
42869 return NULL;
42870 }
42871 static double __Pyx__PyBytes_AsDouble_inf_nan(const char* start, Py_ssize_t length) {
42872 int matches = 1;
42873 char sign = start[0];
42874 int is_signed = (sign == '+') | (sign == '-');
42875 start += is_signed;
42876 length -= is_signed;
42877 switch (start[0]) {
42878 #ifdef Py_NAN
42879 case 'n':
42880 case 'N':
42881 if (unlikely(length != 3)) goto parse_failure;
42882 matches &= (start[1] == 'a' || start[1] == 'A');
42883 matches &= (start[2] == 'n' || start[2] == 'N');
42884 if (unlikely(!matches)) goto parse_failure;
42885 return (sign == '-') ? -Py_NAN : Py_NAN;
42886 #endif
42887 case 'i':
42888 case 'I':
42889 if (unlikely(length < 3)) goto parse_failure;
42890 matches &= (start[1] == 'n' || start[1] == 'N');
42891 matches &= (start[2] == 'f' || start[2] == 'F');
42892 if (likely(length == 3 && matches))
42893 return (sign == '-') ? -Py_HUGE_VAL : Py_HUGE_VAL;
42894 if (unlikely(length != 8)) goto parse_failure;
42895 matches &= (start[3] == 'i' || start[3] == 'I');
42896 matches &= (start[4] == 'n' || start[4] == 'N');
42897 matches &= (start[5] == 'i' || start[5] == 'I');
42898 matches &= (start[6] == 't' || start[6] == 'T');
42899 matches &= (start[7] == 'y' || start[7] == 'Y');
42900 if (unlikely(!matches)) goto parse_failure;
42901 return (sign == '-') ? -Py_HUGE_VAL : Py_HUGE_VAL;
42902 case '.': case '0': case '1': case '2': case '3': case '4': case '5': case '6': case '7': case '8': case '9':
42903 break;
42904 default:
42905 goto parse_failure;
42906 }
42907 return 0.0;
42908 parse_failure:
42909 return -1.0;
42910 }
42911 static CYTHON_INLINE int __Pyx__PyBytes_AsDouble_IsSpace(char ch) {
42912 return (ch == 0x20) | !((ch < 0x9) | (ch > 0xd));
42913 }
42914 CYTHON_UNUSED static double __Pyx__PyBytes_AsDouble(PyObject *obj, const char* start, Py_ssize_t length) {
42915 double value;
42916 Py_ssize_t i, digits;
42917 const char *last = start + length;
42918 char *end;
42919 while (__Pyx__PyBytes_AsDouble_IsSpace(*start))
42920 start++;
42921 while (start < last - 1 && __Pyx__PyBytes_AsDouble_IsSpace(last[-1]))
42922 last--;
42923 length = last - start;
42924 if (unlikely(length <= 0)) goto fallback;
42925 value = __Pyx__PyBytes_AsDouble_inf_nan(start, length);
42926 if (unlikely(value == -1.0)) goto fallback;
42927 if (value != 0.0) return value;
42928 digits = 0;
42929 for (i=0; i < length; digits += start[i++] != '_');
42930 if (likely(digits == length)) {
42931 value = PyOS_string_to_double(start, &end, NULL);
42932 } else if (digits < 40) {
42933 char number[40];
42934 last = __Pyx__PyBytes_AsDouble_Copy(start, number, length);
42935 if (unlikely(!last)) goto fallback;
42936 value = PyOS_string_to_double(number, &end, NULL);
42937 } else {
42938 char *number = (char*) PyMem_Malloc((digits + 1) * sizeof(char));
42939 if (unlikely(!number)) goto fallback;
42940 last = __Pyx__PyBytes_AsDouble_Copy(start, number, length);
42941 if (unlikely(!last)) {
42942 PyMem_Free(number);
42943 goto fallback;
42944 }
42945 value = PyOS_string_to_double(number, &end, NULL);
42946 PyMem_Free(number);
42947 }
42948 if (likely(end == last) || (value == (double)-1 && PyErr_Occurred())) {
42949 return value;
42950 }
42951 fallback:
42952 return __Pyx_SlowPyString_AsDouble(obj);
42953 }
42954
42955 /* pynumber_float */
42956 static CYTHON_INLINE PyObject* __Pyx__PyNumber_Float(PyObject* obj) {
42957 double val;
42958 if (PyLong_CheckExact(obj)) {
42959 #if CYTHON_USE_PYLONG_INTERNALS
42960 if (likely(__Pyx_PyLong_IsCompact(obj))) {
42961 val = (double) __Pyx_PyLong_CompactValue(obj);
42962 goto no_error;
42963 }
42964 #endif
42965 val = PyLong_AsDouble(obj);
42966 } else if (PyUnicode_CheckExact(obj)) {
42967 val = __Pyx_PyUnicode_AsDouble(obj);
42968 } else if (PyBytes_CheckExact(obj)) {
42969 val = __Pyx_PyBytes_AsDouble(obj);
42970 } else if (PyByteArray_CheckExact(obj)) {
42971 val = __Pyx_PyByteArray_AsDouble(obj);
42972 } else {
42973 return PyNumber_Float(obj);
42974 }
42975 if (unlikely(val == -1 && PyErr_Occurred())) {
42976 return NULL;
42977 }
42978 #if CYTHON_USE_PYLONG_INTERNALS
42979 no_error:
42980 #endif
42981 return PyFloat_FromDouble(val);
42982 }
42983
42984 /* RaiseUnboundLocalError */
42985 static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
42986 PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
42987 }
42988
42989 /* ObjectGetItem */
42990 #if CYTHON_USE_TYPE_SLOTS
42991 static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject *index) {
42992 PyObject *runerr = NULL;
42993 Py_ssize_t key_value;
42994 key_value = __Pyx_PyIndex_AsSsize_t(index);
42995 if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) {
42996 return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1);
42997 }
42998 if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) {
42999 __Pyx_TypeName index_type_name = __Pyx_PyType_GetName(Py_TYPE(index));
43000 PyErr_Clear();
43001 PyErr_Format(PyExc_IndexError,
43002 "cannot fit '" __Pyx_FMT_TYPENAME "' into an index-sized integer", index_type_name);
43003 __Pyx_DECREF_TypeName(index_type_name);
43004 }
43005 return NULL;
43006 }
43007 static PyObject *__Pyx_PyObject_GetItem_Slow(PyObject *obj, PyObject *key) {
43008 __Pyx_TypeName obj_type_name;
43009 if (likely(PyType_Check(obj))) {
43010 PyObject *meth = __Pyx_PyObject_GetAttrStrNoError(obj, __pyx_n_s_class_getitem);
43011 if (!meth) {
43012 PyErr_Clear();
43013 } else {
43014 PyObject *result = __Pyx_PyObject_CallOneArg(meth, key);
43015 Py_DECREF(meth);
43016 return result;
43017 }
43018 }
43019 obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj));
43020 PyErr_Format(PyExc_TypeError,
43021 "'" __Pyx_FMT_TYPENAME "' object is not subscriptable", obj_type_name);
43022 __Pyx_DECREF_TypeName(obj_type_name);
43023 return NULL;
43024 }
43025 static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject *key) {
43026 PyTypeObject *tp = Py_TYPE(obj);
43027 PyMappingMethods *mm = tp->tp_as_mapping;
43028 PySequenceMethods *sm = tp->tp_as_sequence;
43029 if (likely(mm && mm->mp_subscript)) {
43030 return mm->mp_subscript(obj, key);
43031 }
43032 if (likely(sm && sm->sq_item)) {
43033 return __Pyx_PyObject_GetIndex(obj, key);
43034 }
43035 return __Pyx_PyObject_GetItem_Slow(obj, key);
43036 }
43037 #endif
43038
43039 /* CIntToDigits */
43040 static const char DIGIT_PAIRS_10[2*10*10+1] = {
43041 "00010203040506070809"
43042 "10111213141516171819"
43043 "20212223242526272829"
43044 "30313233343536373839"
43045 "40414243444546474849"
43046 "50515253545556575859"
43047 "60616263646566676869"
43048 "70717273747576777879"
43049 "80818283848586878889"
43050 "90919293949596979899"
43051 };
43052 static const char DIGIT_PAIRS_8[2*8*8+1] = {
43053 "0001020304050607"
43054 "1011121314151617"
43055 "2021222324252627"
43056 "3031323334353637"
43057 "4041424344454647"
43058 "5051525354555657"
43059 "6061626364656667"
43060 "7071727374757677"
43061 };
43062 static const char DIGITS_HEX[2*16+1] = {
43063 "0123456789abcdef"
43064 "0123456789ABCDEF"
43065 };
43066
43067 /* BuildPyUnicode */
43068 static PyObject* __Pyx_PyUnicode_BuildFromAscii(Py_ssize_t ulength, char* chars, int clength,
43069 int prepend_sign, char padding_char) {
43070 PyObject *uval;
43071 Py_ssize_t uoffset = ulength - clength;
43072 #if CYTHON_USE_UNICODE_INTERNALS
43073 Py_ssize_t i;
43074 #if CYTHON_PEP393_ENABLED
43075 void *udata;
43076 uval = PyUnicode_New(ulength, 127);
43077 if (unlikely(!uval)) return NULL;
43078 udata = PyUnicode_DATA(uval);
43079 #else
43080 Py_UNICODE *udata;
43081 uval = PyUnicode_FromUnicode(NULL, ulength);
43082 if (unlikely(!uval)) return NULL;
43083 udata = PyUnicode_AS_UNICODE(uval);
43084 #endif
43085 if (uoffset > 0) {
43086 i = 0;
43087 if (prepend_sign) {
43088 __Pyx_PyUnicode_WRITE(PyUnicode_1BYTE_KIND, udata, 0, '-');
43089 i++;
43090 }
43091 for (; i < uoffset; i++) {
43092 __Pyx_PyUnicode_WRITE(PyUnicode_1BYTE_KIND, udata, i, padding_char);
43093 }
43094 }
43095 for (i=0; i < clength; i++) {
43096 __Pyx_PyUnicode_WRITE(PyUnicode_1BYTE_KIND, udata, uoffset+i, chars[i]);
43097 }
43098 #else
43099 {
43100 PyObject *sign = NULL, *padding = NULL;
43101 uval = NULL;
43102 if (uoffset > 0) {
43103 prepend_sign = !!prepend_sign;
43104 if (uoffset > prepend_sign) {
43105 padding = PyUnicode_FromOrdinal(padding_char);
43106 if (likely(padding) && uoffset > prepend_sign + 1) {
43107 PyObject *tmp;
43108 PyObject *repeat = PyInt_FromSsize_t(uoffset - prepend_sign);
43109 if (unlikely(!repeat)) goto done_or_error;
43110 tmp = PyNumber_Multiply(padding, repeat);
43111 Py_DECREF(repeat);
43112 Py_DECREF(padding);
43113 padding = tmp;
43114 }
43115 if (unlikely(!padding)) goto done_or_error;
43116 }
43117 if (prepend_sign) {
43118 sign = PyUnicode_FromOrdinal('-');
43119 if (unlikely(!sign)) goto done_or_error;
43120 }
43121 }
43122 uval = PyUnicode_DecodeASCII(chars, clength, NULL);
43123 if (likely(uval) && padding) {
43124 PyObject *tmp = PyNumber_Add(padding, uval);
43125 Py_DECREF(uval);
43126 uval = tmp;
43127 }
43128 if (likely(uval) && sign) {
43129 PyObject *tmp = PyNumber_Add(sign, uval);
43130 Py_DECREF(uval);
43131 uval = tmp;
43132 }
43133 done_or_error:
43134 Py_XDECREF(padding);
43135 Py_XDECREF(sign);
43136 }
43137 #endif
43138 return uval;
43139 }
43140
43141 /* CIntToPyUnicode */
43142 static CYTHON_INLINE PyObject* __Pyx_PyUnicode_From_Py_ssize_t(Py_ssize_t value, Py_ssize_t width, char padding_char, char format_char) {
43143 char digits[sizeof(Py_ssize_t)*3+2];
43144 char *dpos, *end = digits + sizeof(Py_ssize_t)*3+2;
43145 const char *hex_digits = DIGITS_HEX;
43146 Py_ssize_t length, ulength;
43147 int prepend_sign, last_one_off;
43148 Py_ssize_t remaining;
43149 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
43150 #pragma GCC diagnostic push
43151 #pragma GCC diagnostic ignored "-Wconversion"
43152 #endif
43153 const Py_ssize_t neg_one = (Py_ssize_t) -1, const_zero = (Py_ssize_t) 0;
43154 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
43155 #pragma GCC diagnostic pop
43156 #endif
43157 const int is_unsigned = neg_one > const_zero;
43158 if (format_char == 'X') {
43159 hex_digits += 16;
43160 format_char = 'x';
43161 }
43162 remaining = value;
43163 last_one_off = 0;
43164 dpos = end;
43165 do {
43166 int digit_pos;
43167 switch (format_char) {
43168 case 'o':
43169 digit_pos = abs((int)(remaining % (8*8)));
43170 remaining = (Py_ssize_t) (remaining / (8*8));
43171 dpos -= 2;
43172 memcpy(dpos, DIGIT_PAIRS_8 + digit_pos * 2, 2);
43173 last_one_off = (digit_pos < 8);
43174 break;
43175 case 'd':
43176 digit_pos = abs((int)(remaining % (10*10)));
43177 remaining = (Py_ssize_t) (remaining / (10*10));
43178 dpos -= 2;
43179 memcpy(dpos, DIGIT_PAIRS_10 + digit_pos * 2, 2);
43180 last_one_off = (digit_pos < 10);
43181 break;
43182 case 'x':
43183 *(--dpos) = hex_digits[abs((int)(remaining % 16))];
43184 remaining = (Py_ssize_t) (remaining / 16);
43185 break;
43186 default:
43187 assert(0);
43188 break;
43189 }
43190 } while (unlikely(remaining != 0));
43191 assert(!last_one_off || *dpos == '0');
43192 dpos += last_one_off;
43193 length = end - dpos;
43194 ulength = length;
43195 prepend_sign = 0;
43196 if (!is_unsigned && value <= neg_one) {
43197 if (padding_char == ' ' || width <= length + 1) {
43198 *(--dpos) = '-';
43199 ++length;
43200 } else {
43201 prepend_sign = 1;
43202 }
43203 ++ulength;
43204 }
43205 if (width > ulength) {
43206 ulength = width;
43207 }
43208 if (ulength == 1) {
43209 return PyUnicode_FromOrdinal(*dpos);
43210 }
43211 return __Pyx_PyUnicode_BuildFromAscii(ulength, dpos, (int) length, prepend_sign, padding_char);
43212 }
43213
43214 /* PyObjectFormatAndDecref */
43215 static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatSimpleAndDecref(PyObject* s, PyObject* f) {
43216 if (unlikely(!s)) return NULL;
43217 if (likely(PyUnicode_CheckExact(s))) return s;
43218 #if PY_MAJOR_VERSION < 3
43219 if (likely(PyString_CheckExact(s))) {
43220 PyObject *result = PyUnicode_FromEncodedObject(s, NULL, "strict");
43221 Py_DECREF(s);
43222 return result;
43223 }
43224 #endif
43225 return __Pyx_PyObject_FormatAndDecref(s, f);
43226 }
43227 static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatAndDecref(PyObject* s, PyObject* f) {
43228 PyObject *result;
43229 if (unlikely(!s)) return NULL;
43230 result = PyObject_Format(s, f);
43231 Py_DECREF(s);
43232 return result;
43233 }
43234
43235 /* JoinPyUnicode */
43236 static PyObject* __Pyx_PyUnicode_Join(PyObject* value_tuple, Py_ssize_t value_count, Py_ssize_t result_ulength,
43237 Py_UCS4 max_char) {
43238 #if CYTHON_USE_UNICODE_INTERNALS && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
43239 PyObject *result_uval;
43240 int result_ukind, kind_shift;
43241 Py_ssize_t i, char_pos;
43242 void *result_udata;
43243 CYTHON_MAYBE_UNUSED_VAR(max_char);
43244 #if CYTHON_PEP393_ENABLED
43245 result_uval = PyUnicode_New(result_ulength, max_char);
43246 if (unlikely(!result_uval)) return NULL;
43247 result_ukind = (max_char <= 255) ? PyUnicode_1BYTE_KIND : (max_char <= 65535) ? PyUnicode_2BYTE_KIND : PyUnicode_4BYTE_KIND;
43248 kind_shift = (result_ukind == PyUnicode_4BYTE_KIND) ? 2 : result_ukind - 1;
43249 result_udata = PyUnicode_DATA(result_uval);
43250 #else
43251 result_uval = PyUnicode_FromUnicode(NULL, result_ulength);
43252 if (unlikely(!result_uval)) return NULL;
43253 result_ukind = sizeof(Py_UNICODE);
43254 kind_shift = (result_ukind == 4) ? 2 : result_ukind - 1;
43255 result_udata = PyUnicode_AS_UNICODE(result_uval);
43256 #endif
43257 assert(kind_shift == 2 || kind_shift == 1 || kind_shift == 0);
43258 char_pos = 0;
43259 for (i=0; i < value_count; i++) {
43260 int ukind;
43261 Py_ssize_t ulength;
43262 void *udata;
43263 PyObject *uval = PyTuple_GET_ITEM(value_tuple, i);
43264 if (unlikely(__Pyx_PyUnicode_READY(uval)))
43265 goto bad;
43266 ulength = __Pyx_PyUnicode_GET_LENGTH(uval);
43267 if (unlikely(!ulength))
43268 continue;
43269 if (unlikely((PY_SSIZE_T_MAX >> kind_shift) - ulength < char_pos))
43270 goto overflow;
43271 ukind = __Pyx_PyUnicode_KIND(uval);
43272 udata = __Pyx_PyUnicode_DATA(uval);
43273 if (!CYTHON_PEP393_ENABLED || ukind == result_ukind) {
43274 memcpy((char *)result_udata + (char_pos << kind_shift), udata, (size_t) (ulength << kind_shift));
43275 } else {
43276 #if PY_VERSION_HEX >= 0x030d0000
43277 if (unlikely(PyUnicode_CopyCharacters(result_uval, char_pos, uval, 0, ulength) < 0)) goto bad;
43278 #elif CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030300F0 || defined(_PyUnicode_FastCopyCharacters)
43279 _PyUnicode_FastCopyCharacters(result_uval, char_pos, uval, 0, ulength);
43280 #else
43281 Py_ssize_t j;
43282 for (j=0; j < ulength; j++) {
43283 Py_UCS4 uchar = __Pyx_PyUnicode_READ(ukind, udata, j);
43284 __Pyx_PyUnicode_WRITE(result_ukind, result_udata, char_pos+j, uchar);
43285 }
43286 #endif
43287 }
43288 char_pos += ulength;
43289 }
43290 return result_uval;
43291 overflow:
43292 PyErr_SetString(PyExc_OverflowError, "join() result is too long for a Python string");
43293 bad:
43294 Py_DECREF(result_uval);
43295 return NULL;
43296 #else
43297 CYTHON_UNUSED_VAR(max_char);
43298 CYTHON_UNUSED_VAR(result_ulength);
43299 CYTHON_UNUSED_VAR(value_count);
43300 return PyUnicode_Join(__pyx_empty_unicode, value_tuple);
43301 #endif
43302 }
43303
43304 /* PyIntCompare */
43305 static CYTHON_INLINE int __Pyx_PyInt_BoolEqObjC(PyObject *op1, PyObject *op2, long intval, long inplace) {
43306 CYTHON_MAYBE_UNUSED_VAR(intval);
43307 CYTHON_UNUSED_VAR(inplace);
43308 if (op1 == op2) {
43309 return 1;
43310 }
43311 #if PY_MAJOR_VERSION < 3
43312 if (likely(PyInt_CheckExact(op1))) {
43313 const long b = intval;
43314 long a = PyInt_AS_LONG(op1);
43315 return (a == b);
43316 }
43317 #endif
43318 #if CYTHON_USE_PYLONG_INTERNALS
43319 if (likely(PyLong_CheckExact(op1))) {
43320 int unequal;
43321 unsigned long uintval;
43322 Py_ssize_t size = __Pyx_PyLong_DigitCount(op1);
43323 const digit* digits = __Pyx_PyLong_Digits(op1);
43324 if (intval == 0) {
43325 return (__Pyx_PyLong_IsZero(op1) == 1);
43326 } else if (intval < 0) {
43327 if (__Pyx_PyLong_IsNonNeg(op1))
43328 return 0;
43329 intval = -intval;
43330 } else {
43331 if (__Pyx_PyLong_IsNeg(op1))
43332 return 0;
43333 }
43334 uintval = (unsigned long) intval;
43335 #if PyLong_SHIFT * 4 < SIZEOF_LONG*8
43336 if (uintval >> (PyLong_SHIFT * 4)) {
43337 unequal = (size != 5) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
43338 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[4] != ((uintval >> (4 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
43339 } else
43340 #endif
43341 #if PyLong_SHIFT * 3 < SIZEOF_LONG*8
43342 if (uintval >> (PyLong_SHIFT * 3)) {
43343 unequal = (size != 4) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
43344 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
43345 } else
43346 #endif
43347 #if PyLong_SHIFT * 2 < SIZEOF_LONG*8
43348 if (uintval >> (PyLong_SHIFT * 2)) {
43349 unequal = (size != 3) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
43350 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
43351 } else
43352 #endif
43353 #if PyLong_SHIFT * 1 < SIZEOF_LONG*8
43354 if (uintval >> (PyLong_SHIFT * 1)) {
43355 unequal = (size != 2) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
43356 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
43357 } else
43358 #endif
43359 unequal = (size != 1) || (((unsigned long) digits[0]) != (uintval & (unsigned long) PyLong_MASK));
43360 return (unequal == 0);
43361 }
43362 #endif
43363 if (PyFloat_CheckExact(op1)) {
43364 const long b = intval;
43365 #if CYTHON_COMPILING_IN_LIMITED_API
43366 double a = __pyx_PyFloat_AsDouble(op1);
43367 #else
43368 double a = PyFloat_AS_DOUBLE(op1);
43369 #endif
43370 return ((double)a == (double)b);
43371 }
43372 return __Pyx_PyObject_IsTrueAndDecref(
43373 PyObject_RichCompare(op1, op2, Py_EQ));
43374 }
43375
43376 /* PyIntCompare */
43377 static CYTHON_INLINE int __Pyx_PyInt_BoolNeObjC(PyObject *op1, PyObject *op2, long intval, long inplace) {
43378 CYTHON_MAYBE_UNUSED_VAR(intval);
43379 CYTHON_UNUSED_VAR(inplace);
43380 if (op1 == op2) {
43381 return 0;
43382 }
43383 #if PY_MAJOR_VERSION < 3
43384 if (likely(PyInt_CheckExact(op1))) {
43385 const long b = intval;
43386 long a = PyInt_AS_LONG(op1);
43387 return (a != b);
43388 }
43389 #endif
43390 #if CYTHON_USE_PYLONG_INTERNALS
43391 if (likely(PyLong_CheckExact(op1))) {
43392 int unequal;
43393 unsigned long uintval;
43394 Py_ssize_t size = __Pyx_PyLong_DigitCount(op1);
43395 const digit* digits = __Pyx_PyLong_Digits(op1);
43396 if (intval == 0) {
43397 return (__Pyx_PyLong_IsZero(op1) != 1);
43398 } else if (intval < 0) {
43399 if (__Pyx_PyLong_IsNonNeg(op1))
43400 return 1;
43401 intval = -intval;
43402 } else {
43403 if (__Pyx_PyLong_IsNeg(op1))
43404 return 1;
43405 }
43406 uintval = (unsigned long) intval;
43407 #if PyLong_SHIFT * 4 < SIZEOF_LONG*8
43408 if (uintval >> (PyLong_SHIFT * 4)) {
43409 unequal = (size != 5) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
43410 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[4] != ((uintval >> (4 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
43411 } else
43412 #endif
43413 #if PyLong_SHIFT * 3 < SIZEOF_LONG*8
43414 if (uintval >> (PyLong_SHIFT * 3)) {
43415 unequal = (size != 4) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
43416 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
43417 } else
43418 #endif
43419 #if PyLong_SHIFT * 2 < SIZEOF_LONG*8
43420 if (uintval >> (PyLong_SHIFT * 2)) {
43421 unequal = (size != 3) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
43422 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
43423 } else
43424 #endif
43425 #if PyLong_SHIFT * 1 < SIZEOF_LONG*8
43426 if (uintval >> (PyLong_SHIFT * 1)) {
43427 unequal = (size != 2) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
43428 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
43429 } else
43430 #endif
43431 unequal = (size != 1) || (((unsigned long) digits[0]) != (uintval & (unsigned long) PyLong_MASK));
43432 return (unequal != 0);
43433 }
43434 #endif
43435 if (PyFloat_CheckExact(op1)) {
43436 const long b = intval;
43437 #if CYTHON_COMPILING_IN_LIMITED_API
43438 double a = __pyx_PyFloat_AsDouble(op1);
43439 #else
43440 double a = PyFloat_AS_DOUBLE(op1);
43441 #endif
43442 return ((double)a != (double)b);
43443 }
43444 return __Pyx_PyObject_IsTrueAndDecref(
43445 PyObject_RichCompare(op1, op2, Py_NE));
43446 }
43447
43448 /* DictGetItem */
43449 #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
43450 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
43451 PyObject *value;
43452 value = PyDict_GetItemWithError(d, key);
43453 if (unlikely(!value)) {
43454 if (!PyErr_Occurred()) {
43455 if (unlikely(PyTuple_Check(key))) {
43456 PyObject* args = PyTuple_Pack(1, key);
43457 if (likely(args)) {
43458 PyErr_SetObject(PyExc_KeyError, args);
43459 Py_DECREF(args);
43460 }
43461 } else {
43462 PyErr_SetObject(PyExc_KeyError, key);
43463 }
43464 }
43465 return NULL;
43466 }
43467 Py_INCREF(value);
43468 return value;
43469 }
43470 #endif
43471
43472 /* SliceObject */
43473 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj,
43474 Py_ssize_t cstart, Py_ssize_t cstop,
43475 PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
43476 int has_cstart, int has_cstop, int wraparound) {
43477 __Pyx_TypeName obj_type_name;
43478 #if CYTHON_USE_TYPE_SLOTS
43479 PyMappingMethods* mp;
43480 #if PY_MAJOR_VERSION < 3
43481 PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
43482 if (likely(ms && ms->sq_slice)) {
43483 if (!has_cstart) {
43484 if (_py_start && (*_py_start != Py_None)) {
43485 cstart = __Pyx_PyIndex_AsSsize_t(*_py_start);
43486 if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
43487 } else
43488 cstart = 0;
43489 }
43490 if (!has_cstop) {
43491 if (_py_stop && (*_py_stop != Py_None)) {
43492 cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop);
43493 if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
43494 } else
43495 cstop = PY_SSIZE_T_MAX;
43496 }
43497 if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) {
43498 Py_ssize_t l = ms->sq_length(obj);
43499 if (likely(l >= 0)) {
43500 if (cstop < 0) {
43501 cstop += l;
43502 if (cstop < 0) cstop = 0;
43503 }
43504 if (cstart < 0) {
43505 cstart += l;
43506 if (cstart < 0) cstart = 0;
43507 }
43508 } else {
43509 if (!PyErr_ExceptionMatches(PyExc_OverflowError))
43510 goto bad;
43511 PyErr_Clear();
43512 }
43513 }
43514 return ms->sq_slice(obj, cstart, cstop);
43515 }
43516 #else
43517 CYTHON_UNUSED_VAR(wraparound);
43518 #endif
43519 mp = Py_TYPE(obj)->tp_as_mapping;
43520 if (likely(mp && mp->mp_subscript))
43521 #else
43522 CYTHON_UNUSED_VAR(wraparound);
43523 #endif
43524 {
43525 PyObject* result;
43526 PyObject *py_slice, *py_start, *py_stop;
43527 if (_py_slice) {
43528 py_slice = *_py_slice;
43529 } else {
43530 PyObject* owned_start = NULL;
43531 PyObject* owned_stop = NULL;
43532 if (_py_start) {
43533 py_start = *_py_start;
43534 } else {
43535 if (has_cstart) {
43536 owned_start = py_start = PyInt_FromSsize_t(cstart);
43537 if (unlikely(!py_start)) goto bad;
43538 } else
43539 py_start = Py_None;
43540 }
43541 if (_py_stop) {
43542 py_stop = *_py_stop;
43543 } else {
43544 if (has_cstop) {
43545 owned_stop = py_stop = PyInt_FromSsize_t(cstop);
43546 if (unlikely(!py_stop)) {
43547 Py_XDECREF(owned_start);
43548 goto bad;
43549 }
43550 } else
43551 py_stop = Py_None;
43552 }
43553 py_slice = PySlice_New(py_start, py_stop, Py_None);
43554 Py_XDECREF(owned_start);
43555 Py_XDECREF(owned_stop);
43556 if (unlikely(!py_slice)) goto bad;
43557 }
43558 #if CYTHON_USE_TYPE_SLOTS
43559 result = mp->mp_subscript(obj, py_slice);
43560 #else
43561 result = PyObject_GetItem(obj, py_slice);
43562 #endif
43563 if (!_py_slice) {
43564 Py_DECREF(py_slice);
43565 }
43566 return result;
43567 }
43568 obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj));
43569 PyErr_Format(PyExc_TypeError,
43570 "'" __Pyx_FMT_TYPENAME "' object is unsliceable", obj_type_name);
43571 __Pyx_DECREF_TypeName(obj_type_name);
43572 bad:
43573 return NULL;
43574 }
43575
43576 /* KeywordStringCheck */
43577 static int __Pyx_CheckKeywordStrings(
43578 PyObject *kw,
43579 const char* function_name,
43580 int kw_allowed)
43581 {
43582 PyObject* key = 0;
43583 Py_ssize_t pos = 0;
43584 #if CYTHON_COMPILING_IN_PYPY
43585 if (!kw_allowed && PyDict_Next(kw, &pos, &key, 0))
43586 goto invalid_keyword;
43587 return 1;
43588 #else
43589 if (CYTHON_METH_FASTCALL && likely(PyTuple_Check(kw))) {
43590 Py_ssize_t kwsize;
43591 #if CYTHON_ASSUME_SAFE_MACROS
43592 kwsize = PyTuple_GET_SIZE(kw);
43593 #else
43594 kwsize = PyTuple_Size(kw);
43595 if (kwsize < 0) return 0;
43596 #endif
43597 if (unlikely(kwsize == 0))
43598 return 1;
43599 if (!kw_allowed) {
43600 #if CYTHON_ASSUME_SAFE_MACROS
43601 key = PyTuple_GET_ITEM(kw, 0);
43602 #else
43603 key = PyTuple_GetItem(kw, pos);
43604 if (!key) return 0;
43605 #endif
43606 goto invalid_keyword;
43607 }
43608 #if PY_VERSION_HEX < 0x03090000
43609 for (pos = 0; pos < kwsize; pos++) {
43610 #if CYTHON_ASSUME_SAFE_MACROS
43611 key = PyTuple_GET_ITEM(kw, pos);
43612 #else
43613 key = PyTuple_GetItem(kw, pos);
43614 if (!key) return 0;
43615 #endif
43616 if (unlikely(!PyUnicode_Check(key)))
43617 goto invalid_keyword_type;
43618 }
43619 #endif
43620 return 1;
43621 }
43622 while (PyDict_Next(kw, &pos, &key, 0)) {
43623 #if PY_MAJOR_VERSION < 3
43624 if (unlikely(!PyString_Check(key)))
43625 #endif
43626 if (unlikely(!PyUnicode_Check(key)))
43627 goto invalid_keyword_type;
43628 }
43629 if (!kw_allowed && unlikely(key))
43630 goto invalid_keyword;
43631 return 1;
43632 invalid_keyword_type:
43633 PyErr_Format(PyExc_TypeError,
43634 "%.200s() keywords must be strings", function_name);
43635 return 0;
43636 #endif
43637 invalid_keyword:
43638 #if PY_MAJOR_VERSION < 3
43639 PyErr_Format(PyExc_TypeError,
43640 "%.200s() got an unexpected keyword argument '%.200s'",
43641 function_name, PyString_AsString(key));
43642 #else
43643 PyErr_Format(PyExc_TypeError,
43644 "%s() got an unexpected keyword argument '%U'",
43645 function_name, key);
43646 #endif
43647 return 0;
43648 }
43649
43650 /* GetAttr3 */
43651 #if __PYX_LIMITED_VERSION_HEX < 0x030d00A1
43652 static PyObject *__Pyx_GetAttr3Default(PyObject *d) {
43653 __Pyx_PyThreadState_declare
43654 __Pyx_PyThreadState_assign
43655 if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError)))
43656 return NULL;
43657 __Pyx_PyErr_Clear();
43658 Py_INCREF(d);
43659 return d;
43660 }
43661 #endif
43662 static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) {
43663 PyObject *r;
43664 #if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1
43665 int res = PyObject_GetOptionalAttr(o, n, &r);
43666 return (res != 0) ? r : __Pyx_NewRef(d);
43667 #else
43668 #if CYTHON_USE_TYPE_SLOTS
43669 if (likely(PyString_Check(n))) {
43670 r = __Pyx_PyObject_GetAttrStrNoError(o, n);
43671 if (unlikely(!r) && likely(!PyErr_Occurred())) {
43672 r = __Pyx_NewRef(d);
43673 }
43674 return r;
43675 }
43676 #endif
43677 r = PyObject_GetAttr(o, n);
43678 return (likely(r)) ? r : __Pyx_GetAttr3Default(d);
43679 #endif
43680 }
43681
43682 /* RaiseUnexpectedTypeError */
43683 static int
43684 __Pyx_RaiseUnexpectedTypeError(const char *expected, PyObject *obj)
43685 {
43686 __Pyx_TypeName obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj));
43687 PyErr_Format(PyExc_TypeError, "Expected %s, got " __Pyx_FMT_TYPENAME,
43688 expected, obj_type_name);
43689 __Pyx_DECREF_TypeName(obj_type_name);
43690 return 0;
43691 }
43692
43693 /* IterFinish */
43694 static CYTHON_INLINE int __Pyx_IterFinish(void) {
43695 PyObject* exc_type;
43696 __Pyx_PyThreadState_declare
43697 __Pyx_PyThreadState_assign
43698 exc_type = __Pyx_PyErr_CurrentExceptionType();
43699 if (unlikely(exc_type)) {
43700 if (unlikely(!__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)))
43701 return -1;
43702 __Pyx_PyErr_Clear();
43703 return 0;
43704 }
43705 return 0;
43706 }
43707
43708 /* PyObjectCallNoArg */
43709 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
43710 PyObject *arg[2] = {NULL, NULL};
43711 return __Pyx_PyObject_FastCall(func, arg + 1, 0 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET);
43712 }
43713
43714 /* PyObjectGetMethod */
43715 static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method) {
43716 PyObject *attr;
43717 #if CYTHON_UNPACK_METHODS && CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_PYTYPE_LOOKUP
43718 __Pyx_TypeName type_name;
43719 PyTypeObject *tp = Py_TYPE(obj);
43720 PyObject *descr;
43721 descrgetfunc f = NULL;
43722 PyObject **dictptr, *dict;
43723 int meth_found = 0;
43724 assert (*method == NULL);
43725 if (unlikely(tp->tp_getattro != PyObject_GenericGetAttr)) {
43726 attr = __Pyx_PyObject_GetAttrStr(obj, name);
43727 goto try_unpack;
43728 }
43729 if (unlikely(tp->tp_dict == NULL) && unlikely(PyType_Ready(tp) < 0)) {
43730 return 0;
43731 }
43732 descr = _PyType_Lookup(tp, name);
43733 if (likely(descr != NULL)) {
43734 Py_INCREF(descr);
43735 #if defined(Py_TPFLAGS_METHOD_DESCRIPTOR) && Py_TPFLAGS_METHOD_DESCRIPTOR
43736 if (__Pyx_PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_METHOD_DESCRIPTOR))
43737 #elif PY_MAJOR_VERSION >= 3
43738 #ifdef __Pyx_CyFunction_USED
43739 if (likely(PyFunction_Check(descr) || __Pyx_IS_TYPE(descr, &PyMethodDescr_Type) || __Pyx_CyFunction_Check(descr)))
