Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcfaidx.pxd @ 69:33d812a61356
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 # cython: language_level=3 | |
| 2 from libc.stdint cimport int8_t, int16_t, int32_t, int64_t | |
| 3 from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t | |
| 4 from libc.stdlib cimport malloc, calloc, realloc, free | |
| 5 from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup | |
| 6 from libc.stdio cimport FILE, printf | |
| 7 cimport cython | |
| 8 | |
| 9 from cpython cimport array | |
| 10 from pysam.libchtslib cimport faidx_t, kstring_t, BGZF | |
| 11 | |
| 12 # These functions are put here and not in chtslib.pxd in order | |
| 13 # to avoid warnings for unused functions. | |
| 14 cdef extern from "pysam_stream.h" nogil: | |
| 15 | |
| 16 ctypedef struct kstream_t: | |
| 17 pass | |
| 18 | |
| 19 ctypedef struct kseq_t: | |
| 20 kstring_t name | |
| 21 kstring_t comment | |
| 22 kstring_t seq | |
| 23 kstring_t qual | |
| 24 | |
| 25 kseq_t *kseq_init(BGZF *) | |
| 26 int kseq_read(kseq_t *) | |
| 27 void kseq_destroy(kseq_t *) | |
| 28 kstream_t *ks_init(BGZF *) | |
| 29 void ks_destroy(kstream_t *) | |
| 30 | |
| 31 # Retrieve characters from stream until delimiter | |
| 32 # is reached placing results in str. | |
| 33 int ks_getuntil(kstream_t *, | |
| 34 int delimiter, | |
| 35 kstring_t * str, | |
| 36 int * dret) | |
| 37 | |
| 38 cdef class FastaFile: | |
| 39 cdef bint is_remote | |
| 40 cdef object _filename, _references, _lengths, reference2length | |
| 41 cdef faidx_t* fastafile | |
| 42 cdef char* _fetch(self, char* reference, | |
| 43 int start, int end, int* length) except? NULL | |
| 44 | |
| 45 | |
| 46 cdef class FastqProxy: | |
| 47 cdef kseq_t * _delegate | |
| 48 cdef cython.str to_string(self) | |
| 49 cdef cython.str tostring(self) | |
| 50 cpdef array.array get_quality_array(self, int offset=*) | |
| 51 | |
| 52 | |
| 53 cdef class FastxRecord: | |
| 54 """ | |
| 55 Python container for pysam.libcfaidx.FastqProxy with persistence. | |
| 56 """ | |
| 57 cdef public str comment, quality, sequence, name | |
| 58 cdef cython.str to_string(self) | |
| 59 cdef cython.str tostring(self) | |
| 60 cpdef array.array get_quality_array(self, int offset=*) | |
| 61 | |
| 62 cdef class FastxFile: | |
| 63 cdef object _filename | |
| 64 cdef BGZF * fastqfile | |
| 65 cdef kseq_t * entry | |
| 66 cdef bint persist | |
| 67 cdef bint is_remote | |
| 68 | |
| 69 cdef kseq_t * getCurrent(self) | |
| 70 cdef int cnext(self) | |
| 71 | |
| 72 | |
| 73 # Compatibility Layer for pysam 0.8.1 | |
| 74 cdef class FastqFile(FastxFile): | |
| 75 pass | |
| 76 | |
| 77 | |
| 78 # Compatibility Layer for pysam < 0.8 | |
| 79 cdef class Fastafile(FastaFile): | |
| 80 pass | |
| 81 |