X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=pysam%2Fctabix.pxd;fp=pysam%2Fctabix.pxd;h=ef735b64f9230f8851b1ab147a77fcad2835ce1b;hp=0000000000000000000000000000000000000000;hb=6a7c3f175b210cc16d09a5e8e4c1d47333dbe1c6;hpb=aa8ecff068edbb09a03bd874fce716e93e22e53c

diff --git a/pysam/ctabix.pxd b/pysam/ctabix.pxd
new file mode 100644
index 0000000..ef735b6
--- /dev/null
+++ b/pysam/ctabix.pxd
@@ -0,0 +1,171 @@
+
+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)