43740 #else
43741 if (likely(PyFunction_Check(descr) || __Pyx_IS_TYPE(descr, &PyMethodDescr_Type)))
43742 #endif
43743 #else
43744 #ifdef __Pyx_CyFunction_USED
43745 if (likely(PyFunction_Check(descr) || __Pyx_CyFunction_Check(descr)))
43746 #else
43747 if (likely(PyFunction_Check(descr)))
43748 #endif
43749 #endif
43750 {
43751 meth_found = 1;
43752 } else {
43753 f = Py_TYPE(descr)->tp_descr_get;
43754 if (f != NULL && PyDescr_IsData(descr)) {
43755 attr = f(descr, obj, (PyObject *)Py_TYPE(obj));
43756 Py_DECREF(descr);
43757 goto try_unpack;
43758 }
43759 }
43760 }
43761 dictptr = _PyObject_GetDictPtr(obj);
43762 if (dictptr != NULL && (dict = *dictptr) != NULL) {
43763 Py_INCREF(dict);
43764 attr = __Pyx_PyDict_GetItemStr(dict, name);
43765 if (attr != NULL) {
43766 Py_INCREF(attr);
43767 Py_DECREF(dict);
43768 Py_XDECREF(descr);
43769 goto try_unpack;
43770 }
43771 Py_DECREF(dict);
43772 }
43773 if (meth_found) {
43774 *method = descr;
43775 return 1;
43776 }
43777 if (f != NULL) {
43778 attr = f(descr, obj, (PyObject *)Py_TYPE(obj));
43779 Py_DECREF(descr);
43780 goto try_unpack;
43781 }
43782 if (likely(descr != NULL)) {
43783 *method = descr;
43784 return 0;
43785 }
43786 type_name = __Pyx_PyType_GetName(tp);
43787 PyErr_Format(PyExc_AttributeError,
43788 #if PY_MAJOR_VERSION >= 3
43789 "'" __Pyx_FMT_TYPENAME "' object has no attribute '%U'",
43790 type_name, name);
43791 #else
43792 "'" __Pyx_FMT_TYPENAME "' object has no attribute '%.400s'",
43793 type_name, PyString_AS_STRING(name));
43794 #endif
43795 __Pyx_DECREF_TypeName(type_name);
43796 return 0;
43797 #else
43798 attr = __Pyx_PyObject_GetAttrStr(obj, name);
43799 goto try_unpack;
43800 #endif
43801 try_unpack:
43802 #if CYTHON_UNPACK_METHODS
43803 if (likely(attr) && PyMethod_Check(attr) && likely(PyMethod_GET_SELF(attr) == obj)) {
43804 PyObject *function = PyMethod_GET_FUNCTION(attr);
43805 Py_INCREF(function);
43806 Py_DECREF(attr);
43807 *method = function;
43808 return 1;
43809 }
43810 #endif
43811 *method = attr;
43812 return 0;
43813 }
43814
43815 /* PyObjectCallMethod0 */
43816 static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) {
43817 PyObject *method = NULL, *result = NULL;
43818 int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method);
43819 if (likely(is_method)) {
43820 result = __Pyx_PyObject_CallOneArg(method, obj);
43821 Py_DECREF(method);
43822 return result;
43823 }
43824 if (unlikely(!method)) goto bad;
43825 result = __Pyx_PyObject_CallNoArg(method);
43826 Py_DECREF(method);
43827 bad:
43828 return result;
43829 }
43830
43831 /* RaiseNeedMoreValuesToUnpack */
43832 static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
43833 PyErr_Format(PyExc_ValueError,
43834 "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack",
43835 index, (index == 1) ? "" : "s");
43836 }
43837
43838 /* RaiseTooManyValuesToUnpack */
43839 static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
43840 PyErr_Format(PyExc_ValueError,
43841 "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
43842 }
43843
43844 /* UnpackItemEndCheck */
43845 static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
43846 if (unlikely(retval)) {
43847 Py_DECREF(retval);
43848 __Pyx_RaiseTooManyValuesError(expected);
43849 return -1;
43850 }
43851 return __Pyx_IterFinish();
43852 }
43853
43854 /* RaiseNoneIterError */
43855 static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
43856 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
43857 }
43858
43859 /* UnpackTupleError */
43860 static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) {
43861 if (t == Py_None) {
43862 __Pyx_RaiseNoneNotIterableError();
43863 } else if (PyTuple_GET_SIZE(t) < index) {
43864 __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t));
43865 } else {
43866 __Pyx_RaiseTooManyValuesError(index);
43867 }
43868 }
43869
43870 /* UnpackTuple2 */
43871 static CYTHON_INLINE int __Pyx_unpack_tuple2_exact(
43872 PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, int decref_tuple) {
43873 PyObject *value1 = NULL, *value2 = NULL;
43874 #if CYTHON_COMPILING_IN_PYPY
43875 value1 = PySequence_ITEM(tuple, 0); if (unlikely(!value1)) goto bad;
43876 value2 = PySequence_ITEM(tuple, 1); if (unlikely(!value2)) goto bad;
43877 #else
43878 value1 = PyTuple_GET_ITEM(tuple, 0); Py_INCREF(value1);
43879 value2 = PyTuple_GET_ITEM(tuple, 1); Py_INCREF(value2);
43880 #endif
43881 if (decref_tuple) {
43882 Py_DECREF(tuple);
43883 }
43884 *pvalue1 = value1;
43885 *pvalue2 = value2;
43886 return 0;
43887 #if CYTHON_COMPILING_IN_PYPY
43888 bad:
43889 Py_XDECREF(value1);
43890 Py_XDECREF(value2);
43891 if (decref_tuple) { Py_XDECREF(tuple); }
43892 return -1;
43893 #endif
43894 }
43895 static int __Pyx_unpack_tuple2_generic(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2,
43896 int has_known_size, int decref_tuple) {
43897 Py_ssize_t index;
43898 PyObject *value1 = NULL, *value2 = NULL, *iter = NULL;
43899 iternextfunc iternext;
43900 iter = PyObject_GetIter(tuple);
43901 if (unlikely(!iter)) goto bad;
43902 if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; }
43903 iternext = __Pyx_PyObject_GetIterNextFunc(iter);
43904 value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; }
43905 value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; }
43906 if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad;
43907 Py_DECREF(iter);
43908 *pvalue1 = value1;
43909 *pvalue2 = value2;
43910 return 0;
43911 unpacking_failed:
43912 if (!has_known_size && __Pyx_IterFinish() == 0)
43913 __Pyx_RaiseNeedMoreValuesError(index);
43914 bad:
43915 Py_XDECREF(iter);
43916 Py_XDECREF(value1);
43917 Py_XDECREF(value2);
43918 if (decref_tuple) { Py_XDECREF(tuple); }
43919 return -1;
43920 }
43921
43922 /* dict_iter */
43923 #if CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
43924 #include <string.h>
43925 #endif
43926 static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name,
43927 Py_ssize_t* p_orig_length, int* p_source_is_dict) {
43928 is_dict = is_dict || likely(PyDict_CheckExact(iterable));
43929 *p_source_is_dict = is_dict;
43930 if (is_dict) {
43931 #if !CYTHON_COMPILING_IN_PYPY
43932 *p_orig_length = PyDict_Size(iterable);
43933 Py_INCREF(iterable);
43934 return iterable;
43935 #elif PY_MAJOR_VERSION >= 3
43936 static PyObject *py_items = NULL, *py_keys = NULL, *py_values = NULL;
43937 PyObject **pp = NULL;
43938 if (method_name) {
43939 const char *name = PyUnicode_AsUTF8(method_name);
43940 if (strcmp(name, "iteritems") == 0) pp = &py_items;
43941 else if (strcmp(name, "iterkeys") == 0) pp = &py_keys;
43942 else if (strcmp(name, "itervalues") == 0) pp = &py_values;
43943 if (pp) {
43944 if (!*pp) {
43945 *pp = PyUnicode_FromString(name + 4);
43946 if (!*pp)
43947 return NULL;
43948 }
43949 method_name = *pp;
43950 }
43951 }
43952 #endif
43953 }
43954 *p_orig_length = 0;
43955 if (method_name) {
43956 PyObject* iter;
43957 iterable = __Pyx_PyObject_CallMethod0(iterable, method_name);
43958 if (!iterable)
43959 return NULL;
43960 #if !CYTHON_COMPILING_IN_PYPY
43961 if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable))
43962 return iterable;
43963 #endif
43964 iter = PyObject_GetIter(iterable);
43965 Py_DECREF(iterable);
43966 return iter;
43967 }
43968 return PyObject_GetIter(iterable);
43969 }
43970 static CYTHON_INLINE int __Pyx_dict_iter_next(
43971 PyObject* iter_obj, CYTHON_NCP_UNUSED Py_ssize_t orig_length, CYTHON_NCP_UNUSED Py_ssize_t* ppos,
43972 PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) {
43973 PyObject* next_item;
43974 #if !CYTHON_COMPILING_IN_PYPY
43975 if (source_is_dict) {
43976 PyObject *key, *value;
43977 if (unlikely(orig_length != PyDict_Size(iter_obj))) {
43978 PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration");
43979 return -1;
43980 }
43981 if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) {
43982 return 0;
43983 }
43984 if (pitem) {
43985 PyObject* tuple = PyTuple_New(2);
43986 if (unlikely(!tuple)) {
43987 return -1;
43988 }
43989 Py_INCREF(key);
43990 Py_INCREF(value);
43991 PyTuple_SET_ITEM(tuple, 0, key);
43992 PyTuple_SET_ITEM(tuple, 1, value);
43993 *pitem = tuple;
43994 } else {
43995 if (pkey) {
43996 Py_INCREF(key);
43997 *pkey = key;
43998 }
43999 if (pvalue) {
44000 Py_INCREF(value);
44001 *pvalue = value;
44002 }
44003 }
44004 return 1;
44005 } else if (PyTuple_CheckExact(iter_obj)) {
44006 Py_ssize_t pos = *ppos;
44007 if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0;
44008 *ppos = pos + 1;
44009 next_item = PyTuple_GET_ITEM(iter_obj, pos);
44010 Py_INCREF(next_item);
44011 } else if (PyList_CheckExact(iter_obj)) {
44012 Py_ssize_t pos = *ppos;
44013 if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0;
44014 *ppos = pos + 1;
44015 next_item = PyList_GET_ITEM(iter_obj, pos);
44016 Py_INCREF(next_item);
44017 } else
44018 #endif
44019 {
44020 next_item = PyIter_Next(iter_obj);
44021 if (unlikely(!next_item)) {
44022 return __Pyx_IterFinish();
44023 }
44024 }
44025 if (pitem) {
44026 *pitem = next_item;
44027 } else if (pkey && pvalue) {
44028 if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1))
44029 return -1;
44030 } else if (pkey) {
44031 *pkey = next_item;
44032 } else {
44033 *pvalue = next_item;
44034 }
44035 return 1;
44036 }
44037
44038 /* PyObjectSetAttrStr */
44039 #if CYTHON_USE_TYPE_SLOTS
44040 static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) {
44041 PyTypeObject* tp = Py_TYPE(obj);
44042 if (likely(tp->tp_setattro))
44043 return tp->tp_setattro(obj, attr_name, value);
44044 #if PY_MAJOR_VERSION < 3
44045 if (likely(tp->tp_setattr))
44046 return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value);
44047 #endif
44048 return PyObject_SetAttr(obj, attr_name, value);
44049 }
44050 #endif
44051
44052 /* unicode_tailmatch */
44053 static int __Pyx_PyUnicode_TailmatchTuple(PyObject* s, PyObject* substrings,
44054 Py_ssize_t start, Py_ssize_t end, int direction) {
44055 Py_ssize_t i, count = PyTuple_GET_SIZE(substrings);
44056 for (i = 0; i < count; i++) {
44057 Py_ssize_t result;
44058 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
44059 result = PyUnicode_Tailmatch(s, PyTuple_GET_ITEM(substrings, i),
44060 start, end, direction);
44061 #else
44062 PyObject* sub = PySequence_ITEM(substrings, i);
44063 if (unlikely(!sub)) return -1;
44064 result = PyUnicode_Tailmatch(s, sub, start, end, direction);
44065 Py_DECREF(sub);
44066 #endif
44067 if (result) {
44068 return (int) result;
44069 }
44070 }
44071 return 0;
44072 }
44073 static int __Pyx_PyUnicode_Tailmatch(PyObject* s, PyObject* substr,
44074 Py_ssize_t start, Py_ssize_t end, int direction) {
44075 if (unlikely(PyTuple_Check(substr))) {
44076 return __Pyx_PyUnicode_TailmatchTuple(s, substr, start, end, direction);
44077 }
44078 return (int) PyUnicode_Tailmatch(s, substr, start, end, direction);
44079 }
44080
44081 /* PyUnicode_Substring */
44082 static CYTHON_INLINE PyObject* __Pyx_PyUnicode_Substring(
44083 PyObject* text, Py_ssize_t start, Py_ssize_t stop) {
44084 Py_ssize_t length;
44085 if (unlikely(__Pyx_PyUnicode_READY(text) == -1)) return NULL;
44086 length = __Pyx_PyUnicode_GET_LENGTH(text);
44087 if (start < 0) {
44088 start += length;
44089 if (start < 0)
44090 start = 0;
44091 }
44092 if (stop < 0)
44093 stop += length;
44094 else if (stop > length)
44095 stop = length;
44096 if (stop <= start)
44097 return __Pyx_NewRef(__pyx_empty_unicode);
44098 if (start == 0 && stop == length)
44099 return __Pyx_NewRef(text);
44100 #if CYTHON_PEP393_ENABLED
44101 return PyUnicode_FromKindAndData(PyUnicode_KIND(text),
44102 PyUnicode_1BYTE_DATA(text) + start*PyUnicode_KIND(text), stop-start);
44103 #else
44104 return PyUnicode_FromUnicode(PyUnicode_AS_UNICODE(text)+start, stop-start);
44105 #endif
44106 }
44107
44108 /* PyIntBinop */
44109 #if !CYTHON_COMPILING_IN_PYPY
44110 static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check) {
44111 CYTHON_MAYBE_UNUSED_VAR(intval);
44112 CYTHON_MAYBE_UNUSED_VAR(inplace);
44113 CYTHON_UNUSED_VAR(zerodivision_check);
44114 #if PY_MAJOR_VERSION < 3
44115 if (likely(PyInt_CheckExact(op1))) {
44116 const long b = intval;
44117 long x;
44118 long a = PyInt_AS_LONG(op1);
44119
44120 x = (long)((unsigned long)a + (unsigned long)b);
44121 if (likely((x^a) >= 0 || (x^b) >= 0))
44122 return PyInt_FromLong(x);
44123 return PyLong_Type.tp_as_number->nb_add(op1, op2);
44124 }
44125 #endif
44126 #if CYTHON_USE_PYLONG_INTERNALS
44127 if (likely(PyLong_CheckExact(op1))) {
44128 const long b = intval;
44129 long a, x;
44130 #ifdef HAVE_LONG_LONG
44131 const PY_LONG_LONG llb = intval;
44132 PY_LONG_LONG lla, llx;
44133 #endif
44134 if (unlikely(__Pyx_PyLong_IsZero(op1))) {
44135 return __Pyx_NewRef(op2);
44136 }
44137 if (likely(__Pyx_PyLong_IsCompact(op1))) {
44138 a = __Pyx_PyLong_CompactValue(op1);
44139 } else {
44140 const digit* digits = __Pyx_PyLong_Digits(op1);
44141 const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(op1);
44142 switch (size) {
44143 case -2:
44144 if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
44145 a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44146 break;
44147 #ifdef HAVE_LONG_LONG
44148 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
44149 lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44150 goto long_long;
44151 #endif
44152 }
44153 CYTHON_FALLTHROUGH;
44154 case 2:
44155 if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
44156 a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44157 break;
44158 #ifdef HAVE_LONG_LONG
44159 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
44160 lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44161 goto long_long;
44162 #endif
44163 }
44164 CYTHON_FALLTHROUGH;
44165 case -3:
44166 if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
44167 a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44168 break;
44169 #ifdef HAVE_LONG_LONG
44170 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
44171 lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44172 goto long_long;
44173 #endif
44174 }
44175 CYTHON_FALLTHROUGH;
44176 case 3:
44177 if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
44178 a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44179 break;
44180 #ifdef HAVE_LONG_LONG
44181 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
44182 lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44183 goto long_long;
44184 #endif
44185 }
44186 CYTHON_FALLTHROUGH;
44187 case -4:
44188 if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
44189 a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44190 break;
44191 #ifdef HAVE_LONG_LONG
44192 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
44193 lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44194 goto long_long;
44195 #endif
44196 }
44197 CYTHON_FALLTHROUGH;
44198 case 4:
44199 if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
44200 a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44201 break;
44202 #ifdef HAVE_LONG_LONG
44203 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
44204 lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44205 goto long_long;
44206 #endif
44207 }
44208 CYTHON_FALLTHROUGH;
44209 default: return PyLong_Type.tp_as_number->nb_add(op1, op2);
44210 }
44211 }
44212 x = a + b;
44213 return PyLong_FromLong(x);
44214 #ifdef HAVE_LONG_LONG
44215 long_long:
44216 llx = lla + llb;
44217 return PyLong_FromLongLong(llx);
44218 #endif
44219
44220
44221 }
44222 #endif
44223 if (PyFloat_CheckExact(op1)) {
44224 const long b = intval;
44225 #if CYTHON_COMPILING_IN_LIMITED_API
44226 double a = __pyx_PyFloat_AsDouble(op1);
44227 #else
44228 double a = PyFloat_AS_DOUBLE(op1);
44229 #endif
44230 double result;
44231
44232 PyFPE_START_PROTECT("add", return NULL)
44233 result = ((double)a) + (double)b;
44234 PyFPE_END_PROTECT(result)
44235 return PyFloat_FromDouble(result);
44236 }
44237 return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2);
44238 }
44239 #endif
44240
44241 /* UnicodeConcatInPlace */
44242 # if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
44243 static int
44244 __Pyx_unicode_modifiable(PyObject *unicode)
44245 {
44246 if (Py_REFCNT(unicode) != 1)
44247 return 0;
44248 if (!PyUnicode_CheckExact(unicode))
44249 return 0;
44250 if (PyUnicode_CHECK_INTERNED(unicode))
44251 return 0;
44252 return 1;
44253 }
44254 static CYTHON_INLINE PyObject *__Pyx_PyUnicode_ConcatInPlaceImpl(PyObject **p_left, PyObject *right
44255 #if CYTHON_REFNANNY
44256 , void* __pyx_refnanny
44257 #endif
44258 ) {
44259 PyObject *left = *p_left;
44260 Py_ssize_t left_len, right_len, new_len;
44261 if (unlikely(__Pyx_PyUnicode_READY(left) == -1))
44262 return NULL;
44263 if (unlikely(__Pyx_PyUnicode_READY(right) == -1))
44264 return NULL;
44265 left_len = PyUnicode_GET_LENGTH(left);
44266 if (left_len == 0) {
44267 Py_INCREF(right);
44268 return right;
44269 }
44270 right_len = PyUnicode_GET_LENGTH(right);
44271 if (right_len == 0) {
44272 Py_INCREF(left);
44273 return left;
44274 }
44275 if (unlikely(left_len > PY_SSIZE_T_MAX - right_len)) {
44276 PyErr_SetString(PyExc_OverflowError,
44277 "strings are too large to concat");
44278 return NULL;
44279 }
44280 new_len = left_len + right_len;
44281 if (__Pyx_unicode_modifiable(left)
44282 && PyUnicode_CheckExact(right)
44283 && PyUnicode_KIND(right) <= PyUnicode_KIND(left)
44284 && !(PyUnicode_IS_ASCII(left) && !PyUnicode_IS_ASCII(right))) {
44285 int ret;
44286 __Pyx_GIVEREF(*p_left);
44287 ret = PyUnicode_Resize(p_left, new_len);
44288 __Pyx_GOTREF(*p_left);
44289 if (unlikely(ret != 0))
44290 return NULL;
44291 #if PY_VERSION_HEX >= 0x030d0000
44292 if (unlikely(PyUnicode_CopyCharacters(*p_left, left_len, right, 0, right_len) < 0)) return NULL;
44293 #else
44294 _PyUnicode_FastCopyCharacters(*p_left, left_len, right, 0, right_len);
44295 #endif
44296 __Pyx_INCREF(*p_left);
44297 __Pyx_GIVEREF(*p_left);
44298 return *p_left;
44299 } else {
44300 return __Pyx_PyUnicode_Concat(left, right);
44301 }
44302 }
44303 #endif
44304
44305 /* DivInt[Py_ssize_t] */
44306 static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) {
44307 Py_ssize_t q = a / b;
44308 Py_ssize_t r = a - q*b;
44309 q -= ((r != 0) & ((r ^ b) < 0));
44310 return q;
44311 }
44312
44313 /* SliceTupleAndList */
44314 #if CYTHON_COMPILING_IN_CPYTHON
44315 static CYTHON_INLINE void __Pyx_crop_slice(Py_ssize_t* _start, Py_ssize_t* _stop, Py_ssize_t* _length) {
44316 Py_ssize_t start = *_start, stop = *_stop, length = *_length;
44317 if (start < 0) {
44318 start += length;
44319 if (start < 0)
44320 start = 0;
44321 }
44322 if (stop < 0)
44323 stop += length;
44324 else if (stop > length)
44325 stop = length;
44326 *_length = stop - start;
44327 *_start = start;
44328 *_stop = stop;
44329 }
44330 static CYTHON_INLINE PyObject* __Pyx_PyList_GetSlice(
44331 PyObject* src, Py_ssize_t start, Py_ssize_t stop) {
44332 Py_ssize_t length = PyList_GET_SIZE(src);
44333 __Pyx_crop_slice(&start, &stop, &length);
44334 if (length <= 0) {
44335 return PyList_New(0);
44336 }
44337 return __Pyx_PyList_FromArray(((PyListObject*)src)->ob_item + start, length);
44338 }
44339 static CYTHON_INLINE PyObject* __Pyx_PyTuple_GetSlice(
44340 PyObject* src, Py_ssize_t start, Py_ssize_t stop) {
44341 Py_ssize_t length = PyTuple_GET_SIZE(src);
44342 __Pyx_crop_slice(&start, &stop, &length);
44343 return __Pyx_PyTuple_FromArray(((PyTupleObject*)src)->ob_item + start, length);
44344 }
44345 #endif
44346
44347 /* PyObjectCall2Args */
44348 static CYTHON_INLINE PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) {
44349 PyObject *args[3] = {NULL, arg1, arg2};
44350 return __Pyx_PyObject_FastCall(function, args+1, 2 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET);
44351 }
44352
44353 /* PyObjectCallMethod1 */
44354 #if !(CYTHON_VECTORCALL && __PYX_LIMITED_VERSION_HEX >= 0x030C00A2)
44355 static PyObject* __Pyx__PyObject_CallMethod1(PyObject* method, PyObject* arg) {
44356 PyObject *result = __Pyx_PyObject_CallOneArg(method, arg);
44357 Py_DECREF(method);
44358 return result;
44359 }
44360 #endif
44361 static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) {
44362 #if CYTHON_VECTORCALL && __PYX_LIMITED_VERSION_HEX >= 0x030C00A2
44363 PyObject *args[2] = {obj, arg};
44364 (void) __Pyx_PyObject_GetMethod;
44365 (void) __Pyx_PyObject_CallOneArg;
44366 (void) __Pyx_PyObject_Call2Args;
44367 return PyObject_VectorcallMethod(method_name, args, 2 | PY_VECTORCALL_ARGUMENTS_OFFSET, NULL);
44368 #else
44369 PyObject *method = NULL, *result;
44370 int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method);
44371 if (likely(is_method)) {
44372 result = __Pyx_PyObject_Call2Args(method, obj, arg);
44373 Py_DECREF(method);
44374 return result;
44375 }
44376 if (unlikely(!method)) return NULL;
44377 return __Pyx__PyObject_CallMethod1(method, arg);
44378 #endif
44379 }
44380
44381 /* append */
44382 static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
44383 if (likely(PyList_CheckExact(L))) {
44384 if (unlikely(__Pyx_PyList_Append(L, x) < 0)) return -1;
44385 } else {
44386 PyObject* retval = __Pyx_PyObject_CallMethod1(L, __pyx_n_s_append, x);
44387 if (unlikely(!retval))
44388 return -1;
44389 Py_DECREF(retval);
44390 }
44391 return 0;
44392 }
44393
44394 /* PyIntBinop */
44395 #if !CYTHON_COMPILING_IN_PYPY
44396 static PyObject* __Pyx_PyInt_FloorDivideObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check) {
44397 CYTHON_MAYBE_UNUSED_VAR(intval);
44398 CYTHON_MAYBE_UNUSED_VAR(inplace);
44399 CYTHON_UNUSED_VAR(zerodivision_check);
44400 #if PY_MAJOR_VERSION < 3
44401 if (likely(PyInt_CheckExact(op1))) {
44402 const long b = intval;
44403 long x;
44404 long a = PyInt_AS_LONG(op1);
44405
44406 if (unlikely(b == -1 && ((unsigned long)a) == 0-(unsigned long)a))
44407 return PyInt_Type.tp_as_number->nb_floor_divide(op1, op2);
44408 else {
44409 long q, r;
44410 q = a / b;
44411 r = a - q*b;
44412 q -= ((r != 0) & ((r ^ b) < 0));
44413 x = q;
44414 }
44415 return PyInt_FromLong(x);
44416 }
44417 #endif
44418 #if CYTHON_USE_PYLONG_INTERNALS
44419 if (likely(PyLong_CheckExact(op1))) {
44420 const long b = intval;
44421 long a, x;
44422 #ifdef HAVE_LONG_LONG
44423 const PY_LONG_LONG llb = intval;
44424 PY_LONG_LONG lla, llx;
44425 #endif
44426 if (unlikely(__Pyx_PyLong_IsZero(op1))) {
44427 return __Pyx_NewRef(op1);
44428 }
44429 if (likely(__Pyx_PyLong_IsCompact(op1))) {
44430 a = __Pyx_PyLong_CompactValue(op1);
44431 } else {
44432 const digit* digits = __Pyx_PyLong_Digits(op1);
44433 const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(op1);
44434 switch (size) {
44435 case -2:
44436 if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
44437 a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44438 break;
44439 #ifdef HAVE_LONG_LONG
44440 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
44441 lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44442 goto long_long;
44443 #endif
44444 }
44445 CYTHON_FALLTHROUGH;
44446 case 2:
44447 if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
44448 a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44449 break;
44450 #ifdef HAVE_LONG_LONG
44451 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
44452 lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44453 goto long_long;
44454 #endif
44455 }
44456 CYTHON_FALLTHROUGH;
44457 case -3:
44458 if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
44459 a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44460 break;
44461 #ifdef HAVE_LONG_LONG
44462 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
44463 lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44464 goto long_long;
44465 #endif
44466 }
44467 CYTHON_FALLTHROUGH;
44468 case 3:
44469 if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
44470 a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44471 break;
44472 #ifdef HAVE_LONG_LONG
44473 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
44474 lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44475 goto long_long;
44476 #endif
44477 }
44478 CYTHON_FALLTHROUGH;
44479 case -4:
44480 if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
44481 a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44482 break;
44483 #ifdef HAVE_LONG_LONG
44484 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
44485 lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44486 goto long_long;
44487 #endif
44488 }
44489 CYTHON_FALLTHROUGH;
44490 case 4:
44491 if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
44492 a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44493 break;
44494 #ifdef HAVE_LONG_LONG
44495 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
44496 lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44497 goto long_long;
44498 #endif
44499 }
44500 CYTHON_FALLTHROUGH;
44501 default: return PyLong_Type.tp_as_number->nb_floor_divide(op1, op2);
44502 }
44503 }
44504 {
44505 long q, r;
44506 q = a / b;
44507 r = a - q*b;
44508 q -= ((r != 0) & ((r ^ b) < 0));
44509 x = q;
44510 }
44511 return PyLong_FromLong(x);
44512 #ifdef HAVE_LONG_LONG
44513 long_long:
44514 {
44515 PY_LONG_LONG q, r;
44516 q = lla / llb;
44517 r = lla - q*llb;
44518 q -= ((r != 0) & ((r ^ llb) < 0));
44519 llx = q;
44520 }
44521 return PyLong_FromLongLong(llx);
44522 #endif
44523
44524
44525 }
44526 #endif
44527 return (inplace ? PyNumber_InPlaceFloorDivide : PyNumber_FloorDivide)(op1, op2);
44528 }
44529 #endif
44530
44531 /* PyIntBinop */
44532 #if !CYTHON_COMPILING_IN_PYPY
44533 static PyObject* __Pyx_PyInt_RemainderObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check) {
44534 CYTHON_MAYBE_UNUSED_VAR(intval);
44535 CYTHON_MAYBE_UNUSED_VAR(inplace);
44536 CYTHON_UNUSED_VAR(zerodivision_check);
44537 #if PY_MAJOR_VERSION < 3
44538 if (likely(PyInt_CheckExact(op1))) {
44539 const long b = intval;
44540 long x;
44541 long a = PyInt_AS_LONG(op1);
44542
44543 x = a % b;
44544 x += ((x != 0) & ((x ^ b) < 0)) * b;
44545 return PyInt_FromLong(x);
44546 }
44547 #endif
44548 #if CYTHON_USE_PYLONG_INTERNALS
44549 if (likely(PyLong_CheckExact(op1))) {
44550 const long b = intval;
44551 long a, x;
44552 #ifdef HAVE_LONG_LONG
44553 const PY_LONG_LONG llb = intval;
44554 PY_LONG_LONG lla, llx;
44555 #endif
44556 if (unlikely(__Pyx_PyLong_IsZero(op1))) {
44557 return __Pyx_NewRef(op1);
44558 }
44559 if (likely(__Pyx_PyLong_IsCompact(op1))) {
44560 a = __Pyx_PyLong_CompactValue(op1);
44561 } else {
44562 const digit* digits = __Pyx_PyLong_Digits(op1);
44563 const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(op1);
44564 switch (size) {
44565 case -2:
44566 if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
44567 a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44568 break;
44569 #ifdef HAVE_LONG_LONG
44570 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
44571 lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44572 goto long_long;
44573 #endif
44574 }
44575 CYTHON_FALLTHROUGH;
44576 case 2:
44577 if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
44578 a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44579 break;
44580 #ifdef HAVE_LONG_LONG
44581 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
44582 lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44583 goto long_long;
44584 #endif
44585 }
44586 CYTHON_FALLTHROUGH;
44587 case -3:
44588 if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
44589 a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44590 break;
44591 #ifdef HAVE_LONG_LONG
44592 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
44593 lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44594 goto long_long;
44595 #endif
44596 }
44597 CYTHON_FALLTHROUGH;
44598 case 3:
44599 if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
44600 a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44601 break;
44602 #ifdef HAVE_LONG_LONG
44603 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
44604 lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44605 goto long_long;
44606 #endif
44607 }
44608 CYTHON_FALLTHROUGH;
44609 case -4:
44610 if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
44611 a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44612 break;
44613 #ifdef HAVE_LONG_LONG
44614 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
44615 lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44616 goto long_long;
44617 #endif
44618 }
44619 CYTHON_FALLTHROUGH;
44620 case 4:
44621 if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
44622 a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
44623 break;
44624 #ifdef HAVE_LONG_LONG
44625 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
44626 lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
44627 goto long_long;
44628 #endif
44629 }
44630 CYTHON_FALLTHROUGH;
44631 default: return PyLong_Type.tp_as_number->nb_remainder(op1, op2);
44632 }
44633 }
44634 x = a % b;
44635 x += ((x != 0) & ((x ^ b) < 0)) * b;
44636 return PyLong_FromLong(x);
44637 #ifdef HAVE_LONG_LONG
44638 long_long:
44639 llx = lla % llb;
44640 llx += ((llx != 0) & ((llx ^ llb) < 0)) * llb;
44641 return PyLong_FromLongLong(llx);
44642 #endif
44643
44644
44645 }
44646 #endif
44647 return (inplace ? PyNumber_InPlaceRemainder : PyNumber_Remainder)(op1, op2);
44648 }
44649 #endif
44650
44651 /* SetItemInt */
44652 static int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) {
44653 int r;
44654 if (unlikely(!j)) return -1;
44655 r = PyObject_SetItem(o, j, v);
44656 Py_DECREF(j);
44657 return r;
44658 }
44659 static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, int is_list,
44660 CYTHON_NCP_UNUSED int wraparound, CYTHON_NCP_UNUSED int boundscheck) {
44661 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS
44662 if (is_list || PyList_CheckExact(o)) {
44663 Py_ssize_t n = (!wraparound) ? i : ((likely(i >= 0)) ? i : i + PyList_GET_SIZE(o));
44664 if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o)))) {
44665 PyObject* old = PyList_GET_ITEM(o, n);
44666 Py_INCREF(v);
44667 PyList_SET_ITEM(o, n, v);
44668 Py_DECREF(old);
44669 return 1;
44670 }
44671 } else {
44672 PyMappingMethods *mm = Py_TYPE(o)->tp_as_mapping;
44673 PySequenceMethods *sm = Py_TYPE(o)->tp_as_sequence;
44674 if (mm && mm->mp_ass_subscript) {
44675 int r;
44676 PyObject *key = PyInt_FromSsize_t(i);
44677 if (unlikely(!key)) return -1;
44678 r = mm->mp_ass_subscript(o, key, v);
44679 Py_DECREF(key);
44680 return r;
44681 }
44682 if (likely(sm && sm->sq_ass_item)) {
44683 if (wraparound && unlikely(i < 0) && likely(sm->sq_length)) {
44684 Py_ssize_t l = sm->sq_length(o);
44685 if (likely(l >= 0)) {
44686 i += l;
44687 } else {
44688 if (!PyErr_ExceptionMatches(PyExc_OverflowError))
44689 return -1;
44690 PyErr_Clear();
44691 }
44692 }
44693 return sm->sq_ass_item(o, i, v);
44694 }
44695 }
44696 #else
44697 if (is_list || !PyMapping_Check(o))
44698 {
44699 return PySequence_SetItem(o, i, v);
44700 }
44701 #endif
44702 return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
44703 }
44704
44705 /* pyobject_as_double */
44706 static double __Pyx__PyObject_AsDouble(PyObject* obj) {
44707 if (PyUnicode_CheckExact(obj)) {
44708 return __Pyx_PyUnicode_AsDouble(obj);
44709 } else if (PyBytes_CheckExact(obj)) {
44710 return __Pyx_PyBytes_AsDouble(obj);
44711 } else if (PyByteArray_CheckExact(obj)) {
44712 return __Pyx_PyByteArray_AsDouble(obj);
44713 } else {
44714 PyObject* float_value;
44715 #if !CYTHON_USE_TYPE_SLOTS
44716 float_value = PyNumber_Float(obj); if ((0)) goto bad;
44717 (void)__Pyx_PyObject_CallOneArg;
44718 #else
44719 PyNumberMethods *nb = Py_TYPE(obj)->tp_as_number;
44720 if (likely(nb) && likely(nb->nb_float)) {
44721 float_value = nb->nb_float(obj);
44722 if (likely(float_value) && unlikely(!PyFloat_Check(float_value))) {
44723 __Pyx_TypeName float_value_type_name = __Pyx_PyType_GetName(Py_TYPE(float_value));
44724 PyErr_Format(PyExc_TypeError,
44725 "__float__ returned non-float (type " __Pyx_FMT_TYPENAME ")",
44726 float_value_type_name);
44727 __Pyx_DECREF_TypeName(float_value_type_name);
44728 Py_DECREF(float_value);
44729 goto bad;
44730 }
44731 } else {
44732 float_value = __Pyx_PyObject_CallOneArg((PyObject*)&PyFloat_Type, obj);
44733 }
44734 #endif
44735 if (likely(float_value)) {
44736 double value = PyFloat_AS_DOUBLE(float_value);
44737 Py_DECREF(float_value);
44738 return value;
44739 }
44740 }
44741 bad:
44742 return (double)-1;
44743 }
44744
44745 /* PySequenceMultiply */
44746 static PyObject* __Pyx_PySequence_Multiply_Generic(PyObject *seq, Py_ssize_t mul) {
44747 PyObject *result, *pymul = PyInt_FromSsize_t(mul);
44748 if (unlikely(!pymul))
44749 return NULL;
44750 result = PyNumber_Multiply(seq, pymul);
44751 Py_DECREF(pymul);
44752 return result;
44753 }
44754 static CYTHON_INLINE PyObject* __Pyx_PySequence_Multiply(PyObject *seq, Py_ssize_t mul) {
44755 #if CYTHON_USE_TYPE_SLOTS
44756 PyTypeObject *type = Py_TYPE(seq);
44757 if (likely(type->tp_as_sequence && type->tp_as_sequence->sq_repeat)) {
44758 return type->tp_as_sequence->sq_repeat(seq, mul);
44759 } else
44760 #endif
44761 {
44762 return __Pyx_PySequence_Multiply_Generic(seq, mul);
44763 }
44764 }
44765
44766 /* pep479 */
44767 static void __Pyx_Generator_Replace_StopIteration(int in_async_gen) {
44768 PyObject *exc, *val, *tb, *cur_exc;
44769 __Pyx_PyThreadState_declare
44770 #ifdef __Pyx_StopAsyncIteration_USED
44771 int is_async_stopiteration = 0;
44772 #endif
44773 CYTHON_MAYBE_UNUSED_VAR(in_async_gen);
44774 cur_exc = PyErr_Occurred();
44775 if (likely(!__Pyx_PyErr_GivenExceptionMatches(cur_exc, PyExc_StopIteration))) {
44776 #ifdef __Pyx_StopAsyncIteration_USED
44777 if (in_async_gen && unlikely(__Pyx_PyErr_GivenExceptionMatches(cur_exc, __Pyx_PyExc_StopAsyncIteration))) {
44778 is_async_stopiteration = 1;
44779 } else
44780 #endif
44781 return;
44782 }
44783 __Pyx_PyThreadState_assign
44784 __Pyx_GetException(&exc, &val, &tb);
44785 Py_XDECREF(exc);
44786 Py_XDECREF(val);
44787 Py_XDECREF(tb);
44788 PyErr_SetString(PyExc_RuntimeError,
44789 #ifdef __Pyx_StopAsyncIteration_USED
44790 is_async_stopiteration ? "async generator raised StopAsyncIteration" :
44791 in_async_gen ? "async generator raised StopIteration" :
44792 #endif
44793 "generator raised StopIteration");
44794 }
44795
44796 /* Import */
44797 static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
44798 PyObject *module = 0;
44799 PyObject *empty_dict = 0;
44800 PyObject *empty_list = 0;
44801 #if PY_MAJOR_VERSION < 3
44802 PyObject *py_import;
44803 py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
44804 if (unlikely(!py_import))
44805 goto bad;
44806 if (!from_list) {
44807 empty_list = PyList_New(0);
44808 if (unlikely(!empty_list))
44809 goto bad;
44810 from_list = empty_list;
44811 }
44812 #endif
44813 empty_dict = PyDict_New();
44814 if (unlikely(!empty_dict))
44815 goto bad;
44816 {
44817 #if PY_MAJOR_VERSION >= 3
44818 if (level == -1) {
44819 if (strchr(__Pyx_MODULE_NAME, '.') != NULL) {
44820 module = PyImport_ImportModuleLevelObject(
44821 name, __pyx_d, empty_dict, from_list, 1);
44822 if (unlikely(!module)) {
44823 if (unlikely(!PyErr_ExceptionMatches(PyExc_ImportError)))
44824 goto bad;
44825 PyErr_Clear();
44826 }
44827 }
44828 level = 0;
44829 }
44830 #endif
44831 if (!module) {
44832 #if PY_MAJOR_VERSION < 3
44833 PyObject *py_level = PyInt_FromLong(level);
44834 if (unlikely(!py_level))
44835 goto bad;
44836 module = PyObject_CallFunctionObjArgs(py_import,
44837 name, __pyx_d, empty_dict, from_list, py_level, (PyObject *)NULL);
44838 Py_DECREF(py_level);
44839 #else
44840 module = PyImport_ImportModuleLevelObject(
44841 name, __pyx_d, empty_dict, from_list, level);
44842 #endif
44843 }
44844 }
44845 bad:
44846 Py_XDECREF(empty_dict);
44847 Py_XDECREF(empty_list);
44848 #if PY_MAJOR_VERSION < 3
44849 Py_XDECREF(py_import);
44850 #endif
44851 return module;
44852 }
44853
44854 /* ImportFrom */
44855 static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
44856 PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
44857 if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
44858 const char* module_name_str = 0;
44859 PyObject* module_name = 0;
44860 PyObject* module_dot = 0;
44861 PyObject* full_name = 0;
44862 PyErr_Clear();
44863 module_name_str = PyModule_GetName(module);
44864 if (unlikely(!module_name_str)) { goto modbad; }
44865 module_name = PyUnicode_FromString(module_name_str);
44866 if (unlikely(!module_name)) { goto modbad; }
44867 module_dot = PyUnicode_Concat(module_name, __pyx_kp_u__5);
44868 if (unlikely(!module_dot)) { goto modbad; }
44869 full_name = PyUnicode_Concat(module_dot, name);
44870 if (unlikely(!full_name)) { goto modbad; }
44871 #if PY_VERSION_HEX < 0x030700A1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030400)
44872 {
44873 PyObject *modules = PyImport_GetModuleDict();
44874 if (unlikely(!modules))
44875 goto modbad;
44876 value = PyObject_GetItem(modules, full_name);
44877 }
44878 #else
44879 value = PyImport_GetModule(full_name);
44880 #endif
44881 modbad:
44882 Py_XDECREF(full_name);
44883 Py_XDECREF(module_dot);
44884 Py_XDECREF(module_name);
44885 }
44886 if (unlikely(!value)) {
44887 PyErr_Format(PyExc_ImportError,
44888 #if PY_MAJOR_VERSION < 3
44889 "cannot import name %.230s", PyString_AS_STRING(name));
44890 #else
44891 "cannot import name %S", name);
44892 #endif
44893 }
44894 return value;
44895 }
44896
44897 /* GetAttr */
44898 static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) {
44899 #if CYTHON_USE_TYPE_SLOTS
44900 #if PY_MAJOR_VERSION >= 3
44901 if (likely(PyUnicode_Check(n)))
44902 #else
44903 if (likely(PyString_Check(n)))
44904 #endif
44905 return __Pyx_PyObject_GetAttrStr(o, n);
44906 #endif
44907 return PyObject_GetAttr(o, n);
44908 }
44909
44910 /* HasAttr */
44911 static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) {
44912 PyObject *r;
44913 if (unlikely(!__Pyx_PyBaseString_Check(n))) {
44914 PyErr_SetString(PyExc_TypeError,
44915 "hasattr(): attribute name must be string");
44916 return -1;
44917 }
44918 r = __Pyx_GetAttr(o, n);
44919 if (!r) {
44920 PyErr_Clear();
44921 return 0;
44922 } else {
44923 Py_DECREF(r);
44924 return 1;
44925 }
44926 }
44927
44928 /* CallNextTpDealloc */
44929 static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) {
44930 PyTypeObject* type = Py_TYPE(obj);
44931 destructor tp_dealloc = NULL;
44932 while (type && __Pyx_PyType_GetSlot(type, tp_dealloc, destructor) != current_tp_dealloc)
44933 type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*);
44934 while (type && (tp_dealloc = __Pyx_PyType_GetSlot(type, tp_dealloc, destructor)) == current_tp_dealloc)
44935 type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*);
44936 if (type)
44937 tp_dealloc(obj);
44938 }
44939
44940 /* CallNextTpTraverse */
44941 static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
44942 PyTypeObject* type = Py_TYPE(obj);
44943 traverseproc tp_traverse = NULL;
44944 while (type && __Pyx_PyType_GetSlot(type, tp_traverse, traverseproc) != current_tp_traverse)
44945 type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*);
44946 while (type && (tp_traverse = __Pyx_PyType_GetSlot(type, tp_traverse, traverseproc)) == current_tp_traverse)
44947 type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*);
44948 if (type && tp_traverse)
44949 return tp_traverse(obj, v, a);
44950 return 0;
44951 }
44952
44953 /* CallNextTpClear */
44954 static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
44955 PyTypeObject* type = Py_TYPE(obj);
44956 inquiry tp_clear = NULL;
44957 while (type && __Pyx_PyType_GetSlot(type, tp_clear, inquiry) != current_tp_clear)
44958 type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*);
44959 while (type && (tp_clear = __Pyx_PyType_GetSlot(type, tp_clear, inquiry)) == current_tp_clear)
44960 type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*);
44961 if (type && tp_clear)
44962 tp_clear(obj);
44963 }
44964
44965 /* TypeImport */
44966 #ifndef __PYX_HAVE_RT_ImportType_3_0_11
44967 #define __PYX_HAVE_RT_ImportType_3_0_11
44968 static PyTypeObject *__Pyx_ImportType_3_0_11(PyObject *module, const char *module_name, const char *class_name,
44969 size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_11 check_size)
44970 {
44971 PyObject *result = 0;
44972 char warning[200];
44973 Py_ssize_t basicsize;
44974 Py_ssize_t itemsize;
44975 #if CYTHON_COMPILING_IN_LIMITED_API
44976 PyObject *py_basicsize;
44977 PyObject *py_itemsize;
44978 #endif
44979 result = PyObject_GetAttrString(module, class_name);
44980 if (!result)
44981 goto bad;
44982 if (!PyType_Check(result)) {
44983 PyErr_Format(PyExc_TypeError,
44984 "%.200s.%.200s is not a type object",
44985 module_name, class_name);
44986 goto bad;
44987 }
44988 #if !CYTHON_COMPILING_IN_LIMITED_API
44989 basicsize = ((PyTypeObject *)result)->tp_basicsize;
44990 itemsize = ((PyTypeObject *)result)->tp_itemsize;
44991 #else
44992 py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
44993 if (!py_basicsize)
44994 goto bad;
44995 basicsize = PyLong_AsSsize_t(py_basicsize);
44996 Py_DECREF(py_basicsize);
44997 py_basicsize = 0;
44998 if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
44999 goto bad;
45000 py_itemsize = PyObject_GetAttrString(result, "__itemsize__");
45001 if (!py_itemsize)
45002 goto bad;
45003 itemsize = PyLong_AsSsize_t(py_itemsize);
45004 Py_DECREF(py_itemsize);
45005 py_itemsize = 0;
45006 if (itemsize == (Py_ssize_t)-1 && PyErr_Occurred())
45007 goto bad;
45008 #endif
45009 if (itemsize) {
45010 if (size % alignment) {
45011 alignment = size % alignment;
45012 }
45013 if (itemsize < (Py_ssize_t)alignment)
45014 itemsize = (Py_ssize_t)alignment;
45015 }
45016 if ((size_t)(basicsize + itemsize) < size) {
45017 PyErr_Format(PyExc_ValueError,
45018 "%.200s.%.200s size changed, may indicate binary incompatibility. "
45019 "Expected %zd from C header, got %zd from PyObject",
45020 module_name, class_name, size, basicsize+itemsize);
45021 goto bad;
45022 }
45023 if (check_size == __Pyx_ImportType_CheckSize_Error_3_0_11 &&
45024 ((size_t)basicsize > size || (size_t)(basicsize + itemsize) < size)) {
45025 PyErr_Format(PyExc_ValueError,
45026 "%.200s.%.200s size changed, may indicate binary incompatibility. "
45027 "Expected %zd from C header, got %zd-%zd from PyObject",
45028 module_name, class_name, size, basicsize, basicsize+itemsize);
45029 goto bad;
45030 }
45031 else if (check_size == __Pyx_ImportType_CheckSize_Warn_3_0_11 && (size_t)basicsize > size) {
45032 PyOS_snprintf(warning, sizeof(warning),
45033 "%s.%s size changed, may indicate binary incompatibility. "
45034 "Expected %zd from C header, got %zd from PyObject",
45035 module_name, class_name, size, basicsize);
45036 if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
45037 }
45038 return (PyTypeObject *)result;
45039 bad:
45040 Py_XDECREF(result);
45041 return NULL;
45042 }
45043 #endif
45044
45045 /* GetVTable */
45046 static void* __Pyx_GetVtable(PyTypeObject *type) {
45047 void* ptr;
45048 #if CYTHON_COMPILING_IN_LIMITED_API
45049 PyObject *ob = PyObject_GetAttr((PyObject *)type, __pyx_n_s_pyx_vtable);
45050 #else
45051 PyObject *ob = PyObject_GetItem(type->tp_dict, __pyx_n_s_pyx_vtable);
45052 #endif
45053 if (!ob)
45054 goto bad;
45055 ptr = PyCapsule_GetPointer(ob, 0);
45056 if (!ptr && !PyErr_Occurred())
45057 PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
45058 Py_DECREF(ob);
45059 return ptr;
45060 bad:
45061 Py_XDECREF(ob);
45062 return NULL;
45063 }
45064
45065 /* FixUpExtensionType */
45066 #if CYTHON_USE_TYPE_SPECS
45067 static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject *type) {
45068 #if PY_VERSION_HEX > 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
45069 CYTHON_UNUSED_VAR(spec);
45070 CYTHON_UNUSED_VAR(type);
45071 #else
45072 const PyType_Slot *slot = spec->slots;
45073 while (slot && slot->slot && slot->slot != Py_tp_members)
45074 slot++;
45075 if (slot && slot->slot == Py_tp_members) {
45076 int changed = 0;
45077 #if !(PY_VERSION_HEX <= 0x030900b1 && CYTHON_COMPILING_IN_CPYTHON)
45078 const
45079 #endif
45080 PyMemberDef *memb = (PyMemberDef*) slot->pfunc;
45081 while (memb && memb->name) {
45082 if (memb->name[0] == '_' && memb->name[1] == '_') {
45083 #if PY_VERSION_HEX < 0x030900b1
45084 if (strcmp(memb->name, "__weaklistoffset__") == 0) {
45085 assert(memb->type == T_PYSSIZET);
45086 assert(memb->flags == READONLY);
45087 type->tp_weaklistoffset = memb->offset;
45088 changed = 1;
45089 }
45090 else if (strcmp(memb->name, "__dictoffset__") == 0) {
45091 assert(memb->type == T_PYSSIZET);
45092 assert(memb->flags == READONLY);
45093 type->tp_dictoffset = memb->offset;
45094 changed = 1;
45095 }
45096 #if CYTHON_METH_FASTCALL
45097 else if (strcmp(memb->name, "__vectorcalloffset__") == 0) {
45098 assert(memb->type == T_PYSSIZET);
45099 assert(memb->flags == READONLY);
45100 #if PY_VERSION_HEX >= 0x030800b4
45101 type->tp_vectorcall_offset = memb->offset;
45102 #else
45103 type->tp_print = (printfunc) memb->offset;
45104 #endif
45105 changed = 1;
45106 }
45107 #endif
45108 #else
45109 if ((0));
45110 #endif
45111 #if PY_VERSION_HEX <= 0x030900b1 && CYTHON_COMPILING_IN_CPYTHON
45112 else if (strcmp(memb->name, "__module__") == 0) {
45113 PyObject *descr;
45114 assert(memb->type == T_OBJECT);
45115 assert(memb->flags == 0 || memb->flags == READONLY);
45116 descr = PyDescr_NewMember(type, memb);
45117 if (unlikely(!descr))
45118 return -1;
45119 if (unlikely(PyDict_SetItem(type->tp_dict, PyDescr_NAME(descr), descr) < 0)) {
45120 Py_DECREF(descr);
45121 return -1;
45122 }
45123 Py_DECREF(descr);
45124 changed = 1;
45125 }
45126 #endif
45127 }
45128 memb++;
45129 }
45130 if (changed)
45131 PyType_Modified(type);
45132 }
45133 #endif
45134 return 0;
45135 }
45136 #endif
45137
45138 /* ValidateBasesTuple */
45139 #if CYTHON_COMPILING_IN_CPYTHON || CYTHON_COMPILING_IN_LIMITED_API || CYTHON_USE_TYPE_SPECS
45140 static int __Pyx_validate_bases_tuple(const char *type_name, Py_ssize_t dictoffset, PyObject *bases) {
45141 Py_ssize_t i, n;
45142 #if CYTHON_ASSUME_SAFE_MACROS
45143 n = PyTuple_GET_SIZE(bases);
45144 #else
45145 n = PyTuple_Size(bases);
45146 if (n < 0) return -1;
45147 #endif
45148 for (i = 1; i < n; i++)
45149 {
45150 #if CYTHON_AVOID_BORROWED_REFS
45151 PyObject *b0 = PySequence_GetItem(bases, i);
45152 if (!b0) return -1;
45153 #elif CYTHON_ASSUME_SAFE_MACROS
45154 PyObject *b0 = PyTuple_GET_ITEM(bases, i);
45155 #else
45156 PyObject *b0 = PyTuple_GetItem(bases, i);
45157 if (!b0) return -1;
45158 #endif
45159 PyTypeObject *b;
45160 #if PY_MAJOR_VERSION < 3
45161 if (PyClass_Check(b0))
45162 {
45163 PyErr_Format(PyExc_TypeError, "base class '%.200s' is an old-style class",
45164 PyString_AS_STRING(((PyClassObject*)b0)->cl_name));
45165 #if CYTHON_AVOID_BORROWED_REFS
45166 Py_DECREF(b0);
45167 #endif
45168 return -1;
45169 }
45170 #endif
45171 b = (PyTypeObject*) b0;
45172 if (!__Pyx_PyType_HasFeature(b, Py_TPFLAGS_HEAPTYPE))
45173 {
45174 __Pyx_TypeName b_name = __Pyx_PyType_GetName(b);
45175 PyErr_Format(PyExc_TypeError,
45176 "base class '" __Pyx_FMT_TYPENAME "' is not a heap type", b_name);
45177 __Pyx_DECREF_TypeName(b_name);
45178 #if CYTHON_AVOID_BORROWED_REFS
45179 Py_DECREF(b0);
45180 #endif
45181 return -1;
45182 }
45183 if (dictoffset == 0)
45184 {
45185 Py_ssize_t b_dictoffset = 0;
45186 #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY
45187 b_dictoffset = b->tp_dictoffset;
45188 #else
45189 PyObject *py_b_dictoffset = PyObject_GetAttrString((PyObject*)b, "__dictoffset__");
45190 if (!py_b_dictoffset) goto dictoffset_return;
45191 b_dictoffset = PyLong_AsSsize_t(py_b_dictoffset);
45192 Py_DECREF(py_b_dictoffset);
45193 if (b_dictoffset == -1 && PyErr_Occurred()) goto dictoffset_return;
45194 #endif
45195 if (b_dictoffset) {
45196 {
45197 __Pyx_TypeName b_name = __Pyx_PyType_GetName(b);
45198 PyErr_Format(PyExc_TypeError,
45199 "extension type '%.200s' has no __dict__ slot, "
45200 "but base type '" __Pyx_FMT_TYPENAME "' has: "
45201 "either add 'cdef dict __dict__' to the extension type "
45202 "or add '__slots__ = [...]' to the base type",
45203 type_name, b_name);
45204 __Pyx_DECREF_TypeName(b_name);
45205 }
45206 #if !(CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY)
45207 dictoffset_return:
45208 #endif
45209 #if CYTHON_AVOID_BORROWED_REFS
45210 Py_DECREF(b0);
45211 #endif
45212 return -1;
45213 }
45214 }
45215 #if CYTHON_AVOID_BORROWED_REFS
45216 Py_DECREF(b0);
45217 #endif
45218 }
45219 return 0;
45220 }
45221 #endif
45222
45223 /* PyType_Ready */
45224 static int __Pyx_PyType_Ready(PyTypeObject *t) {
45225 #if CYTHON_USE_TYPE_SPECS || !(CYTHON_COMPILING_IN_CPYTHON || CYTHON_COMPILING_IN_LIMITED_API) || defined(PYSTON_MAJOR_VERSION)
45226 (void)__Pyx_PyObject_CallMethod0;
45227 #if CYTHON_USE_TYPE_SPECS
45228 (void)__Pyx_validate_bases_tuple;
45229 #endif
45230 return PyType_Ready(t);
45231 #else
45232 int r;
45233 PyObject *bases = __Pyx_PyType_GetSlot(t, tp_bases, PyObject*);
45234 if (bases && unlikely(__Pyx_validate_bases_tuple(t->tp_name, t->tp_dictoffset, bases) == -1))
45235 return -1;
45236 #if PY_VERSION_HEX >= 0x03050000 && !defined(PYSTON_MAJOR_VERSION)
45237 {
45238 int gc_was_enabled;
45239 #if PY_VERSION_HEX >= 0x030A00b1
45240 gc_was_enabled = PyGC_Disable();
45241 (void)__Pyx_PyObject_CallMethod0;
45242 #else
45243 PyObject *ret, *py_status;
45244 PyObject *gc = NULL;
45245 #if PY_VERSION_HEX >= 0x030700a1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM+0 >= 0x07030400)
45246 gc = PyImport_GetModule(__pyx_kp_u_gc);
45247 #endif
45248 if (unlikely(!gc)) gc = PyImport_Import(__pyx_kp_u_gc);
45249 if (unlikely(!gc)) return -1;
45250 py_status = __Pyx_PyObject_CallMethod0(gc, __pyx_kp_u_isenabled);
45251 if (unlikely(!py_status)) {
45252 Py_DECREF(gc);
45253 return -1;
45254 }
45255 gc_was_enabled = __Pyx_PyObject_IsTrue(py_status);
45256 Py_DECREF(py_status);
45257 if (gc_was_enabled > 0) {
45258 ret = __Pyx_PyObject_CallMethod0(gc, __pyx_kp_u_disable);
45259 if (unlikely(!ret)) {
45260 Py_DECREF(gc);
45261 return -1;
45262 }
45263 Py_DECREF(ret);
45264 } else if (unlikely(gc_was_enabled == -1)) {
45265 Py_DECREF(gc);
45266 return -1;
45267 }
45268 #endif
45269 t->tp_flags |= Py_TPFLAGS_HEAPTYPE;
45270 #if PY_VERSION_HEX >= 0x030A0000
45271 t->tp_flags |= Py_TPFLAGS_IMMUTABLETYPE;
45272 #endif
45273 #else
45274 (void)__Pyx_PyObject_CallMethod0;
45275 #endif
45276 r = PyType_Ready(t);
45277 #if PY_VERSION_HEX >= 0x03050000 && !defined(PYSTON_MAJOR_VERSION)
45278 t->tp_flags &= ~Py_TPFLAGS_HEAPTYPE;
45279 #if PY_VERSION_HEX >= 0x030A00b1
45280 if (gc_was_enabled)
45281 PyGC_Enable();
45282 #else
45283 if (gc_was_enabled) {
45284 PyObject *tp, *v, *tb;
45285 PyErr_Fetch(&tp, &v, &tb);
45286 ret = __Pyx_PyObject_CallMethod0(gc, __pyx_kp_u_enable);
45287 if (likely(ret || r == -1)) {
45288 Py_XDECREF(ret);
45289 PyErr_Restore(tp, v, tb);
45290 } else {
45291 Py_XDECREF(tp);
45292 Py_XDECREF(v);
45293 Py_XDECREF(tb);
45294 r = -1;
45295 }
45296 }
45297 Py_DECREF(gc);
45298 #endif
45299 }
45300 #endif
45301 return r;
45302 #endif
45303 }
45304
45305 /* PyObject_GenericGetAttrNoDict */
45306 #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
45307 static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) {
45308 __Pyx_TypeName type_name = __Pyx_PyType_GetName(tp);
45309 PyErr_Format(PyExc_AttributeError,
45310 #if PY_MAJOR_VERSION >= 3
45311 "'" __Pyx_FMT_TYPENAME "' object has no attribute '%U'",
45312 type_name, attr_name);
45313 #else
45314 "'" __Pyx_FMT_TYPENAME "' object has no attribute '%.400s'",
45315 type_name, PyString_AS_STRING(attr_name));
45316 #endif
45317 __Pyx_DECREF_TypeName(type_name);
45318 return NULL;
45319 }
45320 static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) {
45321 PyObject *descr;
45322 PyTypeObject *tp = Py_TYPE(obj);
45323 if (unlikely(!PyString_Check(attr_name))) {
45324 return PyObject_GenericGetAttr(obj, attr_name);
45325 }
45326 assert(!tp->tp_dictoffset);
45327 descr = _PyType_Lookup(tp, attr_name);
45328 if (unlikely(!descr)) {
45329 return __Pyx_RaiseGenericGetAttributeError(tp, attr_name);
45330 }
45331 Py_INCREF(descr);
45332 #if PY_MAJOR_VERSION < 3
45333 if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS)))
45334 #endif
45335 {
45336 descrgetfunc f = Py_TYPE(descr)->tp_descr_get;
45337 if (unlikely(f)) {
45338 PyObject *res = f(descr, obj, (PyObject *)tp);
45339 Py_DECREF(descr);
45340 return res;
45341 }
45342 }
45343 return descr;
45344 }
45345 #endif
45346
45347 /* PyObject_GenericGetAttr */
45348 #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
45349 static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) {
45350 if (unlikely(Py_TYPE(obj)->tp_dictoffset)) {
45351 return PyObject_GenericGetAttr(obj, attr_name);
45352 }
45353 return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name);
45354 }
45355 #endif
45356
45357 /* SetVTable */
45358 static int __Pyx_SetVtable(PyTypeObject *type, void *vtable) {
45359 PyObject *ob = PyCapsule_New(vtable, 0, 0);
45360 if (unlikely(!ob))
45361 goto bad;
45362 #if CYTHON_COMPILING_IN_LIMITED_API
45363 if (unlikely(PyObject_SetAttr((PyObject *) type, __pyx_n_s_pyx_vtable, ob) < 0))
45364 #else
45365 if (unlikely(PyDict_SetItem(type->tp_dict, __pyx_n_s_pyx_vtable, ob) < 0))
45366 #endif
45367 goto bad;
45368 Py_DECREF(ob);
45369 return 0;
45370 bad:
45371 Py_XDECREF(ob);
45372 return -1;
45373 }
45374
45375 /* MergeVTables */
45376 #if !CYTHON_COMPILING_IN_LIMITED_API
45377 static int __Pyx_MergeVtables(PyTypeObject *type) {
45378 int i;
45379 void** base_vtables;
45380 __Pyx_TypeName tp_base_name;
45381 __Pyx_TypeName base_name;
45382 void* unknown = (void*)-1;
45383 PyObject* bases = type->tp_bases;
45384 int base_depth = 0;
45385 {
45386 PyTypeObject* base = type->tp_base;
45387 while (base) {
45388 base_depth += 1;
45389 base = base->tp_base;
45390 }
45391 }
45392 base_vtables = (void**) malloc(sizeof(void*) * (size_t)(base_depth + 1));
45393 base_vtables[0] = unknown;
45394 for (i = 1; i < PyTuple_GET_SIZE(bases); i++) {
45395 void* base_vtable = __Pyx_GetVtable(((PyTypeObject*)PyTuple_GET_ITEM(bases, i)));
45396 if (base_vtable != NULL) {
45397 int j;
45398 PyTypeObject* base = type->tp_base;
45399 for (j = 0; j < base_depth; j++) {
45400 if (base_vtables[j] == unknown) {
45401 base_vtables[j] = __Pyx_GetVtable(base);
45402 base_vtables[j + 1] = unknown;
45403 }
45404 if (base_vtables[j] == base_vtable) {
45405 break;
45406 } else if (base_vtables[j] == NULL) {
45407 goto bad;
45408 }
45409 base = base->tp_base;
45410 }
45411 }
45412 }
45413 PyErr_Clear();
45414 free(base_vtables);
45415 return 0;
45416 bad:
45417 tp_base_name = __Pyx_PyType_GetName(type->tp_base);
45418 base_name = __Pyx_PyType_GetName((PyTypeObject*)PyTuple_GET_ITEM(bases, i));
45419 PyErr_Format(PyExc_TypeError,
45420 "multiple bases have vtable conflict: '" __Pyx_FMT_TYPENAME "' and '" __Pyx_FMT_TYPENAME "'", tp_base_name, base_name);
45421 __Pyx_DECREF_TypeName(tp_base_name);
45422 __Pyx_DECREF_TypeName(base_name);
45423 free(base_vtables);
45424 return -1;
45425 }
45426 #endif
45427
45428 /* SetupReduce */
45429 #if !CYTHON_COMPILING_IN_LIMITED_API
45430 static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) {
45431 int ret;
45432 PyObject *name_attr;
45433 name_attr = __Pyx_PyObject_GetAttrStrNoError(meth, __pyx_n_s_name);
45434 if (likely(name_attr)) {
45435 ret = PyObject_RichCompareBool(name_attr, name, Py_EQ);
45436 } else {
45437 ret = -1;
45438 }
45439 if (unlikely(ret < 0)) {
45440 PyErr_Clear();
45441 ret = 0;
45442 }
45443 Py_XDECREF(name_attr);
45444 return ret;
45445 }
45446 static int __Pyx_setup_reduce(PyObject* type_obj) {
45447 int ret = 0;
45448 PyObject *object_reduce = NULL;
45449 PyObject *object_getstate = NULL;
45450 PyObject *object_reduce_ex = NULL;
45451 PyObject *reduce = NULL;
45452 PyObject *reduce_ex = NULL;
45453 PyObject *reduce_cython = NULL;
45454 PyObject *setstate = NULL;
45455 PyObject *setstate_cython = NULL;
45456 PyObject *getstate = NULL;
45457 #if CYTHON_USE_PYTYPE_LOOKUP
45458 getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate);
45459 #else
45460 getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate);
45461 if (!getstate && PyErr_Occurred()) {
45462 goto __PYX_BAD;
45463 }
45464 #endif
45465 if (getstate) {
45466 #if CYTHON_USE_PYTYPE_LOOKUP
45467 object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate);
45468 #else
45469 object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate);
45470 if (!object_getstate && PyErr_Occurred()) {
45471 goto __PYX_BAD;
45472 }
45473 #endif
45474 if (object_getstate != getstate) {
45475 goto __PYX_GOOD;
45476 }
45477 }
45478 #if CYTHON_USE_PYTYPE_LOOKUP
45479 object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD;
45480 #else
45481 object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD;
45482 #endif
45483 reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD;
45484 if (reduce_ex == object_reduce_ex) {
45485 #if CYTHON_USE_PYTYPE_LOOKUP
45486 object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD;
45487 #else
45488 object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD;
45489 #endif
45490 reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD;
45491 if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) {
45492 reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython);
45493 if (likely(reduce_cython)) {
45494 ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
45495 ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
45496 } else if (reduce == object_reduce || PyErr_Occurred()) {
45497 goto __PYX_BAD;
45498 }
45499 setstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate);
45500 if (!setstate) PyErr_Clear();
45501 if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
45502 setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython);
45503 if (likely(setstate_cython)) {
45504 ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
45505 ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
45506 } else if (!setstate || PyErr_Occurred()) {
45507 goto __PYX_BAD;
45508 }
45509 }
45510 PyType_Modified((PyTypeObject*)type_obj);
45511 }
45512 }
45513 goto __PYX_GOOD;
45514 __PYX_BAD:
45515 if (!PyErr_Occurred()) {
45516 __Pyx_TypeName type_obj_name =
45517 __Pyx_PyType_GetName((PyTypeObject*)type_obj);
45518 PyErr_Format(PyExc_RuntimeError,
45519 "Unable to initialize pickling for " __Pyx_FMT_TYPENAME, type_obj_name);
45520 __Pyx_DECREF_TypeName(type_obj_name);
45521 }
45522 ret = -1;
45523 __PYX_GOOD:
45524 #if !CYTHON_USE_PYTYPE_LOOKUP
45525 Py_XDECREF(object_reduce);
45526 Py_XDECREF(object_reduce_ex);
45527 Py_XDECREF(object_getstate);
45528 Py_XDECREF(getstate);
45529 #endif
45530 Py_XDECREF(reduce);
45531 Py_XDECREF(reduce_ex);
45532 Py_XDECREF(reduce_cython);
