jpayne@69: # cython: language_level=3
jpayne@69: from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
jpayne@69: from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
jpayne@69: from libc.stdlib cimport malloc, calloc, realloc, free
jpayne@69: from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup
jpayne@69: from libc.stdio cimport FILE, printf
jpayne@69: 
jpayne@69: # Note: this replaces python "open"!
jpayne@69: cdef extern from "fcntl.h":
jpayne@69:     int open(char *pathname, int flags)
jpayne@69: 
jpayne@69: cdef extern from "unistd.h" nogil:
jpayne@69:     ctypedef int ssize_t
jpayne@69:     ssize_t read(int fd, void *buf, size_t count)
jpayne@69:     int close(int fd)
jpayne@69: 
jpayne@69: from pysam.libchtslib cimport hts_idx_t, hts_itr_t, htsFile, \
jpayne@69:     tbx_t, kstring_t, BGZF, HTSFile
jpayne@69: 
jpayne@69: 
jpayne@69: # These functions are put here and not in chtslib.pxd in order
jpayne@69: # to avoid warnings for unused functions.
jpayne@69: cdef extern from "pysam_stream.h" nogil:
jpayne@69: 
jpayne@69:     ctypedef struct kstream_t:
jpayne@69:         pass
jpayne@69: 
jpayne@69:     ctypedef struct kseq_t:
jpayne@69:         kstring_t name
jpayne@69:         kstring_t comment
jpayne@69:         kstring_t seq
jpayne@69:         kstring_t qual
jpayne@69: 
jpayne@69:     kseq_t *kseq_init(BGZF *)
jpayne@69:     int kseq_read(kseq_t *)
jpayne@69:     void kseq_destroy(kseq_t *)
jpayne@69:     kstream_t *ks_init(BGZF *)
jpayne@69:     void ks_destroy(kstream_t *)
jpayne@69: 
jpayne@69:     # Retrieve characters from stream until delimiter
jpayne@69:     # is reached placing results in str.
jpayne@69:     int ks_getuntil(kstream_t *,
jpayne@69:                     int delimiter,
jpayne@69:                     kstring_t * str,
jpayne@69:                     int * dret)
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class tabix_file_iterator:
jpayne@69:     cdef BGZF * fh
jpayne@69:     cdef kstream_t * kstream
jpayne@69:     cdef kstring_t buffer
jpayne@69:     cdef size_t size
jpayne@69:     cdef Parser parser
jpayne@69:     cdef int fd
jpayne@69:     cdef int duplicated_fd
jpayne@69:     cdef infile
jpayne@69: 
jpayne@69:     cdef __cnext__(self)
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class TabixFile(HTSFile):
jpayne@69:     # pointer to index structure
jpayne@69:     cdef tbx_t * index
jpayne@69: 
jpayne@69:     cdef readonly object filename_index
jpayne@69: 
jpayne@69:     cdef Parser parser
jpayne@69: 
jpayne@69:     cdef encoding    
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class Parser:
jpayne@69:     cdef encoding
jpayne@69:     cdef parse(self, char * buffer, int len)
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class asTuple(Parser):
jpayne@69:     cdef parse(self, char * buffer, int len)
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class asGTF(Parser):
jpayne@69:     pass
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class asGFF3(Parser):
jpayne@69:     pass
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class asBed(Parser):
jpayne@69:     pass
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class asVCF(Parser):
jpayne@69:     pass
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class TabixIterator:
jpayne@69:     cdef hts_itr_t * iterator
jpayne@69:     cdef TabixFile tabixfile
jpayne@69:     cdef kstring_t buffer
jpayne@69:     cdef encoding
jpayne@69:     cdef int __cnext__(self)
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class TabixIteratorParsed(TabixIterator):
jpayne@69:     cdef Parser parser
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class GZIterator:
jpayne@69:     cdef object _filename
jpayne@69:     cdef BGZF * gzipfile
jpayne@69:     cdef kstream_t * kstream
jpayne@69:     cdef kstring_t buffer
jpayne@69:     cdef int __cnext__(self)
jpayne@69:     cdef encoding
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class GZIteratorHead(GZIterator):
jpayne@69:     pass
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class GZIteratorParsed(GZIterator):
jpayne@69:     cdef Parser parser
jpayne@69: 
jpayne@69: 
jpayne@69: # Compatibility Layer for pysam < 0.8
jpayne@69: cdef class Tabixfile(TabixFile):
jpayne@69:     pass