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# 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
# Note: this replaces python "open"!
cdef extern from "fcntl.h":
int open(char *pathname, int flags)
cdef extern from "unistd.h" nogil:
ctypedef int ssize_t
ssize_t read(int fd, void *buf, size_t count)
int close(int fd)
from pysam.libchtslib cimport hts_idx_t, hts_itr_t, htsFile, \
tbx_t, kstring_t, BGZF, HTSFile
# 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 tabix_file_iterator:
cdef BGZF * fh
cdef kstream_t * kstream
cdef kstring_t buffer
cdef size_t size
cdef Parser parser
cdef int fd
cdef int duplicated_fd
cdef infile
cdef __cnext__(self)
cdef class TabixFile(HTSFile):
# pointer to index structure
cdef tbx_t * index
cdef readonly object filename_index
cdef Parser parser
cdef encoding
cdef class Parser:
cdef encoding
cdef parse(self, char * buffer, int len)
cdef class asTuple(Parser):
cdef parse(self, char * buffer, int len)
cdef class asGTF(Parser):
pass
cdef class asGFF3(Parser):
pass
cdef class asBed(Parser):
pass
cdef class asVCF(Parser):
pass
cdef class TabixIterator:
cdef hts_itr_t * iterator
cdef TabixFile tabixfile
cdef kstring_t buffer
cdef encoding
cdef int __cnext__(self)
cdef class TabixIteratorParsed(TabixIterator):
cdef Parser parser
cdef class GZIterator:
cdef object _filename
cdef BGZF * gzipfile
cdef kstream_t * kstream
cdef kstring_t buffer
cdef int __cnext__(self)
cdef encoding
cdef class GZIteratorHead(GZIterator):
pass
cdef class GZIteratorParsed(GZIterator):
cdef Parser parser
# Compatibility Layer for pysam < 0.8
cdef class Tabixfile(TabixFile):
pass
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