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in read_utils.py::align_and_fix(), remove supplementary alignments before indel realignment #41

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in read_utils.py::align_and_fix(), remove supplementary alignments before indel realignment #41

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3cb46b3
in read_utils.py::align_and_fix(), remove supplementary alignments be…
tomkinsc Nov 16, 2020
2d1d922
Merge branch 'master' into ct-align_and_fix_without_supplementary_ali…
tomkinsc Dec 6, 2020
7800bd6
Merge branch 'master' into ct-align_and_fix_without_supplementary_ali…
tomkinsc Mar 12, 2024
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22 changes: 17 additions & 5 deletions read_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1182,6 +1182,7 @@ def align_and_fix(
JVMmemory=None,
threads=None,
skip_mark_dupes=False,
include_supplementary_mappings=False,
gatk_path=None,
novoalign_license_path=None
):
Expand Down Expand Up @@ -1245,15 +1246,22 @@ def align_and_fix(
JVMmemory=JVMmemory
)
os.unlink(bam_aligned)

samtools.index(bam_marked)

if samtools.isEmpty(bam_marked):
bam_realigned = bam_marked
if include_supplementary_mappings:
bam_to_be_realigned = bam_marked
else:
bam_realigned = mkstempfname('.realigned.bam')
tools.gatk.GATKTool(path=gatk_path).local_realign(bam_marked, refFastaCopy, bam_realigned, JVMmemory=JVMmemory, threads=threads)
bam_to_be_realigned = mkstempfname('.rmsupplementalmaps.bam')
samtools.view(['-b', '-F', '2048'], bam_marked, bam_to_be_realigned)
os.unlink(bam_marked)
samtools.index(bam_to_be_realigned)

if samtools.isEmpty(bam_to_be_realigned):
bam_realigned = bam_to_be_realigned
else:
bam_realigned = mkstempfname('.realigned.bam')
tools.gatk.GATKTool(path=gatk_path).local_realign(bam_to_be_realigned, refFastaCopy, bam_realigned, JVMmemory=JVMmemory, threads=threads)
os.unlink(bam_to_be_realigned)

if outBamAll:
shutil.copyfile(bam_realigned, outBamAll)
Expand Down Expand Up @@ -1297,6 +1305,10 @@ def parser_align_and_fix(parser=argparse.ArgumentParser()):
help='If specified, duplicate reads will not be marked in the resulting output file.',
dest="skip_mark_dupes",
action='store_true')
parser.add_argument('--includeSupplementaryMappings',
help='If specified, supplementary read mappings will be included.',
dest="include_supplementary_mappings",
action='store_true')
parser.add_argument(
'--GATK_PATH',
default=None,
Expand Down