X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=pysam%2FTabProxies.pxd;fp=pysam%2FTabProxies.pxd;h=32597af090b33ad5c474c0231b4e940c073818c7;hp=0000000000000000000000000000000000000000;hb=bd0c3067c187d1f718004fb38acc093af8810a02;hpb=1b740fc70684c92a5e2293013217d5a2fd661d8a

diff --git a/pysam/TabProxies.pxd b/pysam/TabProxies.pxd
new file mode 100644
index 0000000..32597af
--- /dev/null
+++ b/pysam/TabProxies.pxd
@@ -0,0 +1,97 @@
+cdef extern from "stdlib.h":
+    void free(void *)
+    void *malloc(size_t)       
+    void *calloc(size_t,size_t)
+    void *realloc(void *,size_t)
+    int c_abs "abs" (int)  
+    int c_abs "abs" (int)
+    int atoi( char *nptr)
+    long atol( char *nptr)
+    double atof( char *nptr)
+
+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 "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 )
+  void *memcpy(void *dest, void *src, size_t n)
+  void *memchr(void *s, int c, size_t n)
+
+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 class TupleProxy:
+
+    cdef:
+        char * data
+        char ** fields
+        int nfields
+        int index
+        int nbytes
+        int offset
+        cdef bint is_modified
+
+    cdef int getMaxFields( self, size_t nbytes )
+
+    cdef take( self, char * buffer, size_t nbytes )
+    cdef present( self, char * buffer, size_t nbytes )
+    cdef copy( self, char * buffer, size_t nbytes )
+    cdef update( self, char * buffer, size_t nbytes )
+
+cdef class GTFProxy( TupleProxy) :
+
+    cdef:
+        char * contig
+        char * source
+        char * feature
+        uint32_t start
+        uint32_t end
+        char * score
+        char * strand
+        char * frame
+        char * attributes
+        cdef bint hasOwnAttributes
+
+    cdef int getMaxFields( self, size_t nbytes )
+    cdef update( self, char * buffer, size_t nbytes )
+
+cdef class NamedTupleProxy( TupleProxy) :
+    pass
+
+cdef class BedProxy( NamedTupleProxy) :
+
+    cdef:
+        char * contig
+        uint32_t start
+        uint32_t end
+        int bedfields
+
+    cdef int getMaxFields( self, size_t nbytes )
+    cdef update( self, char * buffer, size_t nbytes )
+
+cdef class VCFProxy( NamedTupleProxy) :
+
+    cdef:
+        char * contig
+        uint32_t pos
+
+    cdef update( self, char * buffer, size_t nbytes )