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Imported Upstream version 0.5
[pysam.git]
/
pysam
/
__init__.py
diff --git
a/pysam/__init__.py
b/pysam/__init__.py
index 9f257c210eca878b0f0039b40f724f3482937284..ec0439f17290876217c610355072aa4f4d074efa 100644
(file)
--- a/
pysam/__init__.py
+++ b/
pysam/__init__.py
@@
-2,6
+2,8
@@
from csamtools import *
from ctabix import *
import csamtools
import ctabix
from ctabix import *
import csamtools
import ctabix
+from cvcf import *
+import cvcf
import Pileup
import sys
import os
import Pileup
import sys
import os
@@
-42,8
+44,8
@@
class SamtoolsDispatcher(object):
self.parsers = parsers
self.stderr = []
self.parsers = parsers
self.stderr = []
- def __call__(self,*args, **kwargs):
- '''execute
the
samtools command
+ def __call__(self,
*args, **kwargs):
+ '''execute
a
samtools command
'''
retval, stderr, stdout = csamtools._samtools_dispatch( self.dispatch, args )
if retval: raise SamtoolsError( "\n".join( stderr ) )
'''
retval, stderr, stdout = csamtools._samtools_dispatch( self.dispatch, args )
if retval: raise SamtoolsError( "\n".join( stderr ) )
@@
-54,8
+56,11
@@
class SamtoolsDispatcher(object):
# for example: [sam_header_read2] 2 sequences loaded.
# Ignore messages like these
stderr = [ x for x in stderr \
# for example: [sam_header_read2] 2 sequences loaded.
# Ignore messages like these
stderr = [ x for x in stderr \
- if not x.startswith( "[sam_header_read2]" ) or \
- x.startswith("[bam_index_load]") ]
+ if not (x.startswith( "[sam_header_read2]" ) or \
+ x.startswith("[bam_index_load]") or \
+ x.startswith("[bam_sort_core]") or \
+ x.startswith("[samopen] SAM header is present") )
+ ]
if stderr: raise SamtoolsError( "\n".join( stderr ) )
# call parser for stdout:
if stderr: raise SamtoolsError( "\n".join( stderr ) )
# call parser for stdout:
@@
-101,9
+106,11
@@
for key, options in SAMTOOLS_DISPATCH.iteritems():
globals()[key] = SamtoolsDispatcher(cmd, parser)
# hack to export all the symbols from csamtools
globals()[key] = SamtoolsDispatcher(cmd, parser)
# hack to export all the symbols from csamtools
-__all__ = csamtools.__all__ + \
+__all__ = \
+ csamtools.__all__ + \
ctabix.__all__ + \
ctabix.__all__ + \
+ cvcf.__all__ +\
[ "SamtoolsError", "SamtoolsDispatcher" ] + list(SAMTOOLS_DISPATCH) +\
[ "SamtoolsError", "SamtoolsDispatcher" ] + list(SAMTOOLS_DISPATCH) +\
- ["Pileup"
,
]
+ ["Pileup"
]
from version import __version__, __samtools_version__
from version import __version__, __samtools_version__