jpayne@68: # cython: language_level=3
jpayne@68: from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
jpayne@68: from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
jpayne@68: from libc.stdlib cimport malloc, calloc, realloc, free
jpayne@68: from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup
jpayne@68: from libc.stdio cimport FILE, printf
jpayne@68: cimport cython
jpayne@68: 
jpayne@68: from cpython cimport array
jpayne@68: from pysam.libchtslib cimport faidx_t, kstring_t, BGZF
jpayne@68: 
jpayne@68: # These functions are put here and not in chtslib.pxd in order
jpayne@68: # to avoid warnings for unused functions.
jpayne@68: cdef extern from "pysam_stream.h" nogil:
jpayne@68: 
jpayne@68:     ctypedef struct kstream_t:
jpayne@68:         pass
jpayne@68: 
jpayne@68:     ctypedef struct kseq_t:
jpayne@68:         kstring_t name
jpayne@68:         kstring_t comment
jpayne@68:         kstring_t seq
jpayne@68:         kstring_t qual
jpayne@68: 
jpayne@68:     kseq_t *kseq_init(BGZF *)
jpayne@68:     int kseq_read(kseq_t *)
jpayne@68:     void kseq_destroy(kseq_t *)
jpayne@68:     kstream_t *ks_init(BGZF *)
jpayne@68:     void ks_destroy(kstream_t *)
jpayne@68: 
jpayne@68:     # Retrieve characters from stream until delimiter
jpayne@68:     # is reached placing results in str.
jpayne@68:     int ks_getuntil(kstream_t *,
jpayne@68:                     int delimiter,
jpayne@68:                     kstring_t * str,
jpayne@68:                     int * dret)
jpayne@68: 
jpayne@68: cdef class FastaFile:
jpayne@68:     cdef bint is_remote
jpayne@68:     cdef object _filename, _references, _lengths, reference2length
jpayne@68:     cdef faidx_t* fastafile
jpayne@68:     cdef char* _fetch(self, char* reference,
jpayne@68:                       int start, int end, int* length) except? NULL
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class FastqProxy:
jpayne@68:     cdef kseq_t * _delegate
jpayne@68:     cdef cython.str to_string(self)
jpayne@68:     cdef cython.str tostring(self)
jpayne@68:     cpdef array.array get_quality_array(self, int offset=*)
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class FastxRecord:
jpayne@68:     """
jpayne@68:     Python container for pysam.libcfaidx.FastqProxy with persistence.
jpayne@68:     """
jpayne@68:     cdef public str comment, quality, sequence, name
jpayne@68:     cdef cython.str to_string(self)
jpayne@68:     cdef cython.str tostring(self)
jpayne@68:     cpdef array.array get_quality_array(self, int offset=*)
jpayne@68: 
jpayne@68: cdef class FastxFile:
jpayne@68:     cdef object _filename
jpayne@68:     cdef BGZF * fastqfile
jpayne@68:     cdef kseq_t * entry
jpayne@68:     cdef bint persist
jpayne@68:     cdef bint is_remote
jpayne@68: 
jpayne@68:     cdef kseq_t * getCurrent(self)
jpayne@68:     cdef int cnext(self)
jpayne@68: 
jpayne@68: 
jpayne@68: # Compatibility Layer for pysam 0.8.1
jpayne@68: cdef class FastqFile(FastxFile):
jpayne@68:     pass
jpayne@68: 
jpayne@68: 
jpayne@68: # Compatibility Layer for pysam < 0.8
jpayne@68: cdef class Fastafile(FastaFile):
jpayne@68:     pass
jpayne@68: