Imported Upstream version 0.3.1

[pysam.git] / pysam / __init__.py

diff --git a/pysam/__init__.py b/pysam/__init__.py
index 9f257c210eca878b0f0039b40f724f3482937284..282ef290770aad31aa1bbba8c3ebd1e1759263ab 100644 (file)
--- a/pysam/__init__.py
+++ b/pysam/__init__.py
@@ -55,7 +55,10 @@ class SamtoolsDispatcher(object):
         # Ignore messages like these
         stderr = [ x for x in stderr \
                        if not x.startswith( "[sam_header_read2]" ) or \
-                       x.startswith("[bam_index_load]") ]
+                       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: