X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=pysam%2F__init__.py;h=ec0439f17290876217c610355072aa4f4d074efa;hp=3062753f295cee7d22ba4e86689063905bb01f0a;hb=e1756c41e7a1d7cc01fb95e42df9dd04da2d2991;hpb=aa8ecff068edbb09a03bd874fce716e93e22e53c

diff --git a/pysam/__init__.py b/pysam/__init__.py
index 3062753..ec0439f 100644
--- a/pysam/__init__.py
+++ b/pysam/__init__.py
@@ -1,4 +1,9 @@
 from csamtools import *
+from ctabix import *
+import csamtools
+import ctabix
+from cvcf import *
+import cvcf
 import Pileup
 import sys
 import os
@@ -39,8 +44,8 @@ class SamtoolsDispatcher(object):
         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 ) )
@@ -50,7 +55,12 @@ class SamtoolsDispatcher(object):
         # Note that there is sometimes output on stderr that is not an error,
         # 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]" ) ]
+        stderr = [ x for x in stderr \
+                       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:
@@ -96,6 +106,11 @@ for key, options in SAMTOOLS_DISPATCH.iteritems():
     globals()[key] = SamtoolsDispatcher(cmd, parser)
 
 # hack to export all the symbols from csamtools
-__all__ = csamtools.__all__ + [ "SamtoolsError", "SamtoolsDispatcher" ] + list(SAMTOOLS_DISPATCH) +\
-    ["Pileup",] 
-
+__all__ = \
+    csamtools.__all__ + \
+    ctabix.__all__ + \
+    cvcf.__all__ +\
+    [ "SamtoolsError", "SamtoolsDispatcher" ] + list(SAMTOOLS_DISPATCH) +\
+    ["Pileup" ] 
+
+from version import __version__, __samtools_version__