45533 Py_XDECREF(setstate);
45534 Py_XDECREF(setstate_cython);
45535 return ret;
45536 }
45537 #endif
45538
45539 /* ImportDottedModule */
45540 #if PY_MAJOR_VERSION >= 3
45541 static PyObject *__Pyx__ImportDottedModule_Error(PyObject *name, PyObject *parts_tuple, Py_ssize_t count) {
45542 PyObject *partial_name = NULL, *slice = NULL, *sep = NULL;
45543 if (unlikely(PyErr_Occurred())) {
45544 PyErr_Clear();
45545 }
45546 if (likely(PyTuple_GET_SIZE(parts_tuple) == count)) {
45547 partial_name = name;
45548 } else {
45549 slice = PySequence_GetSlice(parts_tuple, 0, count);
45550 if (unlikely(!slice))
45551 goto bad;
45552 sep = PyUnicode_FromStringAndSize(".", 1);
45553 if (unlikely(!sep))
45554 goto bad;
45555 partial_name = PyUnicode_Join(sep, slice);
45556 }
45557 PyErr_Format(
45558 #if PY_MAJOR_VERSION < 3
45559 PyExc_ImportError,
45560 "No module named '%s'", PyString_AS_STRING(partial_name));
45561 #else
45562 #if PY_VERSION_HEX >= 0x030600B1
45563 PyExc_ModuleNotFoundError,
45564 #else
45565 PyExc_ImportError,
45566 #endif
45567 "No module named '%U'", partial_name);
45568 #endif
45569 bad:
45570 Py_XDECREF(sep);
45571 Py_XDECREF(slice);
45572 Py_XDECREF(partial_name);
45573 return NULL;
45574 }
45575 #endif
45576 #if PY_MAJOR_VERSION >= 3
45577 static PyObject *__Pyx__ImportDottedModule_Lookup(PyObject *name) {
45578 PyObject *imported_module;
45579 #if PY_VERSION_HEX < 0x030700A1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030400)
45580 PyObject *modules = PyImport_GetModuleDict();
45581 if (unlikely(!modules))
45582 return NULL;
45583 imported_module = __Pyx_PyDict_GetItemStr(modules, name);
45584 Py_XINCREF(imported_module);
45585 #else
45586 imported_module = PyImport_GetModule(name);
45587 #endif
45588 return imported_module;
45589 }
45590 #endif
45591 #if PY_MAJOR_VERSION >= 3
45592 static PyObject *__Pyx_ImportDottedModule_WalkParts(PyObject *module, PyObject *name, PyObject *parts_tuple) {
45593 Py_ssize_t i, nparts;
45594 nparts = PyTuple_GET_SIZE(parts_tuple);
45595 for (i=1; i < nparts && module; i++) {
45596 PyObject *part, *submodule;
45597 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
45598 part = PyTuple_GET_ITEM(parts_tuple, i);
45599 #else
45600 part = PySequence_ITEM(parts_tuple, i);
45601 #endif
45602 submodule = __Pyx_PyObject_GetAttrStrNoError(module, part);
45603 #if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS)
45604 Py_DECREF(part);
45605 #endif
45606 Py_DECREF(module);
45607 module = submodule;
45608 }
45609 if (unlikely(!module)) {
45610 return __Pyx__ImportDottedModule_Error(name, parts_tuple, i);
45611 }
45612 return module;
45613 }
45614 #endif
45615 static PyObject *__Pyx__ImportDottedModule(PyObject *name, PyObject *parts_tuple) {
45616 #if PY_MAJOR_VERSION < 3
45617 PyObject *module, *from_list, *star = __pyx_n_s__33;
45618 CYTHON_UNUSED_VAR(parts_tuple);
45619 from_list = PyList_New(1);
45620 if (unlikely(!from_list))
45621 return NULL;
45622 Py_INCREF(star);
45623 PyList_SET_ITEM(from_list, 0, star);
45624 module = __Pyx_Import(name, from_list, 0);
45625 Py_DECREF(from_list);
45626 return module;
45627 #else
45628 PyObject *imported_module;
45629 PyObject *module = __Pyx_Import(name, NULL, 0);
45630 if (!parts_tuple || unlikely(!module))
45631 return module;
45632 imported_module = __Pyx__ImportDottedModule_Lookup(name);
45633 if (likely(imported_module)) {
45634 Py_DECREF(module);
45635 return imported_module;
45636 }
45637 PyErr_Clear();
45638 return __Pyx_ImportDottedModule_WalkParts(module, name, parts_tuple);
45639 #endif
45640 }
45641 static PyObject *__Pyx_ImportDottedModule(PyObject *name, PyObject *parts_tuple) {
45642 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030400B1
45643 PyObject *module = __Pyx__ImportDottedModule_Lookup(name);
45644 if (likely(module)) {
45645 PyObject *spec = __Pyx_PyObject_GetAttrStrNoError(module, __pyx_n_s_spec);
45646 if (likely(spec)) {
45647 PyObject *unsafe = __Pyx_PyObject_GetAttrStrNoError(spec, __pyx_n_s_initializing);
45648 if (likely(!unsafe || !__Pyx_PyObject_IsTrue(unsafe))) {
45649 Py_DECREF(spec);
45650 spec = NULL;
45651 }
45652 Py_XDECREF(unsafe);
45653 }
45654 if (likely(!spec)) {
45655 PyErr_Clear();
45656 return module;
45657 }
45658 Py_DECREF(spec);
45659 Py_DECREF(module);
45660 } else if (PyErr_Occurred()) {
45661 PyErr_Clear();
45662 }
45663 #endif
45664 return __Pyx__ImportDottedModule(name, parts_tuple);
45665 }
45666
45667 /* FetchSharedCythonModule */
45668 static PyObject *__Pyx_FetchSharedCythonABIModule(void) {
45669 return __Pyx_PyImport_AddModuleRef((char*) __PYX_ABI_MODULE_NAME);
45670 }
45671
45672 /* FetchCommonType */
45673 static int __Pyx_VerifyCachedType(PyObject *cached_type,
45674 const char *name,
45675 Py_ssize_t basicsize,
45676 Py_ssize_t expected_basicsize) {
45677 if (!PyType_Check(cached_type)) {
45678 PyErr_Format(PyExc_TypeError,
45679 "Shared Cython type %.200s is not a type object", name);
45680 return -1;
45681 }
45682 if (basicsize != expected_basicsize) {
45683 PyErr_Format(PyExc_TypeError,
45684 "Shared Cython type %.200s has the wrong size, try recompiling",
45685 name);
45686 return -1;
45687 }
45688 return 0;
45689 }
45690 #if !CYTHON_USE_TYPE_SPECS
45691 static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) {
45692 PyObject* abi_module;
45693 const char* object_name;
45694 PyTypeObject *cached_type = NULL;
45695 abi_module = __Pyx_FetchSharedCythonABIModule();
45696 if (!abi_module) return NULL;
45697 object_name = strrchr(type->tp_name, '.');
45698 object_name = object_name ? object_name+1 : type->tp_name;
45699 cached_type = (PyTypeObject*) PyObject_GetAttrString(abi_module, object_name);
45700 if (cached_type) {
45701 if (__Pyx_VerifyCachedType(
45702 (PyObject *)cached_type,
45703 object_name,
45704 cached_type->tp_basicsize,
45705 type->tp_basicsize) < 0) {
45706 goto bad;
45707 }
45708 goto done;
45709 }
45710 if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad;
45711 PyErr_Clear();
45712 if (PyType_Ready(type) < 0) goto bad;
45713 if (PyObject_SetAttrString(abi_module, object_name, (PyObject *)type) < 0)
45714 goto bad;
45715 Py_INCREF(type);
45716 cached_type = type;
45717 done:
45718 Py_DECREF(abi_module);
45719 return cached_type;
45720 bad:
45721 Py_XDECREF(cached_type);
45722 cached_type = NULL;
45723 goto done;
45724 }
45725 #else
45726 static PyTypeObject *__Pyx_FetchCommonTypeFromSpec(PyObject *module, PyType_Spec *spec, PyObject *bases) {
45727 PyObject *abi_module, *cached_type = NULL;
45728 const char* object_name = strrchr(spec->name, '.');
45729 object_name = object_name ? object_name+1 : spec->name;
45730 abi_module = __Pyx_FetchSharedCythonABIModule();
45731 if (!abi_module) return NULL;
45732 cached_type = PyObject_GetAttrString(abi_module, object_name);
45733 if (cached_type) {
45734 Py_ssize_t basicsize;
45735 #if CYTHON_COMPILING_IN_LIMITED_API
45736 PyObject *py_basicsize;
45737 py_basicsize = PyObject_GetAttrString(cached_type, "__basicsize__");
45738 if (unlikely(!py_basicsize)) goto bad;
45739 basicsize = PyLong_AsSsize_t(py_basicsize);
45740 Py_DECREF(py_basicsize);
45741 py_basicsize = 0;
45742 if (unlikely(basicsize == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
45743 #else
45744 basicsize = likely(PyType_Check(cached_type)) ? ((PyTypeObject*) cached_type)->tp_basicsize : -1;
45745 #endif
45746 if (__Pyx_VerifyCachedType(
45747 cached_type,
45748 object_name,
45749 basicsize,
45750 spec->basicsize) < 0) {
45751 goto bad;
45752 }
45753 goto done;
45754 }
45755 if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad;
45756 PyErr_Clear();
45757 CYTHON_UNUSED_VAR(module);
45758 cached_type = __Pyx_PyType_FromModuleAndSpec(abi_module, spec, bases);
45759 if (unlikely(!cached_type)) goto bad;
45760 if (unlikely(__Pyx_fix_up_extension_type_from_spec(spec, (PyTypeObject *) cached_type) < 0)) goto bad;
45761 if (PyObject_SetAttrString(abi_module, object_name, cached_type) < 0) goto bad;
45762 done:
45763 Py_DECREF(abi_module);
45764 assert(cached_type == NULL || PyType_Check(cached_type));
45765 return (PyTypeObject *) cached_type;
45766 bad:
45767 Py_XDECREF(cached_type);
45768 cached_type = NULL;
45769 goto done;
45770 }
45771 #endif
45772
45773 /* PyVectorcallFastCallDict */
45774 #if CYTHON_METH_FASTCALL
45775 static PyObject *__Pyx_PyVectorcall_FastCallDict_kw(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw)
45776 {
45777 PyObject *res = NULL;
45778 PyObject *kwnames;
45779 PyObject **newargs;
45780 PyObject **kwvalues;
45781 Py_ssize_t i, pos;
45782 size_t j;
45783 PyObject *key, *value;
45784 unsigned long keys_are_strings;
45785 Py_ssize_t nkw = PyDict_GET_SIZE(kw);
45786 newargs = (PyObject **)PyMem_Malloc((nargs + (size_t)nkw) * sizeof(args[0]));
45787 if (unlikely(newargs == NULL)) {
45788 PyErr_NoMemory();
45789 return NULL;
45790 }
45791 for (j = 0; j < nargs; j++) newargs[j] = args[j];
45792 kwnames = PyTuple_New(nkw);
45793 if (unlikely(kwnames == NULL)) {
45794 PyMem_Free(newargs);
45795 return NULL;
45796 }
45797 kwvalues = newargs + nargs;
45798 pos = i = 0;
45799 keys_are_strings = Py_TPFLAGS_UNICODE_SUBCLASS;
45800 while (PyDict_Next(kw, &pos, &key, &value)) {
45801 keys_are_strings &= Py_TYPE(key)->tp_flags;
45802 Py_INCREF(key);
45803 Py_INCREF(value);
45804 PyTuple_SET_ITEM(kwnames, i, key);
45805 kwvalues[i] = value;
45806 i++;
45807 }
45808 if (unlikely(!keys_are_strings)) {
45809 PyErr_SetString(PyExc_TypeError, "keywords must be strings");
45810 goto cleanup;
45811 }
45812 res = vc(func, newargs, nargs, kwnames);
45813 cleanup:
45814 Py_DECREF(kwnames);
45815 for (i = 0; i < nkw; i++)
45816 Py_DECREF(kwvalues[i]);
45817 PyMem_Free(newargs);
45818 return res;
45819 }
45820 static CYTHON_INLINE PyObject *__Pyx_PyVectorcall_FastCallDict(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw)
45821 {
45822 if (likely(kw == NULL) || PyDict_GET_SIZE(kw) == 0) {
45823 return vc(func, args, nargs, NULL);
45824 }
45825 return __Pyx_PyVectorcall_FastCallDict_kw(func, vc, args, nargs, kw);
45826 }
45827 #endif
45828
45829 /* CythonFunctionShared */
45830 #if CYTHON_COMPILING_IN_LIMITED_API
45831 static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc) {
45832 if (__Pyx_CyFunction_Check(func)) {
45833 return PyCFunction_GetFunction(((__pyx_CyFunctionObject*)func)->func) == (PyCFunction) cfunc;
45834 } else if (PyCFunction_Check(func)) {
45835 return PyCFunction_GetFunction(func) == (PyCFunction) cfunc;
45836 }
45837 return 0;
45838 }
45839 #else
45840 static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc) {
45841 return __Pyx_CyOrPyCFunction_Check(func) && __Pyx_CyOrPyCFunction_GET_FUNCTION(func) == (PyCFunction) cfunc;
45842 }
45843 #endif
45844 static CYTHON_INLINE void __Pyx__CyFunction_SetClassObj(__pyx_CyFunctionObject* f, PyObject* classobj) {
45845 #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
45846 __Pyx_Py_XDECREF_SET(
45847 __Pyx_CyFunction_GetClassObj(f),
45848 ((classobj) ? __Pyx_NewRef(classobj) : NULL));
45849 #else
45850 __Pyx_Py_XDECREF_SET(
45851 ((PyCMethodObject *) (f))->mm_class,
45852 (PyTypeObject*)((classobj) ? __Pyx_NewRef(classobj) : NULL));
45853 #endif
45854 }
45855 static PyObject *
45856 __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, void *closure)
45857 {
45858 CYTHON_UNUSED_VAR(closure);
45859 if (unlikely(op->func_doc == NULL)) {
45860 #if CYTHON_COMPILING_IN_LIMITED_API
45861 op->func_doc = PyObject_GetAttrString(op->func, "__doc__");
45862 if (unlikely(!op->func_doc)) return NULL;
45863 #else
45864 if (((PyCFunctionObject*)op)->m_ml->ml_doc) {
45865 #if PY_MAJOR_VERSION >= 3
45866 op->func_doc = PyUnicode_FromString(((PyCFunctionObject*)op)->m_ml->ml_doc);
45867 #else
45868 op->func_doc = PyString_FromString(((PyCFunctionObject*)op)->m_ml->ml_doc);
45869 #endif
45870 if (unlikely(op->func_doc == NULL))
45871 return NULL;
45872 } else {
45873 Py_INCREF(Py_None);
45874 return Py_None;
45875 }
45876 #endif
45877 }
45878 Py_INCREF(op->func_doc);
45879 return op->func_doc;
45880 }
45881 static int
45882 __Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value, void *context)
45883 {
45884 CYTHON_UNUSED_VAR(context);
45885 if (value == NULL) {
45886 value = Py_None;
45887 }
45888 Py_INCREF(value);
45889 __Pyx_Py_XDECREF_SET(op->func_doc, value);
45890 return 0;
45891 }
45892 static PyObject *
45893 __Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op, void *context)
45894 {
45895 CYTHON_UNUSED_VAR(context);
45896 if (unlikely(op->func_name == NULL)) {
45897 #if CYTHON_COMPILING_IN_LIMITED_API
45898 op->func_name = PyObject_GetAttrString(op->func, "__name__");
45899 #elif PY_MAJOR_VERSION >= 3
45900 op->func_name = PyUnicode_InternFromString(((PyCFunctionObject*)op)->m_ml->ml_name);
45901 #else
45902 op->func_name = PyString_InternFromString(((PyCFunctionObject*)op)->m_ml->ml_name);
45903 #endif
45904 if (unlikely(op->func_name == NULL))
45905 return NULL;
45906 }
45907 Py_INCREF(op->func_name);
45908 return op->func_name;
45909 }
45910 static int
45911 __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value, void *context)
45912 {
45913 CYTHON_UNUSED_VAR(context);
45914 #if PY_MAJOR_VERSION >= 3
45915 if (unlikely(value == NULL || !PyUnicode_Check(value)))
45916 #else
45917 if (unlikely(value == NULL || !PyString_Check(value)))
45918 #endif
45919 {
45920 PyErr_SetString(PyExc_TypeError,
45921 "__name__ must be set to a string object");
45922 return -1;
45923 }
45924 Py_INCREF(value);
45925 __Pyx_Py_XDECREF_SET(op->func_name, value);
45926 return 0;
45927 }
45928 static PyObject *
45929 __Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op, void *context)
45930 {
45931 CYTHON_UNUSED_VAR(context);
45932 Py_INCREF(op->func_qualname);
45933 return op->func_qualname;
45934 }
45935 static int
45936 __Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value, void *context)
45937 {
45938 CYTHON_UNUSED_VAR(context);
45939 #if PY_MAJOR_VERSION >= 3
45940 if (unlikely(value == NULL || !PyUnicode_Check(value)))
45941 #else
45942 if (unlikely(value == NULL || !PyString_Check(value)))
45943 #endif
45944 {
45945 PyErr_SetString(PyExc_TypeError,
45946 "__qualname__ must be set to a string object");
45947 return -1;
45948 }
45949 Py_INCREF(value);
45950 __Pyx_Py_XDECREF_SET(op->func_qualname, value);
45951 return 0;
45952 }
45953 static PyObject *
45954 __Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op, void *context)
45955 {
45956 CYTHON_UNUSED_VAR(context);
45957 if (unlikely(op->func_dict == NULL)) {
45958 op->func_dict = PyDict_New();
45959 if (unlikely(op->func_dict == NULL))
45960 return NULL;
45961 }
45962 Py_INCREF(op->func_dict);
45963 return op->func_dict;
45964 }
45965 static int
45966 __Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value, void *context)
45967 {
45968 CYTHON_UNUSED_VAR(context);
45969 if (unlikely(value == NULL)) {
45970 PyErr_SetString(PyExc_TypeError,
45971 "function's dictionary may not be deleted");
45972 return -1;
45973 }
45974 if (unlikely(!PyDict_Check(value))) {
45975 PyErr_SetString(PyExc_TypeError,
45976 "setting function's dictionary to a non-dict");
45977 return -1;
45978 }
45979 Py_INCREF(value);
45980 __Pyx_Py_XDECREF_SET(op->func_dict, value);
45981 return 0;
45982 }
45983 static PyObject *
45984 __Pyx_CyFunction_get_globals(__pyx_CyFunctionObject *op, void *context)
45985 {
45986 CYTHON_UNUSED_VAR(context);
45987 Py_INCREF(op->func_globals);
45988 return op->func_globals;
45989 }
45990 static PyObject *
45991 __Pyx_CyFunction_get_closure(__pyx_CyFunctionObject *op, void *context)
45992 {
45993 CYTHON_UNUSED_VAR(op);
45994 CYTHON_UNUSED_VAR(context);
45995 Py_INCREF(Py_None);
45996 return Py_None;
45997 }
45998 static PyObject *
45999 __Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op, void *context)
46000 {
46001 PyObject* result = (op->func_code) ? op->func_code : Py_None;
46002 CYTHON_UNUSED_VAR(context);
46003 Py_INCREF(result);
46004 return result;
46005 }
46006 static int
46007 __Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) {
46008 int result = 0;
46009 PyObject *res = op->defaults_getter((PyObject *) op);
46010 if (unlikely(!res))
46011 return -1;
46012 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
46013 op->defaults_tuple = PyTuple_GET_ITEM(res, 0);
46014 Py_INCREF(op->defaults_tuple);
46015 op->defaults_kwdict = PyTuple_GET_ITEM(res, 1);
46016 Py_INCREF(op->defaults_kwdict);
46017 #else
46018 op->defaults_tuple = __Pyx_PySequence_ITEM(res, 0);
46019 if (unlikely(!op->defaults_tuple)) result = -1;
46020 else {
46021 op->defaults_kwdict = __Pyx_PySequence_ITEM(res, 1);
46022 if (unlikely(!op->defaults_kwdict)) result = -1;
46023 }
46024 #endif
46025 Py_DECREF(res);
46026 return result;
46027 }
46028 static int
46029 __Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value, void *context) {
46030 CYTHON_UNUSED_VAR(context);
46031 if (!value) {
46032 value = Py_None;
46033 } else if (unlikely(value != Py_None && !PyTuple_Check(value))) {
46034 PyErr_SetString(PyExc_TypeError,
46035 "__defaults__ must be set to a tuple object");
46036 return -1;
46037 }
46038 PyErr_WarnEx(PyExc_RuntimeWarning, "changes to cyfunction.__defaults__ will not "
46039 "currently affect the values used in function calls", 1);
46040 Py_INCREF(value);
46041 __Pyx_Py_XDECREF_SET(op->defaults_tuple, value);
46042 return 0;
46043 }
46044 static PyObject *
46045 __Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op, void *context) {
46046 PyObject* result = op->defaults_tuple;
46047 CYTHON_UNUSED_VAR(context);
46048 if (unlikely(!result)) {
46049 if (op->defaults_getter) {
46050 if (unlikely(__Pyx_CyFunction_init_defaults(op) < 0)) return NULL;
46051 result = op->defaults_tuple;
46052 } else {
46053 result = Py_None;
46054 }
46055 }
46056 Py_INCREF(result);
46057 return result;
46058 }
46059 static int
46060 __Pyx_CyFunction_set_kwdefaults(__pyx_CyFunctionObject *op, PyObject* value, void *context) {
46061 CYTHON_UNUSED_VAR(context);
46062 if (!value) {
46063 value = Py_None;
46064 } else if (unlikely(value != Py_None && !PyDict_Check(value))) {
46065 PyErr_SetString(PyExc_TypeError,
46066 "__kwdefaults__ must be set to a dict object");
46067 return -1;
46068 }
46069 PyErr_WarnEx(PyExc_RuntimeWarning, "changes to cyfunction.__kwdefaults__ will not "
46070 "currently affect the values used in function calls", 1);
46071 Py_INCREF(value);
46072 __Pyx_Py_XDECREF_SET(op->defaults_kwdict, value);
46073 return 0;
46074 }
46075 static PyObject *
46076 __Pyx_CyFunction_get_kwdefaults(__pyx_CyFunctionObject *op, void *context) {
46077 PyObject* result = op->defaults_kwdict;
46078 CYTHON_UNUSED_VAR(context);
46079 if (unlikely(!result)) {
46080 if (op->defaults_getter) {
46081 if (unlikely(__Pyx_CyFunction_init_defaults(op) < 0)) return NULL;
46082 result = op->defaults_kwdict;
46083 } else {
46084 result = Py_None;
46085 }
46086 }
46087 Py_INCREF(result);
46088 return result;
46089 }
46090 static int
46091 __Pyx_CyFunction_set_annotations(__pyx_CyFunctionObject *op, PyObject* value, void *context) {
46092 CYTHON_UNUSED_VAR(context);
46093 if (!value || value == Py_None) {
46094 value = NULL;
46095 } else if (unlikely(!PyDict_Check(value))) {
46096 PyErr_SetString(PyExc_TypeError,
46097 "__annotations__ must be set to a dict object");
46098 return -1;
46099 }
46100 Py_XINCREF(value);
46101 __Pyx_Py_XDECREF_SET(op->func_annotations, value);
46102 return 0;
46103 }
46104 static PyObject *
46105 __Pyx_CyFunction_get_annotations(__pyx_CyFunctionObject *op, void *context) {
46106 PyObject* result = op->func_annotations;
46107 CYTHON_UNUSED_VAR(context);
46108 if (unlikely(!result)) {
46109 result = PyDict_New();
46110 if (unlikely(!result)) return NULL;
46111 op->func_annotations = result;
46112 }
46113 Py_INCREF(result);
46114 return result;
46115 }
46116 static PyObject *
46117 __Pyx_CyFunction_get_is_coroutine(__pyx_CyFunctionObject *op, void *context) {
46118 int is_coroutine;
46119 CYTHON_UNUSED_VAR(context);
46120 if (op->func_is_coroutine) {
46121 return __Pyx_NewRef(op->func_is_coroutine);
46122 }
46123 is_coroutine = op->flags & __Pyx_CYFUNCTION_COROUTINE;
46124 #if PY_VERSION_HEX >= 0x03050000
46125 if (is_coroutine) {
46126 PyObject *module, *fromlist, *marker = __pyx_n_s_is_coroutine;
46127 fromlist = PyList_New(1);
46128 if (unlikely(!fromlist)) return NULL;
46129 Py_INCREF(marker);
46130 #if CYTHON_ASSUME_SAFE_MACROS
46131 PyList_SET_ITEM(fromlist, 0, marker);
46132 #else
46133 if (unlikely(PyList_SetItem(fromlist, 0, marker) < 0)) {
46134 Py_DECREF(marker);
46135 Py_DECREF(fromlist);
46136 return NULL;
46137 }
46138 #endif
46139 module = PyImport_ImportModuleLevelObject(__pyx_n_s_asyncio_coroutines, NULL, NULL, fromlist, 0);
46140 Py_DECREF(fromlist);
46141 if (unlikely(!module)) goto ignore;
46142 op->func_is_coroutine = __Pyx_PyObject_GetAttrStr(module, marker);
46143 Py_DECREF(module);
46144 if (likely(op->func_is_coroutine)) {
46145 return __Pyx_NewRef(op->func_is_coroutine);
46146 }
46147 ignore:
46148 PyErr_Clear();
46149 }
46150 #endif
46151 op->func_is_coroutine = __Pyx_PyBool_FromLong(is_coroutine);
46152 return __Pyx_NewRef(op->func_is_coroutine);
46153 }
46154 #if CYTHON_COMPILING_IN_LIMITED_API
46155 static PyObject *
46156 __Pyx_CyFunction_get_module(__pyx_CyFunctionObject *op, void *context) {
46157 CYTHON_UNUSED_VAR(context);
46158 return PyObject_GetAttrString(op->func, "__module__");
46159 }
46160 static int
46161 __Pyx_CyFunction_set_module(__pyx_CyFunctionObject *op, PyObject* value, void *context) {
46162 CYTHON_UNUSED_VAR(context);
46163 return PyObject_SetAttrString(op->func, "__module__", value);
46164 }
46165 #endif
46166 static PyGetSetDef __pyx_CyFunction_getsets[] = {
46167 {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
46168 {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
46169 {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
46170 {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
46171 {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0},
46172 {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
46173 {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
46174 {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
46175 {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
46176 {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
46177 {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
46178 {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
46179 {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
46180 {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0},
46181 {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0},
46182 {(char *) "__kwdefaults__", (getter)__Pyx_CyFunction_get_kwdefaults, (setter)__Pyx_CyFunction_set_kwdefaults, 0, 0},
46183 {(char *) "__annotations__", (getter)__Pyx_CyFunction_get_annotations, (setter)__Pyx_CyFunction_set_annotations, 0, 0},
46184 {(char *) "_is_coroutine", (getter)__Pyx_CyFunction_get_is_coroutine, 0, 0, 0},
46185 #if CYTHON_COMPILING_IN_LIMITED_API
46186 {"__module__", (getter)__Pyx_CyFunction_get_module, (setter)__Pyx_CyFunction_set_module, 0, 0},
46187 #endif
46188 {0, 0, 0, 0, 0}
46189 };
46190 static PyMemberDef __pyx_CyFunction_members[] = {
46191 #if !CYTHON_COMPILING_IN_LIMITED_API
46192 {(char *) "__module__", T_OBJECT, offsetof(PyCFunctionObject, m_module), 0, 0},
46193 #endif
46194 #if CYTHON_USE_TYPE_SPECS
46195 {(char *) "__dictoffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_dict), READONLY, 0},
46196 #if CYTHON_METH_FASTCALL
46197 #if CYTHON_BACKPORT_VECTORCALL
46198 {(char *) "__vectorcalloffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_vectorcall), READONLY, 0},
46199 #else
46200 #if !CYTHON_COMPILING_IN_LIMITED_API
46201 {(char *) "__vectorcalloffset__", T_PYSSIZET, offsetof(PyCFunctionObject, vectorcall), READONLY, 0},
46202 #endif
46203 #endif
46204 #endif
46205 #if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API
46206 {(char *) "__weaklistoffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_weakreflist), READONLY, 0},
46207 #else
46208 {(char *) "__weaklistoffset__", T_PYSSIZET, offsetof(PyCFunctionObject, m_weakreflist), READONLY, 0},
46209 #endif
46210 #endif
46211 {0, 0, 0, 0, 0}
46212 };
46213 static PyObject *
46214 __Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, PyObject *args)
46215 {
46216 CYTHON_UNUSED_VAR(args);
46217 #if PY_MAJOR_VERSION >= 3
46218 Py_INCREF(m->func_qualname);
46219 return m->func_qualname;
46220 #else
46221 return PyString_FromString(((PyCFunctionObject*)m)->m_ml->ml_name);
46222 #endif
46223 }
46224 static PyMethodDef __pyx_CyFunction_methods[] = {
46225 {"__reduce__", (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
46226 {0, 0, 0, 0}
46227 };
46228 #if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API
46229 #define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func_weakreflist)
46230 #else
46231 #define __Pyx_CyFunction_weakreflist(cyfunc) (((PyCFunctionObject*)cyfunc)->m_weakreflist)
46232 #endif
46233 static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject *op, PyMethodDef *ml, int flags, PyObject* qualname,
46234 PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) {
46235 #if !CYTHON_COMPILING_IN_LIMITED_API
46236 PyCFunctionObject *cf = (PyCFunctionObject*) op;
46237 #endif
46238 if (unlikely(op == NULL))
46239 return NULL;
46240 #if CYTHON_COMPILING_IN_LIMITED_API
46241 op->func = PyCFunction_NewEx(ml, (PyObject*)op, module);
46242 if (unlikely(!op->func)) return NULL;
46243 #endif
46244 op->flags = flags;
46245 __Pyx_CyFunction_weakreflist(op) = NULL;
46246 #if !CYTHON_COMPILING_IN_LIMITED_API
46247 cf->m_ml = ml;
46248 cf->m_self = (PyObject *) op;
46249 #endif
46250 Py_XINCREF(closure);
46251 op->func_closure = closure;
46252 #if !CYTHON_COMPILING_IN_LIMITED_API
46253 Py_XINCREF(module);
46254 cf->m_module = module;
46255 #endif
46256 op->func_dict = NULL;
46257 op->func_name = NULL;
46258 Py_INCREF(qualname);
46259 op->func_qualname = qualname;
46260 op->func_doc = NULL;
46261 #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
46262 op->func_classobj = NULL;
46263 #else
46264 ((PyCMethodObject*)op)->mm_class = NULL;
46265 #endif
46266 op->func_globals = globals;
46267 Py_INCREF(op->func_globals);
46268 Py_XINCREF(code);
46269 op->func_code = code;
46270 op->defaults_pyobjects = 0;
46271 op->defaults_size = 0;
46272 op->defaults = NULL;
46273 op->defaults_tuple = NULL;
46274 op->defaults_kwdict = NULL;
46275 op->defaults_getter = NULL;
46276 op->func_annotations = NULL;
46277 op->func_is_coroutine = NULL;
46278 #if CYTHON_METH_FASTCALL
46279 switch (ml->ml_flags & (METH_VARARGS | METH_FASTCALL | METH_NOARGS | METH_O | METH_KEYWORDS | METH_METHOD)) {
46280 case METH_NOARGS:
46281 __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_NOARGS;
46282 break;
46283 case METH_O:
46284 __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_O;
46285 break;
46286 case METH_METHOD | METH_FASTCALL | METH_KEYWORDS:
46287 __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD;
46288 break;
46289 case METH_FASTCALL | METH_KEYWORDS:
46290 __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS;
46291 break;
46292 case METH_VARARGS | METH_KEYWORDS:
46293 __Pyx_CyFunction_func_vectorcall(op) = NULL;
46294 break;
46295 default:
46296 PyErr_SetString(PyExc_SystemError, "Bad call flags for CyFunction");
46297 Py_DECREF(op);
46298 return NULL;
46299 }
46300 #endif
46301 return (PyObject *) op;
46302 }
46303 static int
46304 __Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
46305 {
46306 Py_CLEAR(m->func_closure);
46307 #if CYTHON_COMPILING_IN_LIMITED_API
46308 Py_CLEAR(m->func);
46309 #else
46310 Py_CLEAR(((PyCFunctionObject*)m)->m_module);
46311 #endif
46312 Py_CLEAR(m->func_dict);
46313 Py_CLEAR(m->func_name);
46314 Py_CLEAR(m->func_qualname);
46315 Py_CLEAR(m->func_doc);
46316 Py_CLEAR(m->func_globals);
46317 Py_CLEAR(m->func_code);
46318 #if !CYTHON_COMPILING_IN_LIMITED_API
46319 #if PY_VERSION_HEX < 0x030900B1
46320 Py_CLEAR(__Pyx_CyFunction_GetClassObj(m));
46321 #else
46322 {
46323 PyObject *cls = (PyObject*) ((PyCMethodObject *) (m))->mm_class;
46324 ((PyCMethodObject *) (m))->mm_class = NULL;
46325 Py_XDECREF(cls);
46326 }
46327 #endif
46328 #endif
46329 Py_CLEAR(m->defaults_tuple);
46330 Py_CLEAR(m->defaults_kwdict);
46331 Py_CLEAR(m->func_annotations);
46332 Py_CLEAR(m->func_is_coroutine);
46333 if (m->defaults) {
46334 PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
46335 int i;
46336 for (i = 0; i < m->defaults_pyobjects; i++)
46337 Py_XDECREF(pydefaults[i]);
46338 PyObject_Free(m->defaults);
46339 m->defaults = NULL;
46340 }
46341 return 0;
46342 }
46343 static void __Pyx__CyFunction_dealloc(__pyx_CyFunctionObject *m)
46344 {
46345 if (__Pyx_CyFunction_weakreflist(m) != NULL)
46346 PyObject_ClearWeakRefs((PyObject *) m);
46347 __Pyx_CyFunction_clear(m);
46348 __Pyx_PyHeapTypeObject_GC_Del(m);
46349 }
46350 static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
46351 {
46352 PyObject_GC_UnTrack(m);
46353 __Pyx__CyFunction_dealloc(m);
46354 }
46355 static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
46356 {
46357 Py_VISIT(m->func_closure);
46358 #if CYTHON_COMPILING_IN_LIMITED_API
46359 Py_VISIT(m->func);
46360 #else
46361 Py_VISIT(((PyCFunctionObject*)m)->m_module);
46362 #endif
46363 Py_VISIT(m->func_dict);
46364 Py_VISIT(m->func_name);
46365 Py_VISIT(m->func_qualname);
46366 Py_VISIT(m->func_doc);
46367 Py_VISIT(m->func_globals);
