remove expected sam output file, do not redirect stderr to stdout

broadinstitute · Dec 5, 2016 · 83a0886 · 83a0886
1 parent c73a5db
commit 83a0886
Show file tree

Hide file tree

Showing 2 changed files with 1 addition and 44 deletions.
diff --git a/test/input/TestToolSamtools/expected_no_leading_trailing_indel_cigars.sam b/test/input/TestToolSamtools/expected_no_leading_trailing_indel_cigars.sam
diff --git a/tools/samtools.py b/tools/samtools.py
@@ -154,8 +154,7 @@ def filterByCigarString(self, inBam, outBam,
         # an input samtools process to read a bam file
         # bufsize 0=unbuffered, 1=linebuffered, -1=system buffered (usually fully)
         in_process = subprocess.Popen(in_args, bufsize=1, stdout=subprocess.PIPE,
-                                    universal_newlines=True,
-                                    stderr=subprocess.STDOUT)
+                                    universal_newlines=True)
 
         # an output samtools process to write filtered output via stdin
         out_args = [self.install_and_get_path(), 'view', '-h', '-o', outBam]