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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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