Unverified Commit ae3c49a0 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #12061 from bernt-matthias/topic/pysam-fix 

[21.01] Fix pysam.view call
parents 572584cb 01eba8ee

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', '--no-PG', '-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', '--no-PG', '-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)

test/functional/tools/sam_to_bam.xml

+1 −1
Original line number Diff line number Diff line
@@ -11,7 +11,7 @@ cat '$input1' > '$out_file1' 
    <tests>

        <test>

            <param name="input1" value="sam_with_header.sam" ftype="sam"/>

            <output name="out_file1" file="bam_from_sam.bam"/>

            <output name="out_file1" file="bam_from_sam.bam" ftype="bam"/>

        </test>

    </tests>

    <help>