|
- # cython: language_level=3
- from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
- from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
- from libc.stdlib cimport malloc, calloc, realloc, free
- from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup
- from libc.stdio cimport FILE, printf
- cimport cython
-
- from cpython cimport array
- from pysam.libchtslib cimport faidx_t, kstring_t, BGZF
-
- # These functions are put here and not in chtslib.pxd in order
- # to avoid warnings for unused functions.
- cdef extern from "pysam_stream.h" nogil:
-
- ctypedef struct kstream_t:
- pass
-
- ctypedef struct kseq_t:
- kstring_t name
- kstring_t comment
- kstring_t seq
- kstring_t qual
-
- kseq_t *kseq_init(BGZF *)
- int kseq_read(kseq_t *)
- void kseq_destroy(kseq_t *)
- kstream_t *ks_init(BGZF *)
- void ks_destroy(kstream_t *)
-
- # Retrieve characters from stream until delimiter
- # is reached placing results in str.
- int ks_getuntil(kstream_t *,
- int delimiter,
- kstring_t * str,
- int * dret)
-
- cdef class FastaFile:
- cdef bint is_remote
- cdef object _filename, _references, _lengths, reference2length
- cdef faidx_t* fastafile
- cdef char* _fetch(self, char* reference,
- int start, int end, int* length) except? NULL
-
-
- cdef class FastqProxy:
- cdef kseq_t * _delegate
- cdef cython.str to_string(self)
- cdef cython.str tostring(self)
- cpdef array.array get_quality_array(self, int offset=*)
-
-
- cdef class FastxRecord:
- """
- Python container for pysam.libcfaidx.FastqProxy with persistence.
- """
- cdef public str comment, quality, sequence, name
- cdef cython.str to_string(self)
- cdef cython.str tostring(self)
- cpdef array.array get_quality_array(self, int offset=*)
-
- cdef class FastxFile:
- cdef object _filename
- cdef BGZF * fastqfile
- cdef kseq_t * entry
- cdef bint persist
- cdef bint is_remote
-
- cdef kseq_t * getCurrent(self)
- cdef int cnext(self)
-
-
- # Compatibility Layer for pysam 0.8.1
- cdef class FastqFile(FastxFile):
- pass
-
-
- # Compatibility Layer for pysam < 0.8
- cdef class Fastafile(FastaFile):
- pass
|
