--- /dev/null
+
+cdef extern from "string.h":
+ 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 "Python.h":
+ ctypedef struct FILE
+ FILE* PyFile_AsFile(object)
+ 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)
+
+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_index_t:
+ pass
+
+ ctypedef struct tabix_t:
+ BGZF *fp
+ ti_index_t *idx
+ char *fn
+ char *fnidx
+
+ ctypedef struct ti_iter_t:
+ pass
+
+ ctypedef struct ti_conf_t:
+ int32_t preset
+ int32_t sc, bc, ec
+ int32_t meta_char, line_skip
+
+ 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)
projects / pysam.git / blobdiff