46368 Py_VISIT(m->func_code);
46369 #if !CYTHON_COMPILING_IN_LIMITED_API
46370 Py_VISIT(__Pyx_CyFunction_GetClassObj(m));
46371 #endif
46372 Py_VISIT(m->defaults_tuple);
46373 Py_VISIT(m->defaults_kwdict);
46374 Py_VISIT(m->func_is_coroutine);
46375 if (m->defaults) {
46376 PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
46377 int i;
46378 for (i = 0; i < m->defaults_pyobjects; i++)
46379 Py_VISIT(pydefaults[i]);
46380 }
46381 return 0;
46382 }
46383 static PyObject*
46384 __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
46385 {
46386 #if PY_MAJOR_VERSION >= 3
46387 return PyUnicode_FromFormat("<cyfunction %U at %p>",
46388 op->func_qualname, (void *)op);
46389 #else
46390 return PyString_FromFormat("<cyfunction %s at %p>",
46391 PyString_AsString(op->func_qualname), (void *)op);
46392 #endif
46393 }
46394 static PyObject * __Pyx_CyFunction_CallMethod(PyObject *func, PyObject *self, PyObject *arg, PyObject *kw) {
46395 #if CYTHON_COMPILING_IN_LIMITED_API
46396 PyObject *f = ((__pyx_CyFunctionObject*)func)->func;
46397 PyObject *py_name = NULL;
46398 PyCFunction meth;
46399 int flags;
46400 meth = PyCFunction_GetFunction(f);
46401 if (unlikely(!meth)) return NULL;
46402 flags = PyCFunction_GetFlags(f);
46403 if (unlikely(flags < 0)) return NULL;
46404 #else
46405 PyCFunctionObject* f = (PyCFunctionObject*)func;
46406 PyCFunction meth = f->m_ml->ml_meth;
46407 int flags = f->m_ml->ml_flags;
46408 #endif
46409 Py_ssize_t size;
46410 switch (flags & (METH_VARARGS | METH_KEYWORDS | METH_NOARGS | METH_O)) {
46411 case METH_VARARGS:
46412 if (likely(kw == NULL || PyDict_Size(kw) == 0))
46413 return (*meth)(self, arg);
46414 break;
46415 case METH_VARARGS | METH_KEYWORDS:
46416 return (*(PyCFunctionWithKeywords)(void*)meth)(self, arg, kw);
46417 case METH_NOARGS:
46418 if (likely(kw == NULL || PyDict_Size(kw) == 0)) {
46419 #if CYTHON_ASSUME_SAFE_MACROS
46420 size = PyTuple_GET_SIZE(arg);
46421 #else
46422 size = PyTuple_Size(arg);
46423 if (unlikely(size < 0)) return NULL;
46424 #endif
46425 if (likely(size == 0))
46426 return (*meth)(self, NULL);
46427 #if CYTHON_COMPILING_IN_LIMITED_API
46428 py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL);
46429 if (!py_name) return NULL;
46430 PyErr_Format(PyExc_TypeError,
46431 "%.200S() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)",
46432 py_name, size);
46433 Py_DECREF(py_name);
46434 #else
46435 PyErr_Format(PyExc_TypeError,
46436 "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)",
46437 f->m_ml->ml_name, size);
46438 #endif
46439 return NULL;
46440 }
46441 break;
46442 case METH_O:
46443 if (likely(kw == NULL || PyDict_Size(kw) == 0)) {
46444 #if CYTHON_ASSUME_SAFE_MACROS
46445 size = PyTuple_GET_SIZE(arg);
46446 #else
46447 size = PyTuple_Size(arg);
46448 if (unlikely(size < 0)) return NULL;
46449 #endif
46450 if (likely(size == 1)) {
46451 PyObject *result, *arg0;
46452 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
46453 arg0 = PyTuple_GET_ITEM(arg, 0);
46454 #else
46455 arg0 = __Pyx_PySequence_ITEM(arg, 0); if (unlikely(!arg0)) return NULL;
46456 #endif
46457 result = (*meth)(self, arg0);
46458 #if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS)
46459 Py_DECREF(arg0);
46460 #endif
46461 return result;
46462 }
46463 #if CYTHON_COMPILING_IN_LIMITED_API
46464 py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL);
46465 if (!py_name) return NULL;
46466 PyErr_Format(PyExc_TypeError,
46467 "%.200S() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)",
46468 py_name, size);
46469 Py_DECREF(py_name);
46470 #else
46471 PyErr_Format(PyExc_TypeError,
46472 "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)",
46473 f->m_ml->ml_name, size);
46474 #endif
46475 return NULL;
46476 }
46477 break;
46478 default:
46479 PyErr_SetString(PyExc_SystemError, "Bad call flags for CyFunction");
46480 return NULL;
46481 }
46482 #if CYTHON_COMPILING_IN_LIMITED_API
46483 py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL);
46484 if (!py_name) return NULL;
46485 PyErr_Format(PyExc_TypeError, "%.200S() takes no keyword arguments",
46486 py_name);
46487 Py_DECREF(py_name);
46488 #else
46489 PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
46490 f->m_ml->ml_name);
46491 #endif
46492 return NULL;
46493 }
46494 static CYTHON_INLINE PyObject *__Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
46495 PyObject *self, *result;
46496 #if CYTHON_COMPILING_IN_LIMITED_API
46497 self = PyCFunction_GetSelf(((__pyx_CyFunctionObject*)func)->func);
46498 if (unlikely(!self) && PyErr_Occurred()) return NULL;
46499 #else
46500 self = ((PyCFunctionObject*)func)->m_self;
46501 #endif
46502 result = __Pyx_CyFunction_CallMethod(func, self, arg, kw);
46503 return result;
46504 }
46505 static PyObject *__Pyx_CyFunction_CallAsMethod(PyObject *func, PyObject *args, PyObject *kw) {
46506 PyObject *result;
46507 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *) func;
46508 #if CYTHON_METH_FASTCALL
46509 __pyx_vectorcallfunc vc = __Pyx_CyFunction_func_vectorcall(cyfunc);
46510 if (vc) {
46511 #if CYTHON_ASSUME_SAFE_MACROS
46512 return __Pyx_PyVectorcall_FastCallDict(func, vc, &PyTuple_GET_ITEM(args, 0), (size_t)PyTuple_GET_SIZE(args), kw);
46513 #else
46514 (void) &__Pyx_PyVectorcall_FastCallDict;
46515 return PyVectorcall_Call(func, args, kw);
46516 #endif
46517 }
46518 #endif
46519 if ((cyfunc->flags & __Pyx_CYFUNCTION_CCLASS) && !(cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD)) {
46520 Py_ssize_t argc;
46521 PyObject *new_args;
46522 PyObject *self;
46523 #if CYTHON_ASSUME_SAFE_MACROS
46524 argc = PyTuple_GET_SIZE(args);
46525 #else
46526 argc = PyTuple_Size(args);
46527 if (unlikely(!argc) < 0) return NULL;
46528 #endif
46529 new_args = PyTuple_GetSlice(args, 1, argc);
46530 if (unlikely(!new_args))
46531 return NULL;
46532 self = PyTuple_GetItem(args, 0);
46533 if (unlikely(!self)) {
46534 Py_DECREF(new_args);
46535 #if PY_MAJOR_VERSION > 2
46536 PyErr_Format(PyExc_TypeError,
46537 "unbound method %.200S() needs an argument",
46538 cyfunc->func_qualname);
46539 #else
46540 PyErr_SetString(PyExc_TypeError,
46541 "unbound method needs an argument");
46542 #endif
46543 return NULL;
46544 }
46545 result = __Pyx_CyFunction_CallMethod(func, self, new_args, kw);
46546 Py_DECREF(new_args);
46547 } else {
46548 result = __Pyx_CyFunction_Call(func, args, kw);
46549 }
46550 return result;
46551 }
46552 #if CYTHON_METH_FASTCALL
46553 static CYTHON_INLINE int __Pyx_CyFunction_Vectorcall_CheckArgs(__pyx_CyFunctionObject *cyfunc, Py_ssize_t nargs, PyObject *kwnames)
46554 {
46555 int ret = 0;
46556 if ((cyfunc->flags & __Pyx_CYFUNCTION_CCLASS) && !(cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD)) {
46557 if (unlikely(nargs < 1)) {
46558 PyErr_Format(PyExc_TypeError, "%.200s() needs an argument",
46559 ((PyCFunctionObject*)cyfunc)->m_ml->ml_name);
46560 return -1;
46561 }
46562 ret = 1;
46563 }
46564 if (unlikely(kwnames) && unlikely(PyTuple_GET_SIZE(kwnames))) {
46565 PyErr_Format(PyExc_TypeError,
46566 "%.200s() takes no keyword arguments", ((PyCFunctionObject*)cyfunc)->m_ml->ml_name);
46567 return -1;
46568 }
46569 return ret;
46570 }
46571 static PyObject * __Pyx_CyFunction_Vectorcall_NOARGS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
46572 {
46573 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func;
46574 PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml;
46575 #if CYTHON_BACKPORT_VECTORCALL
46576 Py_ssize_t nargs = (Py_ssize_t)nargsf;
46577 #else
46578 Py_ssize_t nargs = PyVectorcall_NARGS(nargsf);
46579 #endif
46580 PyObject *self;
46581 switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, kwnames)) {
46582 case 1:
46583 self = args[0];
46584 args += 1;
46585 nargs -= 1;
46586 break;
46587 case 0:
46588 self = ((PyCFunctionObject*)cyfunc)->m_self;
46589 break;
46590 default:
46591 return NULL;
46592 }
46593 if (unlikely(nargs != 0)) {
46594 PyErr_Format(PyExc_TypeError,
46595 "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)",
46596 def->ml_name, nargs);
46597 return NULL;
46598 }
46599 return def->ml_meth(self, NULL);
46600 }
46601 static PyObject * __Pyx_CyFunction_Vectorcall_O(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
46602 {
46603 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func;
46604 PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml;
46605 #if CYTHON_BACKPORT_VECTORCALL
46606 Py_ssize_t nargs = (Py_ssize_t)nargsf;
46607 #else
46608 Py_ssize_t nargs = PyVectorcall_NARGS(nargsf);
46609 #endif
46610 PyObject *self;
46611 switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, kwnames)) {
46612 case 1:
46613 self = args[0];
46614 args += 1;
46615 nargs -= 1;
46616 break;
46617 case 0:
46618 self = ((PyCFunctionObject*)cyfunc)->m_self;
46619 break;
46620 default:
46621 return NULL;
46622 }
46623 if (unlikely(nargs != 1)) {
46624 PyErr_Format(PyExc_TypeError,
46625 "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)",
46626 def->ml_name, nargs);
46627 return NULL;
46628 }
46629 return def->ml_meth(self, args[0]);
46630 }
46631 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
46632 {
46633 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func;
46634 PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml;
46635 #if CYTHON_BACKPORT_VECTORCALL
46636 Py_ssize_t nargs = (Py_ssize_t)nargsf;
46637 #else
46638 Py_ssize_t nargs = PyVectorcall_NARGS(nargsf);
46639 #endif
46640 PyObject *self;
46641 switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, NULL)) {
46642 case 1:
46643 self = args[0];
46644 args += 1;
46645 nargs -= 1;
46646 break;
46647 case 0:
46648 self = ((PyCFunctionObject*)cyfunc)->m_self;
46649 break;
46650 default:
46651 return NULL;
46652 }
46653 return ((__Pyx_PyCFunctionFastWithKeywords)(void(*)(void))def->ml_meth)(self, args, nargs, kwnames);
46654 }
46655 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
46656 {
46657 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func;
46658 PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml;
46659 PyTypeObject *cls = (PyTypeObject *) __Pyx_CyFunction_GetClassObj(cyfunc);
46660 #if CYTHON_BACKPORT_VECTORCALL
46661 Py_ssize_t nargs = (Py_ssize_t)nargsf;
46662 #else
46663 Py_ssize_t nargs = PyVectorcall_NARGS(nargsf);
46664 #endif
46665 PyObject *self;
46666 switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, NULL)) {
46667 case 1:
46668 self = args[0];
46669 args += 1;
46670 nargs -= 1;
46671 break;
46672 case 0:
46673 self = ((PyCFunctionObject*)cyfunc)->m_self;
46674 break;
46675 default:
46676 return NULL;
46677 }
46678 return ((__Pyx_PyCMethod)(void(*)(void))def->ml_meth)(self, cls, args, (size_t)nargs, kwnames);
46679 }
46680 #endif
46681 #if CYTHON_USE_TYPE_SPECS
46682 static PyType_Slot __pyx_CyFunctionType_slots[] = {
46683 {Py_tp_dealloc, (void *)__Pyx_CyFunction_dealloc},
46684 {Py_tp_repr, (void *)__Pyx_CyFunction_repr},
46685 {Py_tp_call, (void *)__Pyx_CyFunction_CallAsMethod},
46686 {Py_tp_traverse, (void *)__Pyx_CyFunction_traverse},
46687 {Py_tp_clear, (void *)__Pyx_CyFunction_clear},
46688 {Py_tp_methods, (void *)__pyx_CyFunction_methods},
46689 {Py_tp_members, (void *)__pyx_CyFunction_members},
46690 {Py_tp_getset, (void *)__pyx_CyFunction_getsets},
46691 {Py_tp_descr_get, (void *)__Pyx_PyMethod_New},
46692 {0, 0},
46693 };
46694 static PyType_Spec __pyx_CyFunctionType_spec = {
46695 __PYX_TYPE_MODULE_PREFIX "cython_function_or_method",
46696 sizeof(__pyx_CyFunctionObject),
46697 0,
46698 #ifdef Py_TPFLAGS_METHOD_DESCRIPTOR
46699 Py_TPFLAGS_METHOD_DESCRIPTOR |
46700 #endif
46701 #if (defined(_Py_TPFLAGS_HAVE_VECTORCALL) && CYTHON_METH_FASTCALL)
46702 _Py_TPFLAGS_HAVE_VECTORCALL |
46703 #endif
46704 Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_BASETYPE,
46705 __pyx_CyFunctionType_slots
46706 };
46707 #else
46708 static PyTypeObject __pyx_CyFunctionType_type = {
46709 PyVarObject_HEAD_INIT(0, 0)
46710 __PYX_TYPE_MODULE_PREFIX "cython_function_or_method",
46711 sizeof(__pyx_CyFunctionObject),
46712 0,
46713 (destructor) __Pyx_CyFunction_dealloc,
46714 #if !CYTHON_METH_FASTCALL
46715 0,
46716 #elif CYTHON_BACKPORT_VECTORCALL
46717 (printfunc)offsetof(__pyx_CyFunctionObject, func_vectorcall),
46718 #else
46719 offsetof(PyCFunctionObject, vectorcall),
46720 #endif
46721 0,
46722 0,
46723 #if PY_MAJOR_VERSION < 3
46724 0,
46725 #else
46726 0,
46727 #endif
46728 (reprfunc) __Pyx_CyFunction_repr,
46729 0,
46730 0,
46731 0,
46732 0,
46733 __Pyx_CyFunction_CallAsMethod,
46734 0,
46735 0,
46736 0,
46737 0,
46738 #ifdef Py_TPFLAGS_METHOD_DESCRIPTOR
46739 Py_TPFLAGS_METHOD_DESCRIPTOR |
46740 #endif
46741 #if defined(_Py_TPFLAGS_HAVE_VECTORCALL) && CYTHON_METH_FASTCALL
46742 _Py_TPFLAGS_HAVE_VECTORCALL |
46743 #endif
46744 Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_BASETYPE,
46745 0,
46746 (traverseproc) __Pyx_CyFunction_traverse,
46747 (inquiry) __Pyx_CyFunction_clear,
46748 0,
46749 #if PY_VERSION_HEX < 0x030500A0
46750 offsetof(__pyx_CyFunctionObject, func_weakreflist),
46751 #else
46752 offsetof(PyCFunctionObject, m_weakreflist),
46753 #endif
46754 0,
46755 0,
46756 __pyx_CyFunction_methods,
46757 __pyx_CyFunction_members,
46758 __pyx_CyFunction_getsets,
46759 0,
46760 0,
46761 __Pyx_PyMethod_New,
46762 0,
46763 offsetof(__pyx_CyFunctionObject, func_dict),
46764 0,
46765 0,
46766 0,
46767 0,
46768 0,
46769 0,
46770 0,
46771 0,
46772 0,
46773 0,
46774 0,
46775 0,
46776 #if PY_VERSION_HEX >= 0x030400a1
46777 0,
46778 #endif
46779 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
46780 0,
46781 #endif
46782 #if __PYX_NEED_TP_PRINT_SLOT
46783 0,
46784 #endif
46785 #if PY_VERSION_HEX >= 0x030C0000
46786 0,
46787 #endif
46788 #if PY_VERSION_HEX >= 0x030d00A4
46789 0,
46790 #endif
46791 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
46792 0,
46793 #endif
46794 };
46795 #endif
46796 static int __pyx_CyFunction_init(PyObject *module) {
46797 #if CYTHON_USE_TYPE_SPECS
46798 __pyx_CyFunctionType = __Pyx_FetchCommonTypeFromSpec(module, &__pyx_CyFunctionType_spec, NULL);
46799 #else
46800 CYTHON_UNUSED_VAR(module);
46801 __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type);
46802 #endif
46803 if (unlikely(__pyx_CyFunctionType == NULL)) {
46804 return -1;
46805 }
46806 return 0;
46807 }
46808 static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
46809 __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
46810 m->defaults = PyObject_Malloc(size);
46811 if (unlikely(!m->defaults))
46812 return PyErr_NoMemory();
46813 memset(m->defaults, 0, size);
46814 m->defaults_pyobjects = pyobjects;
46815 m->defaults_size = size;
46816 return m->defaults;
46817 }
46818 static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
46819 __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
46820 m->defaults_tuple = tuple;
46821 Py_INCREF(tuple);
46822 }
46823 static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *func, PyObject *dict) {
46824 __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
46825 m->defaults_kwdict = dict;
46826 Py_INCREF(dict);
46827 }
46828 static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, PyObject *dict) {
46829 __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
46830 m->func_annotations = dict;
46831 Py_INCREF(dict);
46832 }
46833
46834 /* CythonFunction */
46835 static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml, int flags, PyObject* qualname,
46836 PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) {
46837 PyObject *op = __Pyx_CyFunction_Init(
46838 PyObject_GC_New(__pyx_CyFunctionObject, __pyx_CyFunctionType),
46839 ml, flags, qualname, closure, module, globals, code
46840 );
46841 if (likely(op)) {
46842 PyObject_GC_Track(op);
46843 }
46844 return op;
46845 }
46846
46847 /* Py3UpdateBases */
46848 static PyObject*
46849 __Pyx_PEP560_update_bases(PyObject *bases)
46850 {
46851 Py_ssize_t i, j, size_bases;
46852 PyObject *base, *meth, *new_base, *result, *new_bases = NULL;
46853 size_bases = PyTuple_GET_SIZE(bases);
46854 for (i = 0; i < size_bases; i++) {
46855 base = PyTuple_GET_ITEM(bases, i);
46856 if (PyType_Check(base)) {
46857 if (new_bases) {
46858 if (PyList_Append(new_bases, base) < 0) {
46859 goto error;
46860 }
46861 }
46862 continue;
46863 }
46864 meth = __Pyx_PyObject_GetAttrStrNoError(base, __pyx_n_s_mro_entries);
46865 if (!meth && PyErr_Occurred()) {
46866 goto error;
46867 }
46868 if (!meth) {
46869 if (new_bases) {
46870 if (PyList_Append(new_bases, base) < 0) {
46871 goto error;
46872 }
46873 }
46874 continue;
46875 }
46876 new_base = __Pyx_PyObject_CallOneArg(meth, bases);
46877 Py_DECREF(meth);
46878 if (!new_base) {
46879 goto error;
46880 }
46881 if (!PyTuple_Check(new_base)) {
46882 PyErr_SetString(PyExc_TypeError,
46883 "__mro_entries__ must return a tuple");
46884 Py_DECREF(new_base);
46885 goto error;
46886 }
46887 if (!new_bases) {
46888 if (!(new_bases = PyList_New(i))) {
46889 goto error;
46890 }
46891 for (j = 0; j < i; j++) {
46892 base = PyTuple_GET_ITEM(bases, j);
46893 PyList_SET_ITEM(new_bases, j, base);
46894 Py_INCREF(base);
46895 }
46896 }
46897 j = PyList_GET_SIZE(new_bases);
46898 if (PyList_SetSlice(new_bases, j, j, new_base) < 0) {
46899 goto error;
46900 }
46901 Py_DECREF(new_base);
46902 }
46903 if (!new_bases) {
46904 Py_INCREF(bases);
46905 return bases;
46906 }
46907 result = PyList_AsTuple(new_bases);
46908 Py_DECREF(new_bases);
46909 return result;
46910 error:
46911 Py_XDECREF(new_bases);
46912 return NULL;
46913 }
46914
46915 /* CalculateMetaclass */
46916 static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) {
46917 Py_ssize_t i, nbases;
46918 #if CYTHON_ASSUME_SAFE_MACROS
46919 nbases = PyTuple_GET_SIZE(bases);
46920 #else
46921 nbases = PyTuple_Size(bases);
46922 if (nbases < 0) return NULL;
46923 #endif
46924 for (i=0; i < nbases; i++) {
46925 PyTypeObject *tmptype;
46926 #if CYTHON_ASSUME_SAFE_MACROS
46927 PyObject *tmp = PyTuple_GET_ITEM(bases, i);
46928 #else
46929 PyObject *tmp = PyTuple_GetItem(bases, i);
46930 if (!tmp) return NULL;
46931 #endif
46932 tmptype = Py_TYPE(tmp);
46933 #if PY_MAJOR_VERSION < 3
46934 if (tmptype == &PyClass_Type)
46935 continue;
46936 #endif
46937 if (!metaclass) {
46938 metaclass = tmptype;
46939 continue;
46940 }
46941 if (PyType_IsSubtype(metaclass, tmptype))
46942 continue;
46943 if (PyType_IsSubtype(tmptype, metaclass)) {
46944 metaclass = tmptype;
46945 continue;
46946 }
46947 PyErr_SetString(PyExc_TypeError,
46948 "metaclass conflict: "
46949 "the metaclass of a derived class "
46950 "must be a (non-strict) subclass "
46951 "of the metaclasses of all its bases");
46952 return NULL;
46953 }
46954 if (!metaclass) {
46955 #if PY_MAJOR_VERSION < 3
46956 metaclass = &PyClass_Type;
46957 #else
46958 metaclass = &PyType_Type;
46959 #endif
46960 }
46961 Py_INCREF((PyObject*) metaclass);
46962 return (PyObject*) metaclass;
46963 }
46964
46965 /* PyObjectLookupSpecial */
46966 #if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS
46967 static CYTHON_INLINE PyObject* __Pyx__PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name, int with_error) {
46968 PyObject *res;
46969 PyTypeObject *tp = Py_TYPE(obj);
46970 #if PY_MAJOR_VERSION < 3
46971 if (unlikely(PyInstance_Check(obj)))
46972 return with_error ? __Pyx_PyObject_GetAttrStr(obj, attr_name) : __Pyx_PyObject_GetAttrStrNoError(obj, attr_name);
46973 #endif
46974 res = _PyType_Lookup(tp, attr_name);
46975 if (likely(res)) {
46976 descrgetfunc f = Py_TYPE(res)->tp_descr_get;
46977 if (!f) {
46978 Py_INCREF(res);
46979 } else {
46980 res = f(res, obj, (PyObject *)tp);
46981 }
46982 } else if (with_error) {
46983 PyErr_SetObject(PyExc_AttributeError, attr_name);
46984 }
46985 return res;
46986 }
46987 #endif
46988
46989 /* Py3ClassCreate */
46990 static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name,
46991 PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) {
46992 PyObject *ns;
46993 if (metaclass) {
46994 PyObject *prep = __Pyx_PyObject_GetAttrStrNoError(metaclass, __pyx_n_s_prepare);
46995 if (prep) {
46996 PyObject *pargs[3] = {NULL, name, bases};
46997 ns = __Pyx_PyObject_FastCallDict(prep, pargs+1, 2 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET, mkw);
46998 Py_DECREF(prep);
46999 } else {
47000 if (unlikely(PyErr_Occurred()))
47001 return NULL;
47002 ns = PyDict_New();
47003 }
47004 } else {
47005 ns = PyDict_New();
47006 }
47007 if (unlikely(!ns))
47008 return NULL;
47009 if (unlikely(PyObject_SetItem(ns, __pyx_n_s_module, modname) < 0)) goto bad;
47010 #if PY_VERSION_HEX >= 0x03030000
47011 if (unlikely(PyObject_SetItem(ns, __pyx_n_s_qualname, qualname) < 0)) goto bad;
47012 #else
47013 CYTHON_MAYBE_UNUSED_VAR(qualname);
47014 #endif
47015 if (unlikely(doc && PyObject_SetItem(ns, __pyx_n_s_doc, doc) < 0)) goto bad;
47016 return ns;
47017 bad:
47018 Py_DECREF(ns);
47019 return NULL;
47020 }
47021 #if PY_VERSION_HEX < 0x030600A4 && CYTHON_PEP487_INIT_SUBCLASS
47022 static int __Pyx_SetNamesPEP487(PyObject *type_obj) {
47023 PyTypeObject *type = (PyTypeObject*) type_obj;
47024 PyObject *names_to_set, *key, *value, *set_name, *tmp;
47025 Py_ssize_t i = 0;
47026 #if CYTHON_USE_TYPE_SLOTS
47027 names_to_set = PyDict_Copy(type->tp_dict);
47028 #else
47029 {
47030 PyObject *d = PyObject_GetAttr(type_obj, __pyx_n_s_dict);
47031 names_to_set = NULL;
47032 if (likely(d)) {
47033 PyObject *names_to_set = PyDict_New();
47034 int ret = likely(names_to_set) ? PyDict_Update(names_to_set, d) : -1;
47035 Py_DECREF(d);
47036 if (unlikely(ret < 0))
47037 Py_CLEAR(names_to_set);
47038 }
47039 }
47040 #endif
47041 if (unlikely(names_to_set == NULL))
47042 goto bad;
47043 while (PyDict_Next(names_to_set, &i, &key, &value)) {
47044 set_name = __Pyx_PyObject_LookupSpecialNoError(value, __pyx_n_s_set_name);
47045 if (unlikely(set_name != NULL)) {
47046 tmp = __Pyx_PyObject_Call2Args(set_name, type_obj, key);
47047 Py_DECREF(set_name);
47048 if (unlikely(tmp == NULL)) {
47049 __Pyx_TypeName value_type_name =
47050 __Pyx_PyType_GetName(Py_TYPE(value));
47051 __Pyx_TypeName type_name = __Pyx_PyType_GetName(type);
47052 PyErr_Format(PyExc_RuntimeError,
47053 #if PY_MAJOR_VERSION >= 3
47054 "Error calling __set_name__ on '" __Pyx_FMT_TYPENAME "' instance %R " "in '" __Pyx_FMT_TYPENAME "'",
47055 value_type_name, key, type_name);
47056 #else
47057 "Error calling __set_name__ on '" __Pyx_FMT_TYPENAME "' instance %.100s in '" __Pyx_FMT_TYPENAME "'",
47058 value_type_name,
47059 PyString_Check(key) ? PyString_AS_STRING(key) : "?",
47060 type_name);
47061 #endif
47062 goto bad;
47063 } else {
47064 Py_DECREF(tmp);
47065 }
47066 }
47067 else if (unlikely(PyErr_Occurred())) {
47068 goto bad;
47069 }
47070 }
47071 Py_DECREF(names_to_set);
47072 return 0;
47073 bad:
47074 Py_XDECREF(names_to_set);
47075 return -1;
47076 }
47077 static PyObject *__Pyx_InitSubclassPEP487(PyObject *type_obj, PyObject *mkw) {
47078 #if CYTHON_USE_TYPE_SLOTS && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
47079 PyTypeObject *type = (PyTypeObject*) type_obj;
47080 PyObject *mro = type->tp_mro;
47081 Py_ssize_t i, nbases;
47082 if (unlikely(!mro)) goto done;
47083 (void) &__Pyx_GetBuiltinName;
47084 Py_INCREF(mro);
47085 nbases = PyTuple_GET_SIZE(mro);
47086 assert(PyTuple_GET_ITEM(mro, 0) == type_obj);
47087 for (i = 1; i < nbases-1; i++) {
47088 PyObject *base, *dict, *meth;
47089 base = PyTuple_GET_ITEM(mro, i);
47090 dict = ((PyTypeObject *)base)->tp_dict;
47091 meth = __Pyx_PyDict_GetItemStrWithError(dict, __pyx_n_s_init_subclass);
47092 if (unlikely(meth)) {
47093 descrgetfunc f = Py_TYPE(meth)->tp_descr_get;
47094 PyObject *res;
47095 Py_INCREF(meth);
47096 if (likely(f)) {
47097 res = f(meth, NULL, type_obj);
47098 Py_DECREF(meth);
47099 if (unlikely(!res)) goto bad;
47100 meth = res;
47101 }
47102 res = __Pyx_PyObject_FastCallDict(meth, NULL, 0, mkw);
47103 Py_DECREF(meth);
47104 if (unlikely(!res)) goto bad;
47105 Py_DECREF(res);
47106 goto done;
47107 } else if (unlikely(PyErr_Occurred())) {
47108 goto bad;
47109 }
47110 }
47111 done:
47112 Py_XDECREF(mro);
47113 return type_obj;
47114 bad:
47115 Py_XDECREF(mro);
47116 Py_DECREF(type_obj);
47117 return NULL;
47118 #else
47119 PyObject *super_type, *super, *func, *res;
47120 #if CYTHON_COMPILING_IN_PYPY && !defined(PySuper_Type)
47121 super_type = __Pyx_GetBuiltinName(__pyx_n_s_super);
47122 #else
47123 super_type = (PyObject*) &PySuper_Type;
47124 (void) &__Pyx_GetBuiltinName;
47125 #endif
47126 super = likely(super_type) ? __Pyx_PyObject_Call2Args(super_type, type_obj, type_obj) : NULL;
47127 #if CYTHON_COMPILING_IN_PYPY && !defined(PySuper_Type)
47128 Py_XDECREF(super_type);
47129 #endif
47130 if (unlikely(!super)) {
47131 Py_CLEAR(type_obj);
47132 goto done;
47133 }
47134 func = __Pyx_PyObject_GetAttrStrNoError(super, __pyx_n_s_init_subclass);
47135 Py_DECREF(super);
47136 if (likely(!func)) {
47137 if (unlikely(PyErr_Occurred()))
47138 Py_CLEAR(type_obj);
47139 goto done;
47140 }
47141 res = __Pyx_PyObject_FastCallDict(func, NULL, 0, mkw);
47142 Py_DECREF(func);
47143 if (unlikely(!res))
47144 Py_CLEAR(type_obj);
47145 Py_XDECREF(res);
47146 done:
47147 return type_obj;
47148 #endif
47149 }
47150 #endif
47151 static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases,
47152 PyObject *dict, PyObject *mkw,
47153 int calculate_metaclass, int allow_py2_metaclass) {
47154 PyObject *result;
47155 PyObject *owned_metaclass = NULL;
47156 PyObject *margs[4] = {NULL, name, bases, dict};
47157 if (allow_py2_metaclass) {
47158 owned_metaclass = PyObject_GetItem(dict, __pyx_n_s_metaclass);
47159 if (owned_metaclass) {
47160 metaclass = owned_metaclass;
47161 } else if (likely(PyErr_ExceptionMatches(PyExc_KeyError))) {
47162 PyErr_Clear();
47163 } else {
47164 return NULL;
47165 }
47166 }
47167 if (calculate_metaclass && (!metaclass || PyType_Check(metaclass))) {
47168 metaclass = __Pyx_CalculateMetaclass((PyTypeObject*) metaclass, bases);
47169 Py_XDECREF(owned_metaclass);
47170 if (unlikely(!metaclass))
47171 return NULL;
47172 owned_metaclass = metaclass;
47173 }
47174 result = __Pyx_PyObject_FastCallDict(metaclass, margs+1, 3 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET,
47175 #if PY_VERSION_HEX < 0x030600A4
47176 (metaclass == (PyObject*)&PyType_Type) ? NULL : mkw
47177 #else
47178 mkw
47179 #endif
47180 );
47181 Py_XDECREF(owned_metaclass);
47182 #if PY_VERSION_HEX < 0x030600A4 && CYTHON_PEP487_INIT_SUBCLASS
47183 if (likely(result) && likely(PyType_Check(result))) {
47184 if (unlikely(__Pyx_SetNamesPEP487(result) < 0)) {
47185 Py_CLEAR(result);
47186 } else {
47187 result = __Pyx_InitSubclassPEP487(result, mkw);
47188 }
47189 }
47190 #else
47191 (void) &__Pyx_GetBuiltinName;
47192 #endif
47193 return result;
47194 }
47195
47196 /* CLineInTraceback */
47197 #ifndef CYTHON_CLINE_IN_TRACEBACK
47198 static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line) {
47199 PyObject *use_cline;
47200 PyObject *ptype, *pvalue, *ptraceback;
47201 #if CYTHON_COMPILING_IN_CPYTHON
47202 PyObject **cython_runtime_dict;
47203 #endif
47204 CYTHON_MAYBE_UNUSED_VAR(tstate);
47205 if (unlikely(!__pyx_cython_runtime)) {
47206 return c_line;
47207 }
47208 __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
47209 #if CYTHON_COMPILING_IN_CPYTHON
47210 cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime);
47211 if (likely(cython_runtime_dict)) {
47212 __PYX_PY_DICT_LOOKUP_IF_MODIFIED(
47213 use_cline, *cython_runtime_dict,
47214 __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback))
47215 } else
47216 #endif
47217 {
47218 PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStrNoError(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback);
47219 if (use_cline_obj) {
47220 use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True;
47221 Py_DECREF(use_cline_obj);
47222 } else {
47223 PyErr_Clear();
47224 use_cline = NULL;
47225 }
47226 }
47227 if (!use_cline) {
47228 c_line = 0;
47229 (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False);
47230 }
47231 else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) {
47232 c_line = 0;
47233 }
47234 __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback);
47235 return c_line;
47236 }
47237 #endif
47238
47239 /* CodeObjectCache */
47240 #if !CYTHON_COMPILING_IN_LIMITED_API
47241 static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
47242 int start = 0, mid = 0, end = count - 1;
47243 if (end >= 0 && code_line > entries[end].code_line) {
47244 return count;
47245 }
47246 while (start < end) {
47247 mid = start + (end - start) / 2;
47248 if (code_line < entries[mid].code_line) {
47249 end = mid;
47250 } else if (code_line > entries[mid].code_line) {
47251 start = mid + 1;
47252 } else {
47253 return mid;
47254 }
47255 }
47256 if (code_line <= entries[mid].code_line) {
47257 return mid;
47258 } else {
47259 return mid + 1;
47260 }
47261 }
47262 static PyCodeObject *__pyx_find_code_object(int code_line) {
47263 PyCodeObject* code_object;
47264 int pos;
47265 if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
47266 return NULL;
47267 }
47268 pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
47269 if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
47270 return NULL;
47271 }
47272 code_object = __pyx_code_cache.entries[pos].code_object;
47273 Py_INCREF(code_object);
47274 return code_object;
47275 }
47276 static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
47277 int pos, i;
47278 __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
47279 if (unlikely(!code_line)) {
47280 return;
47281 }
47282 if (unlikely(!entries)) {
47283 entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
47284 if (likely(entries)) {
47285 __pyx_code_cache.entries = entries;
47286 __pyx_code_cache.max_count = 64;
47287 __pyx_code_cache.count = 1;
47288 entries[0].code_line = code_line;
47289 entries[0].code_object = code_object;
47290 Py_INCREF(code_object);
47291 }
47292 return;
47293 }
47294 pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
47295 if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
47296 PyCodeObject* tmp = entries[pos].code_object;
47297 entries[pos].code_object = code_object;
47298 Py_DECREF(tmp);
47299 return;
47300 }
47301 if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
47302 int new_max = __pyx_code_cache.max_count + 64;
47303 entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
47304 __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry));
47305 if (unlikely(!entries)) {
47306 return;
47307 }
47308 __pyx_code_cache.entries = entries;
47309 __pyx_code_cache.max_count = new_max;
47310 }
47311 for (i=__pyx_code_cache.count; i>pos; i--) {
47312 entries[i] = entries[i-1];
47313 }
47314 entries[pos].code_line = code_line;
47315 entries[pos].code_object = code_object;
47316 __pyx_code_cache.count++;
47317 Py_INCREF(code_object);
47318 }
47319 #endif
47320
47321 /* AddTraceback */
47322 #include "compile.h"
47323 #include "frameobject.h"
47324 #include "traceback.h"
47325 #if PY_VERSION_HEX >= 0x030b00a6 && !CYTHON_COMPILING_IN_LIMITED_API
47326 #ifndef Py_BUILD_CORE
47327 #define Py_BUILD_CORE 1
47328 #endif
47329 #include "internal/pycore_frame.h"
47330 #endif
47331 #if CYTHON_COMPILING_IN_LIMITED_API
47332 static PyObject *__Pyx_PyCode_Replace_For_AddTraceback(PyObject *code, PyObject *scratch_dict,
47333 PyObject *firstlineno, PyObject *name) {
47334 PyObject *replace = NULL;
47335 if (unlikely(PyDict_SetItemString(scratch_dict, "co_firstlineno", firstlineno))) return NULL;
47336 if (unlikely(PyDict_SetItemString(scratch_dict, "co_name", name))) return NULL;
47337 replace = PyObject_GetAttrString(code, "replace");
47338 if (likely(replace)) {
47339 PyObject *result;
47340 result = PyObject_Call(replace, __pyx_empty_tuple, scratch_dict);
47341 Py_DECREF(replace);
47342 return result;
47343 }
47344 PyErr_Clear();
47345 #if __PYX_LIMITED_VERSION_HEX < 0x030780000
47346 {
47347 PyObject *compiled = NULL, *result = NULL;
47348 if (unlikely(PyDict_SetItemString(scratch_dict, "code", code))) return NULL;
47349 if (unlikely(PyDict_SetItemString(scratch_dict, "type", (PyObject*)(&PyType_Type)))) return NULL;
47350 compiled = Py_CompileString(
47351 "out = type(code)(\n"
47352 " code.co_argcount, code.co_kwonlyargcount, code.co_nlocals, code.co_stacksize,\n"
47353 " code.co_flags, code.co_code, code.co_consts, code.co_names,\n"
47354 " code.co_varnames, code.co_filename, co_name, co_firstlineno,\n"
47355 " code.co_lnotab)\n", "<dummy>", Py_file_input);
47356 if (!compiled) return NULL;
47357 result = PyEval_EvalCode(compiled, scratch_dict, scratch_dict);
47358 Py_DECREF(compiled);
47359 if (!result) PyErr_Print();
47360 Py_DECREF(result);
47361 result = PyDict_GetItemString(scratch_dict, "out");
47362 if (result) Py_INCREF(result);
47363 return result;
47364 }
47365 #else
47366 return NULL;
47367 #endif
47368 }
47369 static void __Pyx_AddTraceback(const char *funcname, int c_line,
47370 int py_line, const char *filename) {
47371 PyObject *code_object = NULL, *py_py_line = NULL, *py_funcname = NULL, *dict = NULL;
47372 PyObject *replace = NULL, *getframe = NULL, *frame = NULL;
47373 PyObject *exc_type, *exc_value, *exc_traceback;
47374 int success = 0;
47375 if (c_line) {
47376 (void) __pyx_cfilenm;
47377 (void) __Pyx_CLineForTraceback(__Pyx_PyThreadState_Current, c_line);
47378 }
47379 PyErr_Fetch(&exc_type, &exc_value, &exc_traceback);
47380 code_object = Py_CompileString("_getframe()", filename, Py_eval_input);
47381 if (unlikely(!code_object)) goto bad;
47382 py_py_line = PyLong_FromLong(py_line);
47383 if (unlikely(!py_py_line)) goto bad;
47384 py_funcname = PyUnicode_FromString(funcname);
47385 if (unlikely(!py_funcname)) goto bad;
47386 dict = PyDict_New();
47387 if (unlikely(!dict)) goto bad;
47388 {
47389 PyObject *old_code_object = code_object;
47390 code_object = __Pyx_PyCode_Replace_For_AddTraceback(code_object, dict, py_py_line, py_funcname);
47391 Py_DECREF(old_code_object);
47392 }
47393 if (unlikely(!code_object)) goto bad;
47394 getframe = PySys_GetObject("_getframe");
47395 if (unlikely(!getframe)) goto bad;
47396 if (unlikely(PyDict_SetItemString(dict, "_getframe", getframe))) goto bad;
47397 frame = PyEval_EvalCode(code_object, dict, dict);
47398 if (unlikely(!frame) || frame == Py_None) goto bad;
47399 success = 1;
47400 bad:
47401 PyErr_Restore(exc_type, exc_value, exc_traceback);
47402 Py_XDECREF(code_object);
47403 Py_XDECREF(py_py_line);
47404 Py_XDECREF(py_funcname);
47405 Py_XDECREF(dict);
47406 Py_XDECREF(replace);
47407 if (success) {
47408 PyTraceBack_Here(
47409 (struct _frame*)frame);
47410 }
47411 Py_XDECREF(frame);
47412 }
47413 #else
47414 static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
47415 const char *funcname, int c_line,
47416 int py_line, const char *filename) {
47417 PyCodeObject *py_code = NULL;
47418 PyObject *py_funcname = NULL;
47419 #if PY_MAJOR_VERSION < 3
47420 PyObject *py_srcfile = NULL;
47421 py_srcfile = PyString_FromString(filename);
47422 if (!py_srcfile) goto bad;
47423 #endif
47424 if (c_line) {
47425 #if PY_MAJOR_VERSION < 3
47426 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
47427 if (!py_funcname) goto bad;
47428 #else
47429 py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
47430 if (!py_funcname) goto bad;
47431 funcname = PyUnicode_AsUTF8(py_funcname);
47432 if (!funcname) goto bad;
47433 #endif
47434 }
47435 else {
47436 #if PY_MAJOR_VERSION < 3
47437 py_funcname = PyString_FromString(funcname);
47438 if (!py_funcname) goto bad;
47439 #endif
47440 }
47441 #if PY_MAJOR_VERSION < 3
47442 py_code = __Pyx_PyCode_New(
47443 0,
47444 0,
47445 0,
47446 0,
47447 0,
47448 0,
47449 __pyx_empty_bytes, /*PyObject *code,*/
47450 __pyx_empty_tuple, /*PyObject *consts,*/
47451 __pyx_empty_tuple, /*PyObject *names,*/
47452 __pyx_empty_tuple, /*PyObject *varnames,*/
47453 __pyx_empty_tuple, /*PyObject *freevars,*/
47454 __pyx_empty_tuple, /*PyObject *cellvars,*/
47455 py_srcfile, /*PyObject *filename,*/
47456 py_funcname, /*PyObject *name,*/
47457 py_line,
47458 __pyx_empty_bytes /*PyObject *lnotab*/
47459 );
47460 Py_DECREF(py_srcfile);
47461 #else
47462 py_code = PyCode_NewEmpty(filename, funcname, py_line);
47463 #endif
47464 Py_XDECREF(py_funcname);
47465 return py_code;
47466 bad:
47467 Py_XDECREF(py_funcname);
47468 #if PY_MAJOR_VERSION < 3
47469 Py_XDECREF(py_srcfile);
47470 #endif
47471 return NULL;
47472 }
47473 static void __Pyx_AddTraceback(const char *funcname, int c_line,
47474 int py_line, const char *filename) {
47475 PyCodeObject *py_code = 0;
47476 PyFrameObject *py_frame = 0;
47477 PyThreadState *tstate = __Pyx_PyThreadState_Current;
47478 PyObject *ptype, *pvalue, *ptraceback;
47479 if (c_line) {
47480 c_line = __Pyx_CLineForTraceback(tstate, c_line);
47481 }
47482 py_code = __pyx_find_code_object(c_line ? -c_line : py_line);
47483 if (!py_code) {
47484 __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
47485 py_code = __Pyx_CreateCodeObjectForTraceback(
47486 funcname, c_line, py_line, filename);
47487 if (!py_code) {
47488 /* If the code object creation fails, then we should clear the
47489 fetched exception references and propagate the new exception */
47490 Py_XDECREF(ptype);
47491 Py_XDECREF(pvalue);
47492 Py_XDECREF(ptraceback);
47493 goto bad;
47494 }
47495 __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback);
47496 __pyx_insert_code_object(c_line ? -c_line : py_line, py_code);
47497 }
47498 py_frame = PyFrame_New(
47499 tstate, /*PyThreadState *tstate,*/
47500 py_code, /*PyCodeObject *code,*/
47501 __pyx_d, /*PyObject *globals,*/
47502 0 /*PyObject *locals*/
47503 );
47504 if (!py_frame) goto bad;
47505 __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
47506 PyTraceBack_Here(py_frame);
47507 bad:
47508 Py_XDECREF(py_code);
47509 Py_XDECREF(py_frame);
47510 }
47511 #endif
47512
47513 /* CIntFromPyVerify */
47514 #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\
47515 __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0)
47516 #define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\
47517 __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1)
47518 #define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\
47519 {\
47520 func_type value = func_value;\
47521 if (sizeof(target_type) < sizeof(func_type)) {\
47522 if (unlikely(value != (func_type) (target_type) value)) {\
47523 func_type zero = 0;\
47524 if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\
47525 return (target_type) -1;\
47526 if (is_unsigned && unlikely(value < zero))\
47527 goto raise_neg_overflow;\
47528 else\
47529 goto raise_overflow;\
47530 }\
47531 }\
47532 return (target_type) value;\
47533 }
47534
47535 /* CIntFromPy */
47536 static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
47537 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
47538 #pragma GCC diagnostic push
47539 #pragma GCC diagnostic ignored "-Wconversion"
47540 #endif
47541 const long neg_one = (long) -1, const_zero = (long) 0;
47542 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
47543 #pragma GCC diagnostic pop
47544 #endif
47545 const int is_unsigned = neg_one > const_zero;
47546 #if PY_MAJOR_VERSION < 3
47547 if (likely(PyInt_Check(x))) {
47548 if ((sizeof(long) < sizeof(long))) {
47549 __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x))
47550 } else {
47551 long val = PyInt_AS_LONG(x);
47552 if (is_unsigned && unlikely(val < 0)) {
47553 goto raise_neg_overflow;
47554 }
47555 return (long) val;
47556 }
47557 }
47558 #endif
47559 if (unlikely(!PyLong_Check(x))) {
47560 long val;
47561 PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
47562 if (!tmp) return (long) -1;
47563 val = __Pyx_PyInt_As_long(tmp);
47564 Py_DECREF(tmp);
47565 return val;
47566 }
47567 if (is_unsigned) {
47568 #if CYTHON_USE_PYLONG_INTERNALS
47569 if (unlikely(__Pyx_PyLong_IsNeg(x))) {
47570 goto raise_neg_overflow;
47571 } else if (__Pyx_PyLong_IsCompact(x)) {
47572 __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x))
47573 } else {
47574 const digit* digits = __Pyx_PyLong_Digits(x);
47575 assert(__Pyx_PyLong_DigitCount(x) > 1);
47576 switch (__Pyx_PyLong_DigitCount(x)) {
47577 case 2:
47578 if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) {
47579 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
47580 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
47581 } else if ((8 * sizeof(long) >= 2 * PyLong_SHIFT)) {
47582 return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
47583 }
47584 }
47585 break;
47586 case 3:
47587 if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) {
47588 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
47589 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
47590 } else if ((8 * sizeof(long) >= 3 * PyLong_SHIFT)) {
47591 return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
47592 }
47593 }
47594 break;
47595 case 4:
47596 if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) {
47597 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
47598 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
47599 } else if ((8 * sizeof(long) >= 4 * PyLong_SHIFT)) {
47600 return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
47601 }
47602 }
47603 break;
47604 }
47605 }
47606 #endif
47607 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
47608 if (unlikely(Py_SIZE(x) < 0)) {
47609 goto raise_neg_overflow;
47610 }
47611 #else
47612 {
47613 int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
47614 if (unlikely(result < 0))
47615 return (long) -1;
47616 if (unlikely(result == 1))
47617 goto raise_neg_overflow;
47618 }
47619 #endif
47620 if ((sizeof(long) <= sizeof(unsigned long))) {
47621 __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x))
47622 #ifdef HAVE_LONG_LONG
47623 } else if ((sizeof(long) <= sizeof(unsigned PY_LONG_LONG))) {
47624 __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
47625 #endif
47626 }
47627 } else {
47628 #if CYTHON_USE_PYLONG_INTERNALS
47629 if (__Pyx_PyLong_IsCompact(x)) {
47630 __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x))
47631 } else {
47632 const digit* digits = __Pyx_PyLong_Digits(x);
47633 assert(__Pyx_PyLong_DigitCount(x) > 1);
47634 switch (__Pyx_PyLong_SignedDigitCount(x)) {
47635 case -2:
47636 if ((8 * sizeof(long) - 1 > 1 * PyLong_SHIFT)) {
47637 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
47638 __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
47639 } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) {
47640 return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
47641 }
47642 }
47643 break;
47644 case 2:
47645 if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) {
47646 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
47647 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
47648 } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) {
47649 return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
47650 }
47651 }
47652 break;
47653 case -3:
47654 if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) {
47655 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
47656 __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
47657 } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) {
47658 return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
47659 }
47660 }
47661 break;
47662 case 3:
47663 if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) {
47664 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
47665 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
47666 } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) {
47667 return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
47668 }
47669 }
47670 break;
47671 case -4:
47672 if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) {
47673 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
47674 __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
47675 } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) {
47676 return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
47677 }
47678 }
47679 break;
47680 case 4:
47681 if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) {
47682 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
47683 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
47684 } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) {
47685 return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
47686 }
47687 }
47688 break;
47689 }
47690 }
47691 #endif
47692 if ((sizeof(long) <= sizeof(long))) {
47693 __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x))
47694 #ifdef HAVE_LONG_LONG
47695 } else if ((sizeof(long) <= sizeof(PY_LONG_LONG))) {
47696 __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x))
47697 #endif
47698 }
47699 }
47700 {
47701 long val;
47702 int ret = -1;
47703 #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API
47704 Py_ssize_t bytes_copied = PyLong_AsNativeBytes(
47705 x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0));
47706 if (unlikely(bytes_copied == -1)) {
47707 } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) {
47708 goto raise_overflow;
47709 } else {
47710 ret = 0;
47711 }
47712 #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray)
47713 int one = 1; int is_little = (int)*(unsigned char *)&one;
47714 unsigned char *bytes = (unsigned char *)&val;
47715 ret = _PyLong_AsByteArray((PyLongObject *)x,
47716 bytes, sizeof(val),
47717 is_little, !is_unsigned);
47718 #else
47719 PyObject *v;
47720 PyObject *stepval = NULL, *mask = NULL, *shift = NULL;
47721 int bits, remaining_bits, is_negative = 0;
47722 int chunk_size = (sizeof(long) < 8) ? 30 : 62;
47723 if (likely(PyLong_CheckExact(x))) {
47724 v = __Pyx_NewRef(x);
47725 } else {
47726 v = PyNumber_Long(x);
47727 if (unlikely(!v)) return (long) -1;
47728 assert(PyLong_CheckExact(v));
47729 }
47730 {
47731 int result = PyObject_RichCompareBool(v, Py_False, Py_LT);
47732 if (unlikely(result < 0)) {
47733 Py_DECREF(v);
47734 return (long) -1;
47735 }
47736 is_negative = result == 1;
47737 }
47738 if (is_unsigned && unlikely(is_negative)) {
47739 Py_DECREF(v);
47740 goto raise_neg_overflow;
47741 } else if (is_negative) {
47742 stepval = PyNumber_Invert(v);
47743 Py_DECREF(v);
47744 if (unlikely(!stepval))
47745 return (long) -1;
47746 } else {
47747 stepval = v;
47748 }
47749 v = NULL;
47750 val = (long) 0;
47751 mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done;
47752 shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done;
47753 for (bits = 0; bits < (int) sizeof(long) * 8 - chunk_size; bits += chunk_size) {
47754 PyObject *tmp, *digit;
47755 long idigit;
47756 digit = PyNumber_And(stepval, mask);
47757 if (unlikely(!digit)) goto done;
47758 idigit = PyLong_AsLong(digit);
47759 Py_DECREF(digit);
47760 if (unlikely(idigit < 0)) goto done;
47761 val |= ((long) idigit) << bits;
47762 tmp = PyNumber_Rshift(stepval, shift);
47763 if (unlikely(!tmp)) goto done;
47764 Py_DECREF(stepval); stepval = tmp;
47765 }
47766 Py_DECREF(shift); shift = NULL;
47767 Py_DECREF(mask); mask = NULL;
47768 {
47769 long idigit = PyLong_AsLong(stepval);
47770 if (unlikely(idigit < 0)) goto done;
47771 remaining_bits = ((int) sizeof(long) * 8) - bits - (is_unsigned ? 0 : 1);
47772 if (unlikely(idigit >= (1L << remaining_bits)))
47773 goto raise_overflow;
47774 val |= ((long) idigit) << bits;
47775 }
47776 if (!is_unsigned) {
47777 if (unlikely(val & (((long) 1) << (sizeof(long) * 8 - 1))))
47778 goto raise_overflow;
47779 if (is_negative)
47780 val = ~val;
47781 }
47782 ret = 0;
47783 done:
47784 Py_XDECREF(shift);
47785 Py_XDECREF(mask);
47786 Py_XDECREF(stepval);
47787 #endif
47788 if (unlikely(ret))
47789 return (long) -1;
47790 return val;
47791 }
47792 raise_overflow:
47793 PyErr_SetString(PyExc_OverflowError,
47794 "value too large to convert to long");
47795 return (long) -1;
47796 raise_neg_overflow:
47797 PyErr_SetString(PyExc_OverflowError,
47798 "can't convert negative value to long");
47799 return (long) -1;
47800 }
47801
47802 /* CIntToPy */
47803 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
47804 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
47805 #pragma GCC diagnostic push
47806 #pragma GCC diagnostic ignored "-Wconversion"
47807 #endif
47808 const long neg_one = (long) -1, const_zero = (long) 0;
47809 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
47810 #pragma GCC diagnostic pop
47811 #endif
47812 const int is_unsigned = neg_one > const_zero;
47813 if (is_unsigned) {
47814 if (sizeof(long) < sizeof(long)) {
47815 return PyInt_FromLong((long) value);
47816 } else if (sizeof(long) <= sizeof(unsigned long)) {
47817 return PyLong_FromUnsignedLong((unsigned long) value);
47818 #ifdef HAVE_LONG_LONG
47819 } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
47820 return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
47821 #endif
47822 }
47823 } else {
47824 if (sizeof(long) <= sizeof(long)) {
47825 return PyInt_FromLong((long) value);
47826 #ifdef HAVE_LONG_LONG
47827 } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
47828 return PyLong_FromLongLong((PY_LONG_LONG) value);
47829 #endif
47830 }
47831 }
47832 {
47833 unsigned char *bytes = (unsigned char *)&value;
47834 #if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4
47835 if (is_unsigned) {
47836 return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1);
47837 } else {
47838 return PyLong_FromNativeBytes(bytes, sizeof(value), -1);
47839 }
47840 #elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000
47841 int one = 1; int little = (int)*(unsigned char *)&one;
47842 return _PyLong_FromByteArray(bytes, sizeof(long),
47843 little, !is_unsigned);
47844 #else
47845 int one = 1; int little = (int)*(unsigned char *)&one;
47846 PyObject *from_bytes, *result = NULL;
47847 PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL;
47848 from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes");
47849 if (!from_bytes) return NULL;
47850 py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(long));
47851 if (!py_bytes) goto limited_bad;
47852 order_str = PyUnicode_FromString(little ? "little" : "big");
47853 if (!order_str) goto limited_bad;
47854 arg_tuple = PyTuple_Pack(2, py_bytes, order_str);
47855 if (!arg_tuple) goto limited_bad;
47856 if (!is_unsigned) {
47857 kwds = PyDict_New();
47858 if (!kwds) goto limited_bad;
47859 if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad;
47860 }
47861 result = PyObject_Call(from_bytes, arg_tuple, kwds);
47862 limited_bad:
47863 Py_XDECREF(kwds);
47864 Py_XDECREF(arg_tuple);
47865 Py_XDECREF(order_str);
47866 Py_XDECREF(py_bytes);
47867 Py_XDECREF(from_bytes);
47868 return result;
47869 #endif
47870 }
47871 }
47872
47873 /* CIntToPy */
47874 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value) {
47875 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
47876 #pragma GCC diagnostic push
47877 #pragma GCC diagnostic ignored "-Wconversion"
47878 #endif
47879 const uint32_t neg_one = (uint32_t) -1, const_zero = (uint32_t) 0;
47880 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
47881 #pragma GCC diagnostic pop
47882 #endif
47883 const int is_unsigned = neg_one > const_zero;
47884 if (is_unsigned) {
47885 if (sizeof(uint32_t) < sizeof(long)) {
47886 return PyInt_FromLong((long) value);
47887 } else if (sizeof(uint32_t) <= sizeof(unsigned long)) {
47888 return PyLong_FromUnsignedLong((unsigned long) value);
47889 #ifdef HAVE_LONG_LONG
47890 } else if (sizeof(uint32_t) <= sizeof(unsigned PY_LONG_LONG)) {
47891 return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
47892 #endif
47893 }
47894 } else {
47895 if (sizeof(uint32_t) <= sizeof(long)) {
47896 return PyInt_FromLong((long) value);
47897 #ifdef HAVE_LONG_LONG
47898 } else if (sizeof(uint32_t) <= sizeof(PY_LONG_LONG)) {
47899 return PyLong_FromLongLong((PY_LONG_LONG) value);
47900 #endif
47901 }
47902 }
47903 {
47904 unsigned char *bytes = (unsigned char *)&value;
47905 #if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4
47906 if (is_unsigned) {
47907 return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1);
47908 } else {
47909 return PyLong_FromNativeBytes(bytes, sizeof(value), -1);
47910 }
47911 #elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000
47912 int one = 1; int little = (int)*(unsigned char *)&one;
47913 return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
47914 little, !is_unsigned);
47915 #else
47916 int one = 1; int little = (int)*(unsigned char *)&one;
47917 PyObject *from_bytes, *result = NULL;
47918 PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL;
47919 from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes");
47920 if (!from_bytes) return NULL;
47921 py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(uint32_t));
47922 if (!py_bytes) goto limited_bad;
47923 order_str = PyUnicode_FromString(little ? "little" : "big");
47924 if (!order_str) goto limited_bad;
47925 arg_tuple = PyTuple_Pack(2, py_bytes, order_str);
47926 if (!arg_tuple) goto limited_bad;
47927 if (!is_unsigned) {
47928 kwds = PyDict_New();
47929 if (!kwds) goto limited_bad;
47930 if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad;
47931 }
47932 result = PyObject_Call(from_bytes, arg_tuple, kwds);
47933 limited_bad:
47934 Py_XDECREF(kwds);
47935 Py_XDECREF(arg_tuple);
47936 Py_XDECREF(order_str);
47937 Py_XDECREF(py_bytes);
47938 Py_XDECREF(from_bytes);
47939 return result;
47940 #endif
47941 }
47942 }
47943
47944 /* CIntFromPy */
47945 static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
47946 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
47947 #pragma GCC diagnostic push
47948 #pragma GCC diagnostic ignored "-Wconversion"
47949 #endif
47950 const int neg_one = (int) -1, const_zero = (int) 0;
47951 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
47952 #pragma GCC diagnostic pop
47953 #endif
47954 const int is_unsigned = neg_one > const_zero;
47955 #if PY_MAJOR_VERSION < 3
47956 if (likely(PyInt_Check(x))) {
47957 if ((sizeof(int) < sizeof(long))) {
47958 __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x))
47959 } else {
47960 long val = PyInt_AS_LONG(x);
47961 if (is_unsigned && unlikely(val < 0)) {
47962 goto raise_neg_overflow;
47963 }
47964 return (int) val;
47965 }
47966 }
47967 #endif
47968 if (unlikely(!PyLong_Check(x))) {
47969 int val;
47970 PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
47971 if (!tmp) return (int) -1;
47972 val = __Pyx_PyInt_As_int(tmp);
47973 Py_DECREF(tmp);
47974 return val;
47975 }
47976 if (is_unsigned) {
47977 #if CYTHON_USE_PYLONG_INTERNALS
47978 if (unlikely(__Pyx_PyLong_IsNeg(x))) {
47979 goto raise_neg_overflow;
47980 } else if (__Pyx_PyLong_IsCompact(x)) {
47981 __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x))
47982 } else {
47983 const digit* digits = __Pyx_PyLong_Digits(x);
47984 assert(__Pyx_PyLong_DigitCount(x) > 1);
47985 switch (__Pyx_PyLong_DigitCount(x)) {
47986 case 2:
47987 if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) {
47988 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
47989 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
47990 } else if ((8 * sizeof(int) >= 2 * PyLong_SHIFT)) {
47991 return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
47992 }
47993 }
47994 break;
47995 case 3:
47996 if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) {
47997 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
47998 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
47999 } else if ((8 * sizeof(int) >= 3 * PyLong_SHIFT)) {
48000 return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
48001 }
48002 }
48003 break;
48004 case 4:
48005 if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) {
48006 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
48007 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
48008 } else if ((8 * sizeof(int) >= 4 * PyLong_SHIFT)) {
48009 return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
48010 }
48011 }
48012 break;
48013 }
48014 }
48015 #endif
48016 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
48017 if (unlikely(Py_SIZE(x) < 0)) {
48018 goto raise_neg_overflow;
48019 }
48020 #else
48021 {
48022 int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
48023 if (unlikely(result < 0))
48024 return (int) -1;
48025 if (unlikely(result == 1))
48026 goto raise_neg_overflow;
48027 }
48028 #endif
48029 if ((sizeof(int) <= sizeof(unsigned long))) {
48030 __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x))
48031 #ifdef HAVE_LONG_LONG
48032 } else if ((sizeof(int) <= sizeof(unsigned PY_LONG_LONG))) {
48033 __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
48034 #endif
48035 }
48036 } else {
48037 #if CYTHON_USE_PYLONG_INTERNALS
48038 if (__Pyx_PyLong_IsCompact(x)) {
48039 __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x))
48040 } else {
48041 const digit* digits = __Pyx_PyLong_Digits(x);
48042 assert(__Pyx_PyLong_DigitCount(x) > 1);
48043 switch (__Pyx_PyLong_SignedDigitCount(x)) {
48044 case -2:
48045 if ((8 * sizeof(int) - 1 > 1 * PyLong_SHIFT)) {
48046 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
48047 __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
48048 } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) {
48049 return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
48050 }
48051 }
48052 break;
48053 case 2:
48054 if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) {
48055 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
48056 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
48057 } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) {
48058 return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
48059 }
48060 }
48061 break;
48062 case -3:
48063 if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) {
48064 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
48065 __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
48066 } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) {
48067 return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
48068 }
48069 }
48070 break;
48071 case 3:
48072 if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) {
48073 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
48074 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
48075 } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) {
48076 return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
48077 }
48078 }
48079 break;
48080 case -4:
48081 if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) {
48082 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
48083 __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
48084 } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) {
48085 return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
48086 }
48087 }
48088 break;
48089 case 4:
48090 if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) {
48091 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
48092 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
48093 } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) {
