/usr/lib/python2.7/dist-packages/pysam/ctabix.pxd is in python-pysam 0.7.7-1ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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ctypedef int size_t
void *memcpy(void *dst,void *src,size_t len)
void *memmove(void *dst,void *src,size_t len)
void *memset(void *b,int c,size_t len)
char *strtok_r(char *str, char *delim, char **saveptr)
char *strncpy(char *dest, char *src, size_t n)
void *memchr(void *s, int c, size_t n)
cdef extern from "stdlib.h":
void free(void *)
void *malloc(size_t)
void *calloc(size_t,size_t)
void *realloc(void *,size_t)
void qsort(void *base, size_t nmemb, size_t size,
int (*compar)(void *,void *))
int c_abs "abs" (int)
int atoi( char *nptr)
long atol( char *nptr)
double atof( char *nptr)
cdef extern from "stdio.h":
ctypedef struct FILE:
pass
FILE *fopen(char *,char *)
FILE *freopen(char *path, char *mode, FILE *stream)
int fileno(FILE *stream)
int dup2(int oldfd, int newfd)
int fflush(FILE *stream)
FILE * stderr
FILE * stdout
int fclose(FILE *)
int sscanf(char *str,char *fmt,...)
int printf(char *str,char *fmt,...)
int sprintf(char *str,char *fmt,...)
int fprintf(FILE *ifile,char *fmt,...)
char *fgets(char *str,int size,FILE *ifile)
cdef extern from "ctype.h":
int toupper(int c)
int tolower(int c)
cdef extern from "sys/types.h":
pass
cdef extern from "sys/stat.h":
pass
cdef extern from "fcntl.h":
int open(char *pathname, int flags)
cdef extern from "unistd.h":
ctypedef int ssize_t
char *ttyname(int fd)
int isatty(int fd)
ssize_t read(int fd, void *buf, size_t count)
cdef extern from "string.h":
int strcmp(char *s1, char *s2)
int strncmp(char *s1,char *s2,size_t len)
char *strcpy(char *dest,char *src)
char *strncpy(char *dest,char *src, size_t len)
char *strdup(char *)
char *strcat(char *,char *)
size_t strlen(char *s)
int memcmp( void * s1, void *s2, size_t len )
cdef extern from "stdint.h":
ctypedef int int64_t
ctypedef int int32_t
ctypedef int uint32_t
ctypedef int uint8_t
ctypedef int uint64_t
cdef extern from "zlib.h":
ctypedef void * gzFile
ctypedef int64_t z_off_t
int gzclose(gzFile fp)
int gzread(gzFile fp, void *buf, unsigned int n)
char *gzerror(gzFile fp, int *errnum)
gzFile gzopen( char *path, char *mode)
gzFile gzdopen (int fd, char *mode)
char * gzgets(gzFile file, char *buf, int len)
int gzeof( gzFile file )
cdef extern from "Python.h":
ctypedef struct FILE
char *fgets(char *str, int size, FILE *ifile)
int feof(FILE *stream)
size_t strlen(char *s)
size_t getline(char **lineptr, size_t *n, FILE *stream)
char *strstr(char *, char *)
char *strchr(char *string, int c)
int fileno(FILE *stream)
FILE *fdopen(int fd, char *mode)
cdef extern from "bgzf.h":
ctypedef struct BGZF:
pass
int64_t bgzf_seek(BGZF* fp, int64_t pos, int where)
BGZF * bgzf_open(char * path, char * mode)
int bgzf_write(BGZF * fp, void* data, int length)
int bgzf_close(BGZF* fp)
# tabix support
cdef extern from "tabix.h":
ctypedef struct ti_conf_t:
int32_t preset
int32_t sc, bc, ec
int32_t meta_char, line_skip
ctypedef struct ti_index_t:
pass
ctypedef struct tabix_t:
BGZF *fp
ti_index_t *idx
char *fn
char *fnidx
ctypedef struct ti_iter_t:
pass
tabix_t *ti_open(char *fn, char *fnidx)
int ti_lazy_index_load(tabix_t *t)
void ti_close(tabix_t *t)
ti_iter_t ti_query(tabix_t *t, char *name, int beg, int end)
ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end)
ti_iter_t ti_querys(tabix_t *t, char *reg)
char * ti_read(tabix_t *t, ti_iter_t iter, int *len)
# Get the list of sequence names. Each "char*" pointer points to a
# internal member of the index, so DO NOT modify the returned
# pointer; otherwise the index will be corrupted. The returned
# pointer should be freed by a single free() call by the routine
# calling this function. The number of sequences is returned at *n
char **ti_seqname(ti_index_t *idx, int *n)
# Destroy the iterator
void ti_iter_destroy(ti_iter_t iter)
# Build the index for file <fn>. File <fn>.tbi will be generated
# and overwrite the file of the same name. Return -1 on failure. */
int ti_index_build(char *fn, ti_conf_t *conf)
#/* Load the index from file <fn>.tbi. If <fn> is a URL and the index
# * file is not in the working directory, <fn>.tbi will be
# * downloaded. Return NULL on failure. */
ti_index_t *ti_index_load( char *fn)
ti_index_t *ti_index_load_local(char *fnidx)
#/* Destroy the index */
void ti_index_destroy(ti_index_t *idx)
#/* Parse a region like: chr2, chr2:100, chr2:100-200. Return -1 on failure. */
int ti_parse_region( ti_index_t *idx, char *str, int *tid, int *begin, int *end)
int ti_get_tid( ti_index_t *idx, char *name)
# /* Get the iterator pointing to the first record at the current file
# * position. If the file is just openned, the iterator points to the
# * first record in the file. */
ti_iter_t ti_iter_first()
# /* Get the iterator pointing to the first record in region tid:beg-end */
ti_iter_t ti_iter_query( ti_index_t *idx, int tid, int beg, int end)
# /* Get the data line pointed by the iterator and iterate to the next record. */
# char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
cdef extern from "tabix_util.h":
ctypedef struct kstring_t:
size_t l
size_t m
char * s
ctypedef struct kstream_t:
pass
kstream_t * ks_init( gzFile )
int ks_read( kstream_t * )
void ks_destroy( kstream_t * )
int ks_getuntil( kstream_t *, int, kstring_t *, int * )
cdef class tabix_file_iterator:
cdef gzFile fh
cdef kstream_t * ks
cdef kstring_t buffer
cdef size_t size
cdef Parser parser
cdef int fd
cdef infile
cdef __cnext__(self)
cdef class Tabixfile:
# pointer to tabixfile
cdef tabix_t * tabixfile
# flag indicating whether file is remote
cdef int isremote
cdef char * _filename
cdef Parser parser
cdef class TabixIterator:
cdef ti_iter_t iterator
cdef tabix_t * tabixfile
cdef class TabixHeaderIterator:
cdef ti_iter_t iterator
cdef tabix_t * tabixfile
cdef class Parser:
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 asBed(Parser):
pass
cdef class asVCF(Parser):
pass
cdef class TabixIteratorParsed:
cdef ti_iter_t iterator
cdef tabix_t * tabixfile
cdef Parser parser
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