Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libctabixproxies.pxd @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@69 | 1 # cython: language_level=3 |
| jpayne@69 | 2 |
| jpayne@69 | 3 from libc.stdint cimport uint8_t, int32_t, uint32_t, int64_t, uint64_t |
| jpayne@69 | 4 |
| jpayne@69 | 5 cdef class TupleProxy: |
| jpayne@69 | 6 |
| jpayne@69 | 7 cdef: |
| jpayne@69 | 8 char * data |
| jpayne@69 | 9 char ** fields |
| jpayne@69 | 10 int nfields |
| jpayne@69 | 11 int nbytes |
| jpayne@69 | 12 int offset |
| jpayne@69 | 13 bint is_modified |
| jpayne@69 | 14 |
| jpayne@69 | 15 cdef encoding |
| jpayne@69 | 16 |
| jpayne@69 | 17 cpdef int getMaxFields(self) |
| jpayne@69 | 18 cpdef int getMinFields(self) |
| jpayne@69 | 19 # cdef char * _getindex(self, int idx) |
| jpayne@69 | 20 |
| jpayne@69 | 21 cdef take(self, char * buffer, size_t nbytes) |
| jpayne@69 | 22 cdef present(self, char * buffer, size_t nbytes) |
| jpayne@69 | 23 cdef copy(self, char * buffer, size_t nbytes, bint reset=*) |
| jpayne@69 | 24 cdef update(self, char * buffer, size_t nbytes) |
| jpayne@69 | 25 |
| jpayne@69 | 26 |
| jpayne@69 | 27 cdef class TupleProxyIterator: |
| jpayne@69 | 28 cdef TupleProxy proxy |
| jpayne@69 | 29 cdef int index |
| jpayne@69 | 30 |
| jpayne@69 | 31 |
| jpayne@69 | 32 cdef class NamedTupleProxy(TupleProxy): |
| jpayne@69 | 33 pass |
| jpayne@69 | 34 |
| jpayne@69 | 35 |
| jpayne@69 | 36 cdef class GTFProxy(NamedTupleProxy): |
| jpayne@69 | 37 cdef object attribute_dict |
| jpayne@69 | 38 cpdef int getMaxFields(self) |
| jpayne@69 | 39 cpdef int getMinFields(self) |
| jpayne@69 | 40 |
| jpayne@69 | 41 |
| jpayne@69 | 42 cdef class GFF3Proxy(GTFProxy): |
| jpayne@69 | 43 pass |
| jpayne@69 | 44 |
| jpayne@69 | 45 |
| jpayne@69 | 46 cdef class BedProxy(NamedTupleProxy): |
| jpayne@69 | 47 |
| jpayne@69 | 48 cdef: |
| jpayne@69 | 49 char * contig |
| jpayne@69 | 50 uint32_t start |
| jpayne@69 | 51 uint32_t end |
| jpayne@69 | 52 int bedfields |
| jpayne@69 | 53 |
| jpayne@69 | 54 cpdef int getMaxFields(self) |
| jpayne@69 | 55 cpdef int getMinFields(self) |
| jpayne@69 | 56 cdef update(self, char * buffer, size_t nbytes) |
| jpayne@69 | 57 |
| jpayne@69 | 58 cdef class VCFProxy(NamedTupleProxy) : |
| jpayne@69 | 59 |
| jpayne@69 | 60 cdef: |
| jpayne@69 | 61 char * contig |
| jpayne@69 | 62 uint32_t pos |
| jpayne@69 | 63 |
| jpayne@69 | 64 cdef update(self, char * buffer, size_t nbytes) |