48094 return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
48095 }
48096 }
48097 break;
48098 }
48099 }
48100 #endif
48101 if ((sizeof(int) <= sizeof(long))) {
48102 __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x))
48103 #ifdef HAVE_LONG_LONG
48104 } else if ((sizeof(int) <= sizeof(PY_LONG_LONG))) {
48105 __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x))
48106 #endif
48107 }
48108 }
48109 {
48110 int val;
48111 int ret = -1;
48112 #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API
48113 Py_ssize_t bytes_copied = PyLong_AsNativeBytes(
48114 x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0));
48115 if (unlikely(bytes_copied == -1)) {
48116 } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) {
48117 goto raise_overflow;
48118 } else {
48119 ret = 0;
48120 }
48121 #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray)
48122 int one = 1; int is_little = (int)*(unsigned char *)&one;
48123 unsigned char *bytes = (unsigned char *)&val;
48124 ret = _PyLong_AsByteArray((PyLongObject *)x,
48125 bytes, sizeof(val),
48126 is_little, !is_unsigned);
48127 #else
48128 PyObject *v;
48129 PyObject *stepval = NULL, *mask = NULL, *shift = NULL;
48130 int bits, remaining_bits, is_negative = 0;
48131 int chunk_size = (sizeof(long) < 8) ? 30 : 62;
48132 if (likely(PyLong_CheckExact(x))) {
48133 v = __Pyx_NewRef(x);
48134 } else {
48135 v = PyNumber_Long(x);
48136 if (unlikely(!v)) return (int) -1;
48137 assert(PyLong_CheckExact(v));
48138 }
48139 {
48140 int result = PyObject_RichCompareBool(v, Py_False, Py_LT);
48141 if (unlikely(result < 0)) {
48142 Py_DECREF(v);
48143 return (int) -1;
48144 }
48145 is_negative = result == 1;
48146 }
48147 if (is_unsigned && unlikely(is_negative)) {
48148 Py_DECREF(v);
48149 goto raise_neg_overflow;
48150 } else if (is_negative) {
48151 stepval = PyNumber_Invert(v);
48152 Py_DECREF(v);
48153 if (unlikely(!stepval))
48154 return (int) -1;
48155 } else {
48156 stepval = v;
48157 }
48158 v = NULL;
48159 val = (int) 0;
48160 mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done;
48161 shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done;
48162 for (bits = 0; bits < (int) sizeof(int) * 8 - chunk_size; bits += chunk_size) {
48163 PyObject *tmp, *digit;
48164 long idigit;
48165 digit = PyNumber_And(stepval, mask);
48166 if (unlikely(!digit)) goto done;
48167 idigit = PyLong_AsLong(digit);
48168 Py_DECREF(digit);
48169 if (unlikely(idigit < 0)) goto done;
48170 val |= ((int) idigit) << bits;
48171 tmp = PyNumber_Rshift(stepval, shift);
48172 if (unlikely(!tmp)) goto done;
48173 Py_DECREF(stepval); stepval = tmp;
48174 }
48175 Py_DECREF(shift); shift = NULL;
48176 Py_DECREF(mask); mask = NULL;
48177 {
48178 long idigit = PyLong_AsLong(stepval);
48179 if (unlikely(idigit < 0)) goto done;
48180 remaining_bits = ((int) sizeof(int) * 8) - bits - (is_unsigned ? 0 : 1);
48181 if (unlikely(idigit >= (1L << remaining_bits)))
48182 goto raise_overflow;
48183 val |= ((int) idigit) << bits;
48184 }
48185 if (!is_unsigned) {
48186 if (unlikely(val & (((int) 1) << (sizeof(int) * 8 - 1))))
48187 goto raise_overflow;
48188 if (is_negative)
48189 val = ~val;
48190 }
48191 ret = 0;
48192 done:
48193 Py_XDECREF(shift);
48194 Py_XDECREF(mask);
48195 Py_XDECREF(stepval);
48196 #endif
48197 if (unlikely(ret))
48198 return (int) -1;
48199 return val;
48200 }
48201 raise_overflow:
48202 PyErr_SetString(PyExc_OverflowError,
48203 "value too large to convert to int");
48204 return (int) -1;
48205 raise_neg_overflow:
48206 PyErr_SetString(PyExc_OverflowError,
48207 "can't convert negative value to int");
48208 return (int) -1;
48209 }
48210
48211 /* FormatTypeName */
48212 #if CYTHON_COMPILING_IN_LIMITED_API
48213 static __Pyx_TypeName
48214 __Pyx_PyType_GetName(PyTypeObject* tp)
48215 {
48216 PyObject *name = __Pyx_PyObject_GetAttrStr((PyObject *)tp,
48217 __pyx_n_s_name);
48218 if (unlikely(name == NULL) || unlikely(!PyUnicode_Check(name))) {
48219 PyErr_Clear();
48220 Py_XDECREF(name);
48221 name = __Pyx_NewRef(__pyx_n_s__139);
48222 }
48223 return name;
48224 }
48225 #endif
48226
48227 /* FastTypeChecks */
48228 #if CYTHON_COMPILING_IN_CPYTHON
48229 static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) {
48230 while (a) {
48231 a = __Pyx_PyType_GetSlot(a, tp_base, PyTypeObject*);
48232 if (a == b)
48233 return 1;
48234 }
48235 return b == &PyBaseObject_Type;
48236 }
48237 static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) {
48238 PyObject *mro;
48239 if (a == b) return 1;
48240 mro = a->tp_mro;
48241 if (likely(mro)) {
48242 Py_ssize_t i, n;
48243 n = PyTuple_GET_SIZE(mro);
48244 for (i = 0; i < n; i++) {
48245 if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b)
48246 return 1;
48247 }
48248 return 0;
48249 }
48250 return __Pyx_InBases(a, b);
48251 }
48252 static CYTHON_INLINE int __Pyx_IsAnySubtype2(PyTypeObject *cls, PyTypeObject *a, PyTypeObject *b) {
48253 PyObject *mro;
48254 if (cls == a || cls == b) return 1;
48255 mro = cls->tp_mro;
48256 if (likely(mro)) {
48257 Py_ssize_t i, n;
48258 n = PyTuple_GET_SIZE(mro);
48259 for (i = 0; i < n; i++) {
48260 PyObject *base = PyTuple_GET_ITEM(mro, i);
48261 if (base == (PyObject *)a || base == (PyObject *)b)
48262 return 1;
48263 }
48264 return 0;
48265 }
48266 return __Pyx_InBases(cls, a) || __Pyx_InBases(cls, b);
48267 }
48268 #if PY_MAJOR_VERSION == 2
48269 static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) {
48270 PyObject *exception, *value, *tb;
48271 int res;
48272 __Pyx_PyThreadState_declare
48273 __Pyx_PyThreadState_assign
48274 __Pyx_ErrFetch(&exception, &value, &tb);
48275 res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0;
48276 if (unlikely(res == -1)) {
48277 PyErr_WriteUnraisable(err);
48278 res = 0;
48279 }
48280 if (!res) {
48281 res = PyObject_IsSubclass(err, exc_type2);
48282 if (unlikely(res == -1)) {
48283 PyErr_WriteUnraisable(err);
48284 res = 0;
48285 }
48286 }
48287 __Pyx_ErrRestore(exception, value, tb);
48288 return res;
48289 }
48290 #else
48291 static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) {
48292 if (exc_type1) {
48293 return __Pyx_IsAnySubtype2((PyTypeObject*)err, (PyTypeObject*)exc_type1, (PyTypeObject*)exc_type2);
48294 } else {
48295 return __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2);
48296 }
48297 }
48298 #endif
48299 static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) {
48300 Py_ssize_t i, n;
48301 assert(PyExceptionClass_Check(exc_type));
48302 n = PyTuple_GET_SIZE(tuple);
48303 #if PY_MAJOR_VERSION >= 3
48304 for (i=0; i<n; i++) {
48305 if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1;
48306 }
48307 #endif
48308 for (i=0; i<n; i++) {
48309 PyObject *t = PyTuple_GET_ITEM(tuple, i);
48310 #if PY_MAJOR_VERSION < 3
48311 if (likely(exc_type == t)) return 1;
48312 #endif
48313 if (likely(PyExceptionClass_Check(t))) {
48314 if (__Pyx_inner_PyErr_GivenExceptionMatches2(exc_type, NULL, t)) return 1;
48315 } else {
48316 }
48317 }
48318 return 0;
48319 }
48320 static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject* exc_type) {
48321 if (likely(err == exc_type)) return 1;
48322 if (likely(PyExceptionClass_Check(err))) {
48323 if (likely(PyExceptionClass_Check(exc_type))) {
48324 return __Pyx_inner_PyErr_GivenExceptionMatches2(err, NULL, exc_type);
48325 } else if (likely(PyTuple_Check(exc_type))) {
48326 return __Pyx_PyErr_GivenExceptionMatchesTuple(err, exc_type);
48327 } else {
48328 }
48329 }
48330 return PyErr_GivenExceptionMatches(err, exc_type);
48331 }
48332 static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *exc_type1, PyObject *exc_type2) {
48333 assert(PyExceptionClass_Check(exc_type1));
48334 assert(PyExceptionClass_Check(exc_type2));
48335 if (likely(err == exc_type1 || err == exc_type2)) return 1;
48336 if (likely(PyExceptionClass_Check(err))) {
48337 return __Pyx_inner_PyErr_GivenExceptionMatches2(err, exc_type1, exc_type2);
48338 }
48339 return (PyErr_GivenExceptionMatches(err, exc_type1) || PyErr_GivenExceptionMatches(err, exc_type2));
48340 }
48341 #endif
48342
48343 /* SwapException */
48344 #if CYTHON_FAST_THREAD_STATE
48345 static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
48346 PyObject *tmp_type, *tmp_value, *tmp_tb;
48347 #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4
48348 _PyErr_StackItem *exc_info = tstate->exc_info;
48349 tmp_value = exc_info->exc_value;
48350 exc_info->exc_value = *value;
48351 if (tmp_value == NULL || tmp_value == Py_None) {
48352 Py_XDECREF(tmp_value);
48353 tmp_value = NULL;
48354 tmp_type = NULL;
48355 tmp_tb = NULL;
48356 } else {
48357 tmp_type = (PyObject*) Py_TYPE(tmp_value);
48358 Py_INCREF(tmp_type);
48359 #if CYTHON_COMPILING_IN_CPYTHON
48360 tmp_tb = ((PyBaseExceptionObject*) tmp_value)->traceback;
48361 Py_XINCREF(tmp_tb);
48362 #else
48363 tmp_tb = PyException_GetTraceback(tmp_value);
48364 #endif
48365 }
48366 #elif CYTHON_USE_EXC_INFO_STACK
48367 _PyErr_StackItem *exc_info = tstate->exc_info;
48368 tmp_type = exc_info->exc_type;
48369 tmp_value = exc_info->exc_value;
48370 tmp_tb = exc_info->exc_traceback;
48371 exc_info->exc_type = *type;
48372 exc_info->exc_value = *value;
48373 exc_info->exc_traceback = *tb;
48374 #else
48375 tmp_type = tstate->exc_type;
48376 tmp_value = tstate->exc_value;
48377 tmp_tb = tstate->exc_traceback;
48378 tstate->exc_type = *type;
48379 tstate->exc_value = *value;
48380 tstate->exc_traceback = *tb;
48381 #endif
48382 *type = tmp_type;
48383 *value = tmp_value;
48384 *tb = tmp_tb;
48385 }
48386 #else
48387 static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
48388 PyObject *tmp_type, *tmp_value, *tmp_tb;
48389 PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
48390 PyErr_SetExcInfo(*type, *value, *tb);
48391 *type = tmp_type;
48392 *value = tmp_value;
48393 *tb = tmp_tb;
48394 }
48395 #endif
48396
48397 /* CoroutineBase */
48398 #include <frameobject.h>
48399 #if PY_VERSION_HEX >= 0x030b00a6
48400 #ifndef Py_BUILD_CORE
48401 #define Py_BUILD_CORE 1
48402 #endif
48403 #include "internal/pycore_frame.h"
48404 #endif
48405 #define __Pyx_Coroutine_Undelegate(gen) Py_CLEAR((gen)->yieldfrom)
48406 static int __Pyx_PyGen__FetchStopIterationValue(PyThreadState *__pyx_tstate, PyObject **pvalue) {
48407 PyObject *et, *ev, *tb;
48408 PyObject *value = NULL;
48409 CYTHON_UNUSED_VAR(__pyx_tstate);
48410 __Pyx_ErrFetch(&et, &ev, &tb);
48411 if (!et) {
48412 Py_XDECREF(tb);
48413 Py_XDECREF(ev);
48414 Py_INCREF(Py_None);
48415 *pvalue = Py_None;
48416 return 0;
48417 }
48418 if (likely(et == PyExc_StopIteration)) {
48419 if (!ev) {
48420 Py_INCREF(Py_None);
48421 value = Py_None;
48422 }
48423 #if PY_VERSION_HEX >= 0x030300A0
48424 else if (likely(__Pyx_IS_TYPE(ev, (PyTypeObject*)PyExc_StopIteration))) {
48425 value = ((PyStopIterationObject *)ev)->value;
48426 Py_INCREF(value);
48427 Py_DECREF(ev);
48428 }
48429 #endif
48430 else if (unlikely(PyTuple_Check(ev))) {
48431 if (PyTuple_GET_SIZE(ev) >= 1) {
48432 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
48433 value = PyTuple_GET_ITEM(ev, 0);
48434 Py_INCREF(value);
48435 #else
48436 value = PySequence_ITEM(ev, 0);
48437 #endif
48438 } else {
48439 Py_INCREF(Py_None);
48440 value = Py_None;
48441 }
48442 Py_DECREF(ev);
48443 }
48444 else if (!__Pyx_TypeCheck(ev, (PyTypeObject*)PyExc_StopIteration)) {
48445 value = ev;
48446 }
48447 if (likely(value)) {
48448 Py_XDECREF(tb);
48449 Py_DECREF(et);
48450 *pvalue = value;
48451 return 0;
48452 }
48453 } else if (!__Pyx_PyErr_GivenExceptionMatches(et, PyExc_StopIteration)) {
48454 __Pyx_ErrRestore(et, ev, tb);
48455 return -1;
48456 }
48457 PyErr_NormalizeException(&et, &ev, &tb);
48458 if (unlikely(!PyObject_TypeCheck(ev, (PyTypeObject*)PyExc_StopIteration))) {
48459 __Pyx_ErrRestore(et, ev, tb);
48460 return -1;
48461 }
48462 Py_XDECREF(tb);
48463 Py_DECREF(et);
48464 #if PY_VERSION_HEX >= 0x030300A0
48465 value = ((PyStopIterationObject *)ev)->value;
48466 Py_INCREF(value);
48467 Py_DECREF(ev);
48468 #else
48469 {
48470 PyObject* args = __Pyx_PyObject_GetAttrStr(ev, __pyx_n_s_args);
48471 Py_DECREF(ev);
48472 if (likely(args)) {
48473 value = PySequence_GetItem(args, 0);
48474 Py_DECREF(args);
48475 }
48476 if (unlikely(!value)) {
48477 __Pyx_ErrRestore(NULL, NULL, NULL);
48478 Py_INCREF(Py_None);
48479 value = Py_None;
48480 }
48481 }
48482 #endif
48483 *pvalue = value;
48484 return 0;
48485 }
48486 static CYTHON_INLINE
48487 void __Pyx_Coroutine_ExceptionClear(__Pyx_ExcInfoStruct *exc_state) {
48488 #if PY_VERSION_HEX >= 0x030B00a4
48489 Py_CLEAR(exc_state->exc_value);
48490 #else
48491 PyObject *t, *v, *tb;
48492 t = exc_state->exc_type;
48493 v = exc_state->exc_value;
48494 tb = exc_state->exc_traceback;
48495 exc_state->exc_type = NULL;
48496 exc_state->exc_value = NULL;
48497 exc_state->exc_traceback = NULL;
48498 Py_XDECREF(t);
48499 Py_XDECREF(v);
48500 Py_XDECREF(tb);
48501 #endif
48502 }
48503 #define __Pyx_Coroutine_AlreadyRunningError(gen) (__Pyx__Coroutine_AlreadyRunningError(gen), (PyObject*)NULL)
48504 static void __Pyx__Coroutine_AlreadyRunningError(__pyx_CoroutineObject *gen) {
48505 const char *msg;
48506 CYTHON_MAYBE_UNUSED_VAR(gen);
48507 if ((0)) {
48508 #ifdef __Pyx_Coroutine_USED
48509 } else if (__Pyx_Coroutine_Check((PyObject*)gen)) {
48510 msg = "coroutine already executing";
48511 #endif
48512 #ifdef __Pyx_AsyncGen_USED
48513 } else if (__Pyx_AsyncGen_CheckExact((PyObject*)gen)) {
48514 msg = "async generator already executing";
48515 #endif
48516 } else {
48517 msg = "generator already executing";
48518 }
48519 PyErr_SetString(PyExc_ValueError, msg);
48520 }
48521 #define __Pyx_Coroutine_NotStartedError(gen) (__Pyx__Coroutine_NotStartedError(gen), (PyObject*)NULL)
48522 static void __Pyx__Coroutine_NotStartedError(PyObject *gen) {
48523 const char *msg;
48524 CYTHON_MAYBE_UNUSED_VAR(gen);
48525 if ((0)) {
48526 #ifdef __Pyx_Coroutine_USED
48527 } else if (__Pyx_Coroutine_Check(gen)) {
48528 msg = "can't send non-None value to a just-started coroutine";
48529 #endif
48530 #ifdef __Pyx_AsyncGen_USED
48531 } else if (__Pyx_AsyncGen_CheckExact(gen)) {
48532 msg = "can't send non-None value to a just-started async generator";
48533 #endif
48534 } else {
48535 msg = "can't send non-None value to a just-started generator";
48536 }
48537 PyErr_SetString(PyExc_TypeError, msg);
48538 }
48539 #define __Pyx_Coroutine_AlreadyTerminatedError(gen, value, closing) (__Pyx__Coroutine_AlreadyTerminatedError(gen, value, closing), (PyObject*)NULL)
48540 static void __Pyx__Coroutine_AlreadyTerminatedError(PyObject *gen, PyObject *value, int closing) {
48541 CYTHON_MAYBE_UNUSED_VAR(gen);
48542 CYTHON_MAYBE_UNUSED_VAR(closing);
48543 #ifdef __Pyx_Coroutine_USED
48544 if (!closing && __Pyx_Coroutine_Check(gen)) {
48545 PyErr_SetString(PyExc_RuntimeError, "cannot reuse already awaited coroutine");
48546 } else
48547 #endif
48548 if (value) {
48549 #ifdef __Pyx_AsyncGen_USED
48550 if (__Pyx_AsyncGen_CheckExact(gen))
48551 PyErr_SetNone(__Pyx_PyExc_StopAsyncIteration);
48552 else
48553 #endif
48554 PyErr_SetNone(PyExc_StopIteration);
48555 }
48556 }
48557 static
48558 PyObject *__Pyx_Coroutine_SendEx(__pyx_CoroutineObject *self, PyObject *value, int closing) {
48559 __Pyx_PyThreadState_declare
48560 PyThreadState *tstate;
48561 __Pyx_ExcInfoStruct *exc_state;
48562 PyObject *retval;
48563 assert(!self->is_running);
48564 if (unlikely(self->resume_label == 0)) {
48565 if (unlikely(value && value != Py_None)) {
48566 return __Pyx_Coroutine_NotStartedError((PyObject*)self);
48567 }
48568 }
48569 if (unlikely(self->resume_label == -1)) {
48570 return __Pyx_Coroutine_AlreadyTerminatedError((PyObject*)self, value, closing);
48571 }
48572 #if CYTHON_FAST_THREAD_STATE
48573 __Pyx_PyThreadState_assign
48574 tstate = __pyx_tstate;
48575 #else
48576 tstate = __Pyx_PyThreadState_Current;
48577 #endif
48578 exc_state = &self->gi_exc_state;
48579 if (exc_state->exc_value) {
48580 #if CYTHON_COMPILING_IN_PYPY
48581 #else
48582 PyObject *exc_tb;
48583 #if PY_VERSION_HEX >= 0x030B00a4 && !CYTHON_COMPILING_IN_CPYTHON
48584 exc_tb = PyException_GetTraceback(exc_state->exc_value);
48585 #elif PY_VERSION_HEX >= 0x030B00a4
48586 exc_tb = ((PyBaseExceptionObject*) exc_state->exc_value)->traceback;
48587 #else
48588 exc_tb = exc_state->exc_traceback;
48589 #endif
48590 if (exc_tb) {
48591 PyTracebackObject *tb = (PyTracebackObject *) exc_tb;
48592 PyFrameObject *f = tb->tb_frame;
48593 assert(f->f_back == NULL);
48594 #if PY_VERSION_HEX >= 0x030B00A1
48595 f->f_back = PyThreadState_GetFrame(tstate);
48596 #else
48597 Py_XINCREF(tstate->frame);
48598 f->f_back = tstate->frame;
48599 #endif
48600 #if PY_VERSION_HEX >= 0x030B00a4 && !CYTHON_COMPILING_IN_CPYTHON
48601 Py_DECREF(exc_tb);
48602 #endif
48603 }
48604 #endif
48605 }
48606 #if CYTHON_USE_EXC_INFO_STACK
48607 exc_state->previous_item = tstate->exc_info;
48608 tstate->exc_info = exc_state;
48609 #else
48610 if (exc_state->exc_type) {
48611 __Pyx_ExceptionSwap(&exc_state->exc_type, &exc_state->exc_value, &exc_state->exc_traceback);
48612 } else {
48613 __Pyx_Coroutine_ExceptionClear(exc_state);
48614 __Pyx_ExceptionSave(&exc_state->exc_type, &exc_state->exc_value, &exc_state->exc_traceback);
48615 }
48616 #endif
48617 self->is_running = 1;
48618 retval = self->body(self, tstate, value);
48619 self->is_running = 0;
48620 #if CYTHON_USE_EXC_INFO_STACK
48621 exc_state = &self->gi_exc_state;
48622 tstate->exc_info = exc_state->previous_item;
48623 exc_state->previous_item = NULL;
48624 __Pyx_Coroutine_ResetFrameBackpointer(exc_state);
48625 #endif
48626 return retval;
48627 }
48628 static CYTHON_INLINE void __Pyx_Coroutine_ResetFrameBackpointer(__Pyx_ExcInfoStruct *exc_state) {
48629 #if CYTHON_COMPILING_IN_PYPY
48630 CYTHON_UNUSED_VAR(exc_state);
48631 #else
48632 PyObject *exc_tb;
48633 #if PY_VERSION_HEX >= 0x030B00a4
48634 if (!exc_state->exc_value) return;
48635 exc_tb = PyException_GetTraceback(exc_state->exc_value);
48636 #else
48637 exc_tb = exc_state->exc_traceback;
48638 #endif
48639 if (likely(exc_tb)) {
48640 PyTracebackObject *tb = (PyTracebackObject *) exc_tb;
48641 PyFrameObject *f = tb->tb_frame;
48642 Py_CLEAR(f->f_back);
48643 #if PY_VERSION_HEX >= 0x030B00a4
48644 Py_DECREF(exc_tb);
48645 #endif
48646 }
48647 #endif
48648 }
48649 static CYTHON_INLINE
48650 PyObject *__Pyx_Coroutine_MethodReturn(PyObject* gen, PyObject *retval) {
48651 CYTHON_MAYBE_UNUSED_VAR(gen);
48652 if (unlikely(!retval)) {
48653 __Pyx_PyThreadState_declare
48654 __Pyx_PyThreadState_assign
48655 if (!__Pyx_PyErr_Occurred()) {
48656 PyObject *exc = PyExc_StopIteration;
48657 #ifdef __Pyx_AsyncGen_USED
48658 if (__Pyx_AsyncGen_CheckExact(gen))
48659 exc = __Pyx_PyExc_StopAsyncIteration;
48660 #endif
48661 __Pyx_PyErr_SetNone(exc);
48662 }
48663 }
48664 return retval;
48665 }
48666 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03030000 && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3)
48667 static CYTHON_INLINE
48668 PyObject *__Pyx_PyGen_Send(PyGenObject *gen, PyObject *arg) {
48669 #if PY_VERSION_HEX <= 0x030A00A1
48670 return _PyGen_Send(gen, arg);
48671 #else
48672 PyObject *result;
48673 if (PyIter_Send((PyObject*)gen, arg ? arg : Py_None, &result) == PYGEN_RETURN) {
48674 if (PyAsyncGen_CheckExact(gen)) {
48675 assert(result == Py_None);
48676 PyErr_SetNone(PyExc_StopAsyncIteration);
48677 }
48678 else if (result == Py_None) {
48679 PyErr_SetNone(PyExc_StopIteration);
48680 }
48681 else {
48682 #if PY_VERSION_HEX < 0x030d00A1
48683 _PyGen_SetStopIterationValue(result);
48684 #else
48685 if (!PyTuple_Check(result) && !PyExceptionInstance_Check(result)) {
48686 PyErr_SetObject(PyExc_StopIteration, result);
48687 } else {
48688 PyObject *exc = __Pyx_PyObject_CallOneArg(PyExc_StopIteration, result);
48689 if (likely(exc != NULL)) {
48690 PyErr_SetObject(PyExc_StopIteration, exc);
48691 Py_DECREF(exc);
48692 }
48693 }
48694 #endif
48695 }
48696 Py_DECREF(result);
48697 result = NULL;
48698 }
48699 return result;
48700 #endif
48701 }
48702 #endif
48703 static CYTHON_INLINE
48704 PyObject *__Pyx_Coroutine_FinishDelegation(__pyx_CoroutineObject *gen) {
48705 PyObject *ret;
48706 PyObject *val = NULL;
48707 __Pyx_Coroutine_Undelegate(gen);
48708 __Pyx_PyGen__FetchStopIterationValue(__Pyx_PyThreadState_Current, &val);
48709 ret = __Pyx_Coroutine_SendEx(gen, val, 0);
48710 Py_XDECREF(val);
48711 return ret;
48712 }
48713 static PyObject *__Pyx_Coroutine_Send(PyObject *self, PyObject *value) {
48714 PyObject *retval;
48715 __pyx_CoroutineObject *gen = (__pyx_CoroutineObject*) self;
48716 PyObject *yf = gen->yieldfrom;
48717 if (unlikely(gen->is_running))
48718 return __Pyx_Coroutine_AlreadyRunningError(gen);
48719 if (yf) {
48720 PyObject *ret;
48721 gen->is_running = 1;
48722 #ifdef __Pyx_Generator_USED
48723 if (__Pyx_Generator_CheckExact(yf)) {
48724 ret = __Pyx_Coroutine_Send(yf, value);
48725 } else
48726 #endif
48727 #ifdef __Pyx_Coroutine_USED
48728 if (__Pyx_Coroutine_Check(yf)) {
48729 ret = __Pyx_Coroutine_Send(yf, value);
48730 } else
48731 #endif
48732 #ifdef __Pyx_AsyncGen_USED
48733 if (__pyx_PyAsyncGenASend_CheckExact(yf)) {
48734 ret = __Pyx_async_gen_asend_send(yf, value);
48735 } else
48736 #endif
48737 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03030000 && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3)
48738 if (PyGen_CheckExact(yf)) {
48739 ret = __Pyx_PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value);
48740 } else
48741 #endif
48742 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03050000 && defined(PyCoro_CheckExact) && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3)
48743 if (PyCoro_CheckExact(yf)) {
48744 ret = __Pyx_PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value);
48745 } else
48746 #endif
48747 {
48748 if (value == Py_None)
48749 ret = __Pyx_PyObject_GetIterNextFunc(yf)(yf);
48750 else
48751 ret = __Pyx_PyObject_CallMethod1(yf, __pyx_n_s_send, value);
48752 }
48753 gen->is_running = 0;
48754 if (likely(ret)) {
48755 return ret;
48756 }
48757 retval = __Pyx_Coroutine_FinishDelegation(gen);
48758 } else {
48759 retval = __Pyx_Coroutine_SendEx(gen, value, 0);
48760 }
48761 return __Pyx_Coroutine_MethodReturn(self, retval);
48762 }
48763 static int __Pyx_Coroutine_CloseIter(__pyx_CoroutineObject *gen, PyObject *yf) {
48764 PyObject *retval = NULL;
48765 int err = 0;
48766 #ifdef __Pyx_Generator_USED
48767 if (__Pyx_Generator_CheckExact(yf)) {
48768 retval = __Pyx_Coroutine_Close(yf);
48769 if (!retval)
48770 return -1;
48771 } else
48772 #endif
48773 #ifdef __Pyx_Coroutine_USED
48774 if (__Pyx_Coroutine_Check(yf)) {
48775 retval = __Pyx_Coroutine_Close(yf);
48776 if (!retval)
48777 return -1;
48778 } else
48779 if (__Pyx_CoroutineAwait_CheckExact(yf)) {
48780 retval = __Pyx_CoroutineAwait_Close((__pyx_CoroutineAwaitObject*)yf, NULL);
48781 if (!retval)
48782 return -1;
48783 } else
48784 #endif
48785 #ifdef __Pyx_AsyncGen_USED
48786 if (__pyx_PyAsyncGenASend_CheckExact(yf)) {
48787 retval = __Pyx_async_gen_asend_close(yf, NULL);
48788 } else
48789 if (__pyx_PyAsyncGenAThrow_CheckExact(yf)) {
48790 retval = __Pyx_async_gen_athrow_close(yf, NULL);
48791 } else
48792 #endif
48793 {
48794 PyObject *meth;
48795 gen->is_running = 1;
48796 meth = __Pyx_PyObject_GetAttrStrNoError(yf, __pyx_n_s_close);
48797 if (unlikely(!meth)) {
48798 if (unlikely(PyErr_Occurred())) {
48799 PyErr_WriteUnraisable(yf);
48800 }
48801 } else {
48802 retval = __Pyx_PyObject_CallNoArg(meth);
48803 Py_DECREF(meth);
48804 if (unlikely(!retval))
48805 err = -1;
48806 }
48807 gen->is_running = 0;
48808 }
48809 Py_XDECREF(retval);
48810 return err;
48811 }
48812 static PyObject *__Pyx_Generator_Next(PyObject *self) {
48813 __pyx_CoroutineObject *gen = (__pyx_CoroutineObject*) self;
48814 PyObject *yf = gen->yieldfrom;
48815 if (unlikely(gen->is_running))
48816 return __Pyx_Coroutine_AlreadyRunningError(gen);
48817 if (yf) {
48818 PyObject *ret;
48819 gen->is_running = 1;
48820 #ifdef __Pyx_Generator_USED
48821 if (__Pyx_Generator_CheckExact(yf)) {
48822 ret = __Pyx_Generator_Next(yf);
48823 } else
48824 #endif
48825 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03030000 && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3)
48826 if (PyGen_CheckExact(yf)) {
48827 ret = __Pyx_PyGen_Send((PyGenObject*)yf, NULL);
48828 } else
48829 #endif
48830 #ifdef __Pyx_Coroutine_USED
48831 if (__Pyx_Coroutine_Check(yf)) {
48832 ret = __Pyx_Coroutine_Send(yf, Py_None);
48833 } else
48834 #endif
48835 ret = __Pyx_PyObject_GetIterNextFunc(yf)(yf);
48836 gen->is_running = 0;
48837 if (likely(ret)) {
48838 return ret;
48839 }
48840 return __Pyx_Coroutine_FinishDelegation(gen);
48841 }
48842 return __Pyx_Coroutine_SendEx(gen, Py_None, 0);
48843 }
48844 static PyObject *__Pyx_Coroutine_Close_Method(PyObject *self, PyObject *arg) {
48845 CYTHON_UNUSED_VAR(arg);
48846 return __Pyx_Coroutine_Close(self);
48847 }
48848 static PyObject *__Pyx_Coroutine_Close(PyObject *self) {
48849 __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self;
48850 PyObject *retval, *raised_exception;
48851 PyObject *yf = gen->yieldfrom;
48852 int err = 0;
48853 if (unlikely(gen->is_running))
48854 return __Pyx_Coroutine_AlreadyRunningError(gen);
48855 if (yf) {
48856 Py_INCREF(yf);
48857 err = __Pyx_Coroutine_CloseIter(gen, yf);
48858 __Pyx_Coroutine_Undelegate(gen);
48859 Py_DECREF(yf);
48860 }
48861 if (err == 0)
48862 PyErr_SetNone(PyExc_GeneratorExit);
48863 retval = __Pyx_Coroutine_SendEx(gen, NULL, 1);
48864 if (unlikely(retval)) {
48865 const char *msg;
48866 Py_DECREF(retval);
48867 if ((0)) {
48868 #ifdef __Pyx_Coroutine_USED
48869 } else if (__Pyx_Coroutine_Check(self)) {
48870 msg = "coroutine ignored GeneratorExit";
48871 #endif
48872 #ifdef __Pyx_AsyncGen_USED
48873 } else if (__Pyx_AsyncGen_CheckExact(self)) {
48874 #if PY_VERSION_HEX < 0x03060000
48875 msg = "async generator ignored GeneratorExit - might require Python 3.6+ finalisation (PEP 525)";
48876 #else
48877 msg = "async generator ignored GeneratorExit";
48878 #endif
48879 #endif
48880 } else {
48881 msg = "generator ignored GeneratorExit";
48882 }
48883 PyErr_SetString(PyExc_RuntimeError, msg);
48884 return NULL;
48885 }
48886 raised_exception = PyErr_Occurred();
48887 if (likely(!raised_exception || __Pyx_PyErr_GivenExceptionMatches2(raised_exception, PyExc_GeneratorExit, PyExc_StopIteration))) {
48888 if (raised_exception) PyErr_Clear();
48889 Py_INCREF(Py_None);
48890 return Py_None;
48891 }
48892 return NULL;
48893 }
48894 static PyObject *__Pyx__Coroutine_Throw(PyObject *self, PyObject *typ, PyObject *val, PyObject *tb,
48895 PyObject *args, int close_on_genexit) {
48896 __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self;
48897 PyObject *yf = gen->yieldfrom;
48898 if (unlikely(gen->is_running))
48899 return __Pyx_Coroutine_AlreadyRunningError(gen);
48900 if (yf) {
48901 PyObject *ret;
48902 Py_INCREF(yf);
48903 if (__Pyx_PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit) && close_on_genexit) {
48904 int err = __Pyx_Coroutine_CloseIter(gen, yf);
48905 Py_DECREF(yf);
48906 __Pyx_Coroutine_Undelegate(gen);
48907 if (err < 0)
48908 return __Pyx_Coroutine_MethodReturn(self, __Pyx_Coroutine_SendEx(gen, NULL, 0));
48909 goto throw_here;
48910 }
48911 gen->is_running = 1;
48912 if (0
48913 #ifdef __Pyx_Generator_USED
48914 || __Pyx_Generator_CheckExact(yf)
48915 #endif
48916 #ifdef __Pyx_Coroutine_USED
48917 || __Pyx_Coroutine_Check(yf)
48918 #endif
48919 ) {
48920 ret = __Pyx__Coroutine_Throw(yf, typ, val, tb, args, close_on_genexit);
48921 #ifdef __Pyx_Coroutine_USED
48922 } else if (__Pyx_CoroutineAwait_CheckExact(yf)) {
48923 ret = __Pyx__Coroutine_Throw(((__pyx_CoroutineAwaitObject*)yf)->coroutine, typ, val, tb, args, close_on_genexit);
48924 #endif
48925 } else {
48926 PyObject *meth = __Pyx_PyObject_GetAttrStrNoError(yf, __pyx_n_s_throw);
48927 if (unlikely(!meth)) {
48928 Py_DECREF(yf);
48929 if (unlikely(PyErr_Occurred())) {
48930 gen->is_running = 0;
48931 return NULL;
48932 }
48933 __Pyx_Coroutine_Undelegate(gen);
48934 gen->is_running = 0;
48935 goto throw_here;
48936 }
48937 if (likely(args)) {
48938 ret = __Pyx_PyObject_Call(meth, args, NULL);
48939 } else {
48940 PyObject *cargs[4] = {NULL, typ, val, tb};
48941 ret = __Pyx_PyObject_FastCall(meth, cargs+1, 3 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET);
48942 }
48943 Py_DECREF(meth);
48944 }
48945 gen->is_running = 0;
48946 Py_DECREF(yf);
48947 if (!ret) {
48948 ret = __Pyx_Coroutine_FinishDelegation(gen);
48949 }
48950 return __Pyx_Coroutine_MethodReturn(self, ret);
48951 }
48952 throw_here:
48953 __Pyx_Raise(typ, val, tb, NULL);
48954 return __Pyx_Coroutine_MethodReturn(self, __Pyx_Coroutine_SendEx(gen, NULL, 0));
48955 }
48956 static PyObject *__Pyx_Coroutine_Throw(PyObject *self, PyObject *args) {
48957 PyObject *typ;
48958 PyObject *val = NULL;
48959 PyObject *tb = NULL;
48960 if (unlikely(!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb)))
48961 return NULL;
48962 return __Pyx__Coroutine_Throw(self, typ, val, tb, args, 1);
48963 }
48964 static CYTHON_INLINE int __Pyx_Coroutine_traverse_excstate(__Pyx_ExcInfoStruct *exc_state, visitproc visit, void *arg) {
48965 #if PY_VERSION_HEX >= 0x030B00a4
48966 Py_VISIT(exc_state->exc_value);
48967 #else
48968 Py_VISIT(exc_state->exc_type);
48969 Py_VISIT(exc_state->exc_value);
48970 Py_VISIT(exc_state->exc_traceback);
48971 #endif
48972 return 0;
48973 }
