Commit ecbce136 authored by Matthias Bernt's avatar Matthias Bernt
Browse files

fix pysam.view call 

otherwise samtools output is the return value of `pysam.view`
and the output stays empty.

see also https://github.com/pysam-developers/pysam/issues/677
parent 572584cb

lib/galaxy/tool_util/verify/__init__.py

+2 −2
Original line number Diff line number Diff line
@@ -184,12 +184,12 @@ def _bam_to_sam(local_name, temp_name): 
    temp_local = tempfile.NamedTemporaryFile(suffix='.sam', prefix='local_bam_converted_to_sam_')

    with tempfile.NamedTemporaryFile(suffix='.sam', prefix='history_bam_converted_to_sam_', delete=False) as temp:

        try:

            pysam.view('-h', '-o%s' % temp_local.name, local_name)

            pysam.view('-h', '-o', temp_local.name, local_name, catch_stdout=False)

        except Exception as e:

            msg = "Converting local (test-data) BAM to SAM failed: %s" % unicodify(e)

            raise Exception(msg)

        try:

            pysam.view('-h', '-o%s' % temp.name, temp_name)

            pysam.view('-h', '-o', temp.name, temp_name, catch_stdout=False)

        except Exception as e:

            msg = "Converting history BAM to SAM failed: %s" % unicodify(e)

            raise Exception(msg)