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"""
Seekable access to BGZ files based on samtools code. Does not yet implement
complete file-like interface.
"""
from cpython.version cimport PY_MAJOR_VERSION
ctypedef unsigned long long int64_t
cdef extern from "Python.h":
char * PyBytes_AsString( object )
object PyBytes_FromStringAndSize( char *, Py_ssize_t )
cdef extern from "bgzf.h":
ctypedef struct BGZF
BGZF * bgzf_open( const char * path, const char * mode )
int bgzf_close( BGZF * fp )
int bgzf_read( BGZF * fp, void * data, int length )
int64_t bgzf_tell( BGZF * fp )
int64_t bgzf_seek( BGZF * fp, int64_t pos, int where )
cdef class BGZFFile( object ):
cdef BGZF * bgzf
def __init__( self, path, mode="r" ):
if PY_MAJOR_VERSION >= 3:
bytes_path, bytes_mode = path.encode(), mode.encode()
else:
bytes_path, bytes_mode = path, mode
self.bgzf = bgzf_open( bytes_path, bytes_mode )
if not self.bgzf:
raise IOError( "Could not open file" )
def close( self ):
if self.bgzf:
bgzf_close( self.bgzf )
def read( self, int length ):
cdef object rval
rval = PyBytes_FromStringAndSize( NULL, length )
bgzf_read( self.bgzf, PyBytes_AsString( rval ), length )
return rval
def tell( self ):
return bgzf_tell( self.bgzf )
def seek( self, int64_t pos, int where=0 ):
return bgzf_seek( self.bgzf, pos, where )
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