48974 static int __Pyx_Coroutine_traverse(__pyx_CoroutineObject *gen, visitproc visit, void *arg) {
48975 Py_VISIT(gen->closure);
48976 Py_VISIT(gen->classobj);
48977 Py_VISIT(gen->yieldfrom);
48978 return __Pyx_Coroutine_traverse_excstate(&gen->gi_exc_state, visit, arg);
48979 }
48980 static int __Pyx_Coroutine_clear(PyObject *self) {
48981 __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self;
48982 Py_CLEAR(gen->closure);
48983 Py_CLEAR(gen->classobj);
48984 Py_CLEAR(gen->yieldfrom);
48985 __Pyx_Coroutine_ExceptionClear(&gen->gi_exc_state);
48986 #ifdef __Pyx_AsyncGen_USED
48987 if (__Pyx_AsyncGen_CheckExact(self)) {
48988 Py_CLEAR(((__pyx_PyAsyncGenObject*)gen)->ag_finalizer);
48989 }
48990 #endif
48991 Py_CLEAR(gen->gi_code);
48992 Py_CLEAR(gen->gi_frame);
48993 Py_CLEAR(gen->gi_name);
48994 Py_CLEAR(gen->gi_qualname);
48995 Py_CLEAR(gen->gi_modulename);
48996 return 0;
48997 }
48998 static void __Pyx_Coroutine_dealloc(PyObject *self) {
48999 __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self;
49000 PyObject_GC_UnTrack(gen);
49001 if (gen->gi_weakreflist != NULL)
49002 PyObject_ClearWeakRefs(self);
49003 if (gen->resume_label >= 0) {
49004 PyObject_GC_Track(self);
49005 #if PY_VERSION_HEX >= 0x030400a1 && CYTHON_USE_TP_FINALIZE
49006 if (unlikely(PyObject_CallFinalizerFromDealloc(self)))
49007 #else
49008 Py_TYPE(gen)->tp_del(self);
49009 if (unlikely(Py_REFCNT(self) > 0))
49010 #endif
49011 {
49012 return;
49013 }
49014 PyObject_GC_UnTrack(self);
49015 }
49016 #ifdef __Pyx_AsyncGen_USED
49017 if (__Pyx_AsyncGen_CheckExact(self)) {
49018 /* We have to handle this case for asynchronous generators
49019 right here, because this code has to be between UNTRACK
49020 and GC_Del. */
49021 Py_CLEAR(((__pyx_PyAsyncGenObject*)self)->ag_finalizer);
49022 }
49023 #endif
49024 __Pyx_Coroutine_clear(self);
49025 __Pyx_PyHeapTypeObject_GC_Del(gen);
49026 }
49027 static void __Pyx_Coroutine_del(PyObject *self) {
49028 PyObject *error_type, *error_value, *error_traceback;
49029 __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self;
49030 __Pyx_PyThreadState_declare
49031 if (gen->resume_label < 0) {
49032 return;
49033 }
49034 #if !CYTHON_USE_TP_FINALIZE
49035 assert(self->ob_refcnt == 0);
49036 __Pyx_SET_REFCNT(self, 1);
49037 #endif
49038 __Pyx_PyThreadState_assign
49039 __Pyx_ErrFetch(&error_type, &error_value, &error_traceback);
49040 #ifdef __Pyx_AsyncGen_USED
49041 if (__Pyx_AsyncGen_CheckExact(self)) {
49042 __pyx_PyAsyncGenObject *agen = (__pyx_PyAsyncGenObject*)self;
49043 PyObject *finalizer = agen->ag_finalizer;
49044 if (finalizer && !agen->ag_closed) {
49045 PyObject *res = __Pyx_PyObject_CallOneArg(finalizer, self);
49046 if (unlikely(!res)) {
49047 PyErr_WriteUnraisable(self);
49048 } else {
49049 Py_DECREF(res);
49050 }
49051 __Pyx_ErrRestore(error_type, error_value, error_traceback);
49052 return;
49053 }
49054 }
49055 #endif
49056 if (unlikely(gen->resume_label == 0 && !error_value)) {
49057 #ifdef __Pyx_Coroutine_USED
49058 #ifdef __Pyx_Generator_USED
49059 if (!__Pyx_Generator_CheckExact(self))
49060 #endif
49061 {
49062 PyObject_GC_UnTrack(self);
49063 #if PY_MAJOR_VERSION >= 3 || defined(PyErr_WarnFormat)
49064 if (unlikely(PyErr_WarnFormat(PyExc_RuntimeWarning, 1, "coroutine '%.50S' was never awaited", gen->gi_qualname) < 0))
49065 PyErr_WriteUnraisable(self);
49066 #else
49067 {PyObject *msg;
49068 char *cmsg;
49069 #if CYTHON_COMPILING_IN_PYPY
49070 msg = NULL;
49071 cmsg = (char*) "coroutine was never awaited";
49072 #else
49073 char *cname;
49074 PyObject *qualname;
49075 qualname = gen->gi_qualname;
49076 cname = PyString_AS_STRING(qualname);
49077 msg = PyString_FromFormat("coroutine '%.50s' was never awaited", cname);
49078 if (unlikely(!msg)) {
49079 PyErr_Clear();
49080 cmsg = (char*) "coroutine was never awaited";
49081 } else {
49082 cmsg = PyString_AS_STRING(msg);
49083 }
49084 #endif
49085 if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning, cmsg, 1) < 0))
49086 PyErr_WriteUnraisable(self);
49087 Py_XDECREF(msg);}
49088 #endif
49089 PyObject_GC_Track(self);
49090 }
49091 #endif
49092 } else {
49093 PyObject *res = __Pyx_Coroutine_Close(self);
49094 if (unlikely(!res)) {
49095 if (PyErr_Occurred())
49096 PyErr_WriteUnraisable(self);
49097 } else {
49098 Py_DECREF(res);
49099 }
49100 }
49101 __Pyx_ErrRestore(error_type, error_value, error_traceback);
49102 #if !CYTHON_USE_TP_FINALIZE
49103 assert(Py_REFCNT(self) > 0);
49104 if (likely(--self->ob_refcnt == 0)) {
49105 return;
49106 }
49107 {
49108 Py_ssize_t refcnt = Py_REFCNT(self);
49109 _Py_NewReference(self);
49110 __Pyx_SET_REFCNT(self, refcnt);
49111 }
49112 #if CYTHON_COMPILING_IN_CPYTHON
49113 assert(PyType_IS_GC(Py_TYPE(self)) &&
49114 _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
49115 _Py_DEC_REFTOTAL;
49116 #endif
49117 #ifdef COUNT_ALLOCS
49118 --Py_TYPE(self)->tp_frees;
49119 --Py_TYPE(self)->tp_allocs;
49120 #endif
49121 #endif
49122 }
49123 static PyObject *
49124 __Pyx_Coroutine_get_name(__pyx_CoroutineObject *self, void *context)
49125 {
49126 PyObject *name = self->gi_name;
49127 CYTHON_UNUSED_VAR(context);
49128 if (unlikely(!name)) name = Py_None;
49129 Py_INCREF(name);
49130 return name;
49131 }
49132 static int
49133 __Pyx_Coroutine_set_name(__pyx_CoroutineObject *self, PyObject *value, void *context)
49134 {
49135 CYTHON_UNUSED_VAR(context);
49136 #if PY_MAJOR_VERSION >= 3
49137 if (unlikely(value == NULL || !PyUnicode_Check(value)))
49138 #else
49139 if (unlikely(value == NULL || !PyString_Check(value)))
49140 #endif
49141 {
49142 PyErr_SetString(PyExc_TypeError,
49143 "__name__ must be set to a string object");
49144 return -1;
49145 }
49146 Py_INCREF(value);
49147 __Pyx_Py_XDECREF_SET(self->gi_name, value);
49148 return 0;
49149 }
49150 static PyObject *
49151 __Pyx_Coroutine_get_qualname(__pyx_CoroutineObject *self, void *context)
49152 {
49153 PyObject *name = self->gi_qualname;
49154 CYTHON_UNUSED_VAR(context);
49155 if (unlikely(!name)) name = Py_None;
49156 Py_INCREF(name);
49157 return name;
49158 }
49159 static int
49160 __Pyx_Coroutine_set_qualname(__pyx_CoroutineObject *self, PyObject *value, void *context)
49161 {
49162 CYTHON_UNUSED_VAR(context);
49163 #if PY_MAJOR_VERSION >= 3
49164 if (unlikely(value == NULL || !PyUnicode_Check(value)))
49165 #else
49166 if (unlikely(value == NULL || !PyString_Check(value)))
49167 #endif
49168 {
49169 PyErr_SetString(PyExc_TypeError,
49170 "__qualname__ must be set to a string object");
49171 return -1;
49172 }
49173 Py_INCREF(value);
49174 __Pyx_Py_XDECREF_SET(self->gi_qualname, value);
49175 return 0;
49176 }
49177 static PyObject *
49178 __Pyx_Coroutine_get_frame(__pyx_CoroutineObject *self, void *context)
49179 {
49180 PyObject *frame = self->gi_frame;
49181 CYTHON_UNUSED_VAR(context);
49182 if (!frame) {
49183 if (unlikely(!self->gi_code)) {
49184 Py_RETURN_NONE;
49185 }
49186 frame = (PyObject *) PyFrame_New(
49187 PyThreadState_Get(), /*PyThreadState *tstate,*/
49188 (PyCodeObject*) self->gi_code, /*PyCodeObject *code,*/
49189 __pyx_d, /*PyObject *globals,*/
49190 0 /*PyObject *locals*/
49191 );
49192 if (unlikely(!frame))
49193 return NULL;
49194 self->gi_frame = frame;
49195 }
49196 Py_INCREF(frame);
49197 return frame;
49198 }
49199 static __pyx_CoroutineObject *__Pyx__Coroutine_New(
49200 PyTypeObject* type, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure,
49201 PyObject *name, PyObject *qualname, PyObject *module_name) {
49202 __pyx_CoroutineObject *gen = PyObject_GC_New(__pyx_CoroutineObject, type);
49203 if (unlikely(!gen))
49204 return NULL;
49205 return __Pyx__Coroutine_NewInit(gen, body, code, closure, name, qualname, module_name);
49206 }
49207 static __pyx_CoroutineObject *__Pyx__Coroutine_NewInit(
49208 __pyx_CoroutineObject *gen, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure,
49209 PyObject *name, PyObject *qualname, PyObject *module_name) {
49210 gen->body = body;
49211 gen->closure = closure;
49212 Py_XINCREF(closure);
49213 gen->is_running = 0;
49214 gen->resume_label = 0;
49215 gen->classobj = NULL;
49216 gen->yieldfrom = NULL;
49217 #if PY_VERSION_HEX >= 0x030B00a4
49218 gen->gi_exc_state.exc_value = NULL;
49219 #else
49220 gen->gi_exc_state.exc_type = NULL;
49221 gen->gi_exc_state.exc_value = NULL;
49222 gen->gi_exc_state.exc_traceback = NULL;
49223 #endif
49224 #if CYTHON_USE_EXC_INFO_STACK
49225 gen->gi_exc_state.previous_item = NULL;
49226 #endif
49227 gen->gi_weakreflist = NULL;
49228 Py_XINCREF(qualname);
49229 gen->gi_qualname = qualname;
49230 Py_XINCREF(name);
49231 gen->gi_name = name;
49232 Py_XINCREF(module_name);
49233 gen->gi_modulename = module_name;
49234 Py_XINCREF(code);
49235 gen->gi_code = code;
49236 gen->gi_frame = NULL;
49237 PyObject_GC_Track(gen);
49238 return gen;
49239 }
49240
49241 /* PatchModuleWithCoroutine */
49242 static PyObject* __Pyx_Coroutine_patch_module(PyObject* module, const char* py_code) {
49243 #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
49244 int result;
49245 PyObject *globals, *result_obj;
49246 globals = PyDict_New(); if (unlikely(!globals)) goto ignore;
49247 result = PyDict_SetItemString(globals, "_cython_coroutine_type",
49248 #ifdef __Pyx_Coroutine_USED
49249 (PyObject*)__pyx_CoroutineType);
49250 #else
49251 Py_None);
49252 #endif
49253 if (unlikely(result < 0)) goto ignore;
49254 result = PyDict_SetItemString(globals, "_cython_generator_type",
49255 #ifdef __Pyx_Generator_USED
49256 (PyObject*)__pyx_GeneratorType);
49257 #else
49258 Py_None);
49259 #endif
49260 if (unlikely(result < 0)) goto ignore;
49261 if (unlikely(PyDict_SetItemString(globals, "_module", module) < 0)) goto ignore;
49262 if (unlikely(PyDict_SetItemString(globals, "__builtins__", __pyx_b) < 0)) goto ignore;
49263 result_obj = PyRun_String(py_code, Py_file_input, globals, globals);
49264 if (unlikely(!result_obj)) goto ignore;
49265 Py_DECREF(result_obj);
49266 Py_DECREF(globals);
49267 return module;
49268 ignore:
49269 Py_XDECREF(globals);
49270 PyErr_WriteUnraisable(module);
49271 if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning, "Cython module failed to patch module with custom type", 1) < 0)) {
49272 Py_DECREF(module);
49273 module = NULL;
49274 }
49275 #else
49276 py_code++;
49277 #endif
49278 return module;
49279 }
49280
49281 /* PatchGeneratorABC */
49282 #ifndef CYTHON_REGISTER_ABCS
49283 #define CYTHON_REGISTER_ABCS 1
49284 #endif
49285 #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
49286 static PyObject* __Pyx_patch_abc_module(PyObject *module);
49287 static PyObject* __Pyx_patch_abc_module(PyObject *module) {
49288 module = __Pyx_Coroutine_patch_module(
49289 module, ""
49290 "if _cython_generator_type is not None:\n"
49291 " try: Generator = _module.Generator\n"
49292 " except AttributeError: pass\n"
49293 " else: Generator.register(_cython_generator_type)\n"
49294 "if _cython_coroutine_type is not None:\n"
49295 " try: Coroutine = _module.Coroutine\n"
49296 " except AttributeError: pass\n"
49297 " else: Coroutine.register(_cython_coroutine_type)\n"
49298 );
49299 return module;
49300 }
49301 #endif
49302 static int __Pyx_patch_abc(void) {
49303 #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
49304 static int abc_patched = 0;
49305 if (CYTHON_REGISTER_ABCS && !abc_patched) {
49306 PyObject *module;
49307 module = PyImport_ImportModule((PY_MAJOR_VERSION >= 3) ? "collections.abc" : "collections");
49308 if (unlikely(!module)) {
49309 PyErr_WriteUnraisable(NULL);
49310 if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning,
49311 ((PY_MAJOR_VERSION >= 3) ?
49312 "Cython module failed to register with collections.abc module" :
49313 "Cython module failed to register with collections module"), 1) < 0)) {
49314 return -1;
49315 }
49316 } else {
49317 module = __Pyx_patch_abc_module(module);
49318 abc_patched = 1;
49319 if (unlikely(!module))
49320 return -1;
49321 Py_DECREF(module);
49322 }
49323 module = PyImport_ImportModule("backports_abc");
49324 if (module) {
49325 module = __Pyx_patch_abc_module(module);
49326 Py_XDECREF(module);
49327 }
49328 if (!module) {
49329 PyErr_Clear();
49330 }
49331 }
49332 #else
49333 if ((0)) __Pyx_Coroutine_patch_module(NULL, NULL);
49334 #endif
49335 return 0;
49336 }
49337
49338 /* Generator */
49339 static PyMethodDef __pyx_Generator_methods[] = {
49340 {"send", (PyCFunction) __Pyx_Coroutine_Send, METH_O,
49341 (char*) PyDoc_STR("send(arg) -> send 'arg' into generator,\nreturn next yielded value or raise StopIteration.")},
49342 {"throw", (PyCFunction) __Pyx_Coroutine_Throw, METH_VARARGS,
49343 (char*) PyDoc_STR("throw(typ[,val[,tb]]) -> raise exception in generator,\nreturn next yielded value or raise StopIteration.")},
49344 {"close", (PyCFunction) __Pyx_Coroutine_Close_Method, METH_NOARGS,
49345 (char*) PyDoc_STR("close() -> raise GeneratorExit inside generator.")},
49346 {0, 0, 0, 0}
49347 };
49348 static PyMemberDef __pyx_Generator_memberlist[] = {
49349 {(char *) "gi_running", T_BOOL, offsetof(__pyx_CoroutineObject, is_running), READONLY, NULL},
49350 {(char*) "gi_yieldfrom", T_OBJECT, offsetof(__pyx_CoroutineObject, yieldfrom), READONLY,
49351 (char*) PyDoc_STR("object being iterated by 'yield from', or None")},
49352 {(char*) "gi_code", T_OBJECT, offsetof(__pyx_CoroutineObject, gi_code), READONLY, NULL},
49353 {(char *) "__module__", T_OBJECT, offsetof(__pyx_CoroutineObject, gi_modulename), 0, 0},
49354 #if CYTHON_USE_TYPE_SPECS
49355 {(char *) "__weaklistoffset__", T_PYSSIZET, offsetof(__pyx_CoroutineObject, gi_weakreflist), READONLY, 0},
49356 #endif
49357 {0, 0, 0, 0, 0}
49358 };
49359 static PyGetSetDef __pyx_Generator_getsets[] = {
49360 {(char *) "__name__", (getter)__Pyx_Coroutine_get_name, (setter)__Pyx_Coroutine_set_name,
49361 (char*) PyDoc_STR("name of the generator"), 0},
49362 {(char *) "__qualname__", (getter)__Pyx_Coroutine_get_qualname, (setter)__Pyx_Coroutine_set_qualname,
49363 (char*) PyDoc_STR("qualified name of the generator"), 0},
49364 {(char *) "gi_frame", (getter)__Pyx_Coroutine_get_frame, NULL,
49365 (char*) PyDoc_STR("Frame of the generator"), 0},
49366 {0, 0, 0, 0, 0}
49367 };
49368 #if CYTHON_USE_TYPE_SPECS
49369 static PyType_Slot __pyx_GeneratorType_slots[] = {
49370 {Py_tp_dealloc, (void *)__Pyx_Coroutine_dealloc},
49371 {Py_tp_traverse, (void *)__Pyx_Coroutine_traverse},
49372 {Py_tp_iter, (void *)PyObject_SelfIter},
49373 {Py_tp_iternext, (void *)__Pyx_Generator_Next},
49374 {Py_tp_methods, (void *)__pyx_Generator_methods},
49375 {Py_tp_members, (void *)__pyx_Generator_memberlist},
49376 {Py_tp_getset, (void *)__pyx_Generator_getsets},
49377 {Py_tp_getattro, (void *) __Pyx_PyObject_GenericGetAttrNoDict},
49378 #if CYTHON_USE_TP_FINALIZE
49379 {Py_tp_finalize, (void *)__Pyx_Coroutine_del},
49380 #endif
49381 {0, 0},
49382 };
49383 static PyType_Spec __pyx_GeneratorType_spec = {
49384 __PYX_TYPE_MODULE_PREFIX "generator",
49385 sizeof(__pyx_CoroutineObject),
49386 0,
49387 Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_HAVE_FINALIZE,
49388 __pyx_GeneratorType_slots
49389 };
49390 #else
49391 static PyTypeObject __pyx_GeneratorType_type = {
49392 PyVarObject_HEAD_INIT(0, 0)
49393 __PYX_TYPE_MODULE_PREFIX "generator",
49394 sizeof(__pyx_CoroutineObject),
49395 0,
49396 (destructor) __Pyx_Coroutine_dealloc,
49397 0,
49398 0,
49399 0,
49400 0,
49401 0,
49402 0,
49403 0,
49404 0,
49405 0,
49406 0,
49407 0,
49408 0,
49409 0,
49410 0,
49411 Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_HAVE_FINALIZE,
49412 0,
49413 (traverseproc) __Pyx_Coroutine_traverse,
49414 0,
49415 0,
49416 offsetof(__pyx_CoroutineObject, gi_weakreflist),
49417 0,
49418 (iternextfunc) __Pyx_Generator_Next,
49419 __pyx_Generator_methods,
49420 __pyx_Generator_memberlist,
49421 __pyx_Generator_getsets,
49422 0,
49423 0,
49424 0,
49425 0,
49426 0,
49427 0,
49428 0,
49429 0,
49430 0,
49431 0,
49432 0,
49433 0,
49434 0,
49435 0,
49436 0,
49437 #if CYTHON_USE_TP_FINALIZE
49438 0,
49439 #else
49440 __Pyx_Coroutine_del,
49441 #endif
49442 0,
49443 #if CYTHON_USE_TP_FINALIZE
49444 __Pyx_Coroutine_del,
49445 #elif PY_VERSION_HEX >= 0x030400a1
49446 0,
49447 #endif
49448 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
49449 0,
49450 #endif
49451 #if __PYX_NEED_TP_PRINT_SLOT
49452 0,
49453 #endif
49454 #if PY_VERSION_HEX >= 0x030C0000
49455 0,
49456 #endif
49457 #if PY_VERSION_HEX >= 0x030d00A4
49458 0,
49459 #endif
49460 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
49461 0,
49462 #endif
49463 };
49464 #endif
49465 static int __pyx_Generator_init(PyObject *module) {
49466 #if CYTHON_USE_TYPE_SPECS
49467 __pyx_GeneratorType = __Pyx_FetchCommonTypeFromSpec(module, &__pyx_GeneratorType_spec, NULL);
49468 #else
49469 CYTHON_UNUSED_VAR(module);
49470 __pyx_GeneratorType_type.tp_getattro = __Pyx_PyObject_GenericGetAttrNoDict;
49471 __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
49472 __pyx_GeneratorType = __Pyx_FetchCommonType(&__pyx_GeneratorType_type);
49473 #endif
49474 if (unlikely(!__pyx_GeneratorType)) {
49475 return -1;
49476 }
49477 return 0;
49478 }
49479
49480 /* CheckBinaryVersion */
49481 static unsigned long __Pyx_get_runtime_version(void) {
49482 #if __PYX_LIMITED_VERSION_HEX >= 0x030B00A4
49483 return Py_Version & ~0xFFUL;
49484 #else
49485 const char* rt_version = Py_GetVersion();
49486 unsigned long version = 0;
49487 unsigned long factor = 0x01000000UL;
49488 unsigned int digit = 0;
49489 int i = 0;
49490 while (factor) {
49491 while ('0' <= rt_version[i] && rt_version[i] <= '9') {
49492 digit = digit * 10 + (unsigned int) (rt_version[i] - '0');
49493 ++i;
49494 }
49495 version += factor * digit;
49496 if (rt_version[i] != '.')
49497 break;
49498 digit = 0;
49499 factor >>= 8;
49500 ++i;
49501 }
49502 return version;
49503 #endif
49504 }
49505 static int __Pyx_check_binary_version(unsigned long ct_version, unsigned long rt_version, int allow_newer) {
49506 const unsigned long MAJOR_MINOR = 0xFFFF0000UL;
49507 if ((rt_version & MAJOR_MINOR) == (ct_version & MAJOR_MINOR))
49508 return 0;
49509 if (likely(allow_newer && (rt_version & MAJOR_MINOR) > (ct_version & MAJOR_MINOR)))
49510 return 1;
49511 {
49512 char message[200];
49513 PyOS_snprintf(message, sizeof(message),
49514 "compile time Python version %d.%d "
49515 "of module '%.100s' "
49516 "%s "
49517 "runtime version %d.%d",
49518 (int) (ct_version >> 24), (int) ((ct_version >> 16) & 0xFF),
49519 __Pyx_MODULE_NAME,
49520 (allow_newer) ? "was newer than" : "does not match",
49521 (int) (rt_version >> 24), (int) ((rt_version >> 16) & 0xFF)
49522 );
49523 return PyErr_WarnEx(NULL, message, 1);
49524 }
49525 }
49526
49527 /* FunctionImport */
49528 #ifndef __PYX_HAVE_RT_ImportFunction_3_0_11
49529 #define __PYX_HAVE_RT_ImportFunction_3_0_11
49530 static int __Pyx_ImportFunction_3_0_11(PyObject *module, const char *funcname, void (**f)(void), const char *sig) {
49531 PyObject *d = 0;
49532 PyObject *cobj = 0;
49533 union {
49534 void (*fp)(void);
49535 void *p;
49536 } tmp;
49537 d = PyObject_GetAttrString(module, (char *)"__pyx_capi__");
49538 if (!d)
49539 goto bad;
49540 cobj = PyDict_GetItemString(d, funcname);
49541 if (!cobj) {
49542 PyErr_Format(PyExc_ImportError,
49543 "%.200s does not export expected C function %.200s",
49544 PyModule_GetName(module), funcname);
49545 goto bad;
49546 }
49547 if (!PyCapsule_IsValid(cobj, sig)) {
49548 PyErr_Format(PyExc_TypeError,
49549 "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)",
49550 PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj));
49551 goto bad;
49552 }
49553 tmp.p = PyCapsule_GetPointer(cobj, sig);
49554 *f = tmp.fp;
49555 if (!(*f))
49556 goto bad;
49557 Py_DECREF(d);
49558 return 0;
49559 bad:
49560 Py_XDECREF(d);
49561 return -1;
49562 }
49563 #endif
49564
49565 /* InitStrings */
49566 #if PY_MAJOR_VERSION >= 3
49567 static int __Pyx_InitString(__Pyx_StringTabEntry t, PyObject **str) {
49568 if (t.is_unicode | t.is_str) {
49569 if (t.intern) {
49570 *str = PyUnicode_InternFromString(t.s);
49571 } else if (t.encoding) {
49572 *str = PyUnicode_Decode(t.s, t.n - 1, t.encoding, NULL);
49573 } else {
49574 *str = PyUnicode_FromStringAndSize(t.s, t.n - 1);
49575 }
49576 } else {
49577 *str = PyBytes_FromStringAndSize(t.s, t.n - 1);
49578 }
49579 if (!*str)
49580 return -1;
49581 if (PyObject_Hash(*str) == -1)
49582 return -1;
49583 return 0;
49584 }
49585 #endif
49586 static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
49587 while (t->p) {
49588 #if PY_MAJOR_VERSION >= 3
49589 __Pyx_InitString(*t, t->p);
49590 #else
49591 if (t->is_unicode) {
49592 *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
49593 } else if (t->intern) {
49594 *t->p = PyString_InternFromString(t->s);
49595 } else {
49596 *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
49597 }
49598 if (!*t->p)
49599 return -1;
49600 if (PyObject_Hash(*t->p) == -1)
49601 return -1;
49602 #endif
49603 ++t;
49604 }
49605 return 0;
49606 }
49607
49608 #include <string.h>
49609 static CYTHON_INLINE Py_ssize_t __Pyx_ssize_strlen(const char *s) {
49610 size_t len = strlen(s);
49611 if (unlikely(len > (size_t) PY_SSIZE_T_MAX)) {
49612 PyErr_SetString(PyExc_OverflowError, "byte string is too long");
49613 return -1;
49614 }
49615 return (Py_ssize_t) len;
49616 }
49617 static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
49618 Py_ssize_t len = __Pyx_ssize_strlen(c_str);
49619 if (unlikely(len < 0)) return NULL;
49620 return __Pyx_PyUnicode_FromStringAndSize(c_str, len);
49621 }
49622 static CYTHON_INLINE PyObject* __Pyx_PyByteArray_FromString(const char* c_str) {
49623 Py_ssize_t len = __Pyx_ssize_strlen(c_str);
49624 if (unlikely(len < 0)) return NULL;
49625 return PyByteArray_FromStringAndSize(c_str, len);
49626 }
49627 static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) {
49628 Py_ssize_t ignore;
49629 return __Pyx_PyObject_AsStringAndSize(o, &ignore);
49630 }
49631 #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
49632 #if !CYTHON_PEP393_ENABLED
49633 static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
49634 char* defenc_c;
49635 PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
49636 if (!defenc) return NULL;
49637 defenc_c = PyBytes_AS_STRING(defenc);
49638 #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
49639 {
49640 char* end = defenc_c + PyBytes_GET_SIZE(defenc);
49641 char* c;
49642 for (c = defenc_c; c < end; c++) {
49643 if ((unsigned char) (*c) >= 128) {
49644 PyUnicode_AsASCIIString(o);
49645 return NULL;
49646 }
49647 }
49648 }
49649 #endif
49650 *length = PyBytes_GET_SIZE(defenc);
49651 return defenc_c;
49652 }
49653 #else
49654 static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
49655 if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL;
49656 #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
49657 if (likely(PyUnicode_IS_ASCII(o))) {
49658 *length = PyUnicode_GET_LENGTH(o);
49659 return PyUnicode_AsUTF8(o);
49660 } else {
49661 PyUnicode_AsASCIIString(o);
49662 return NULL;
49663 }
49664 #else
49665 return PyUnicode_AsUTF8AndSize(o, length);
49666 #endif
49667 }
49668 #endif
49669 #endif
49670 static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
49671 #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
49672 if (
49673 #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
49674 __Pyx_sys_getdefaultencoding_not_ascii &&
49675 #endif
49676 PyUnicode_Check(o)) {
49677 return __Pyx_PyUnicode_AsStringAndSize(o, length);
49678 } else
49679 #endif
49680 #if (!CYTHON_COMPILING_IN_PYPY && !CYTHON_COMPILING_IN_LIMITED_API) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE))
49681 if (PyByteArray_Check(o)) {
49682 *length = PyByteArray_GET_SIZE(o);
49683 return PyByteArray_AS_STRING(o);
49684 } else
49685 #endif
49686 {
49687 char* result;
49688 int r = PyBytes_AsStringAndSize(o, &result, length);
49689 if (unlikely(r < 0)) {
49690 return NULL;
49691 } else {
49692 return result;
49693 }
49694 }
49695 }
49696 static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
49697 int is_true = x == Py_True;
49698 if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
49699 else return PyObject_IsTrue(x);
49700 }
49701 static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) {
49702 int retval;
49703 if (unlikely(!x)) return -1;
49704 retval = __Pyx_PyObject_IsTrue(x);
49705 Py_DECREF(x);
49706 return retval;
49707 }
49708 static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) {
49709 __Pyx_TypeName result_type_name = __Pyx_PyType_GetName(Py_TYPE(result));
49710 #if PY_MAJOR_VERSION >= 3
49711 if (PyLong_Check(result)) {
49712 if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1,
49713 "__int__ returned non-int (type " __Pyx_FMT_TYPENAME "). "
49714 "The ability to return an instance of a strict subclass of int is deprecated, "
49715 "and may be removed in a future version of Python.",
49716 result_type_name)) {
49717 __Pyx_DECREF_TypeName(result_type_name);
49718 Py_DECREF(result);
49719 return NULL;
49720 }
49721 __Pyx_DECREF_TypeName(result_type_name);
49722 return result;
49723 }
49724 #endif
49725 PyErr_Format(PyExc_TypeError,
49726 "__%.4s__ returned non-%.4s (type " __Pyx_FMT_TYPENAME ")",
49727 type_name, type_name, result_type_name);
49728 __Pyx_DECREF_TypeName(result_type_name);
49729 Py_DECREF(result);
49730 return NULL;
49731 }
49732 static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
49733 #if CYTHON_USE_TYPE_SLOTS
49734 PyNumberMethods *m;
49735 #endif
49736 const char *name = NULL;
49737 PyObject *res = NULL;
49738 #if PY_MAJOR_VERSION < 3
49739 if (likely(PyInt_Check(x) || PyLong_Check(x)))
49740 #else
49741 if (likely(PyLong_Check(x)))
49742 #endif
49743 return __Pyx_NewRef(x);
49744 #if CYTHON_USE_TYPE_SLOTS
49745 m = Py_TYPE(x)->tp_as_number;
49746 #if PY_MAJOR_VERSION < 3
49747 if (m && m->nb_int) {
49748 name = "int";
49749 res = m->nb_int(x);
49750 }
49751 else if (m && m->nb_long) {
49752 name = "long";
49753 res = m->nb_long(x);
49754 }
49755 #else
49756 if (likely(m && m->nb_int)) {
49757 name = "int";
49758 res = m->nb_int(x);
49759 }
49760 #endif
49761 #else
49762 if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) {
49763 res = PyNumber_Int(x);
49764 }
49765 #endif
49766 if (likely(res)) {
49767 #if PY_MAJOR_VERSION < 3
49768 if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) {
49769 #else
49770 if (unlikely(!PyLong_CheckExact(res))) {
49771 #endif
49772 return __Pyx_PyNumber_IntOrLongWrongResultType(res, name);
49773 }
49774 }
49775 else if (!PyErr_Occurred()) {
49776 PyErr_SetString(PyExc_TypeError,
49777 "an integer is required");
49778 }
49779 return res;
49780 }
49781 static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
49782 Py_ssize_t ival;
49783 PyObject *x;
49784 #if PY_MAJOR_VERSION < 3
49785 if (likely(PyInt_CheckExact(b))) {
49786 if (sizeof(Py_ssize_t) >= sizeof(long))
49787 return PyInt_AS_LONG(b);
49788 else
49789 return PyInt_AsSsize_t(b);
49790 }
49791 #endif
49792 if (likely(PyLong_CheckExact(b))) {
49793 #if CYTHON_USE_PYLONG_INTERNALS
49794 if (likely(__Pyx_PyLong_IsCompact(b))) {
49795 return __Pyx_PyLong_CompactValue(b);
49796 } else {
49797 const digit* digits = __Pyx_PyLong_Digits(b);
49798 const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(b);
49799 switch (size) {
49800 case 2:
49801 if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
49802 return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
49803 }
49804 break;
49805 case -2:
49806 if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
49807 return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
49808 }
49809 break;
49810 case 3:
49811 if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
49812 return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
49813 }
49814 break;
49815 case -3:
49816 if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
49817 return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
49818 }
49819 break;
49820 case 4:
49821 if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
49822 return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
49823 }
49824 break;
49825 case -4:
49826 if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
49827 return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
49828 }
49829 break;
49830 }
49831 }
49832 #endif
49833 return PyLong_AsSsize_t(b);
49834 }
49835 x = PyNumber_Index(b);
49836 if (!x) return -1;
49837 ival = PyInt_AsSsize_t(x);
49838 Py_DECREF(x);
49839 return ival;
49840 }
49841 static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) {
49842 if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) {
49843 return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o);
49844 #if PY_MAJOR_VERSION < 3
49845 } else if (likely(PyInt_CheckExact(o))) {
49846 return PyInt_AS_LONG(o);
49847 #endif
49848 } else {
49849 Py_ssize_t ival;
49850 PyObject *x;
49851 x = PyNumber_Index(o);
49852 if (!x) return -1;
49853 ival = PyInt_AsLong(x);
49854 Py_DECREF(x);
49855 return ival;
49856 }
49857 }
49858 static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) {
49859 return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False);
49860 }
49861 static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
49862 return PyInt_FromSize_t(ival);
49863 }
49864
49865
49866 /* #### Code section: utility_code_pragmas_end ### */
49867 #ifdef _MSC_VER
49868 #pragma warning( pop )
49869 #endif
49870
49871
49872
49873 /* #### Code section: end ### */
49874 #endif /* Py_PYTHON_H */