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alignmentSieve: Adding the option to keep the original tags in the processed BAM #1255

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alignmentSieve: Adding the option to keep the original tags in the processed BAM #1255

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2748326
Add the option to keep the tags in the new BAM
samuelruizperez Sep 14, 2023
6acbcb8
Removing extra spaces
samuelruizperez Sep 14, 2023
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7 changes: 7 additions & 0 deletions deeptools/alignmentSieve.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,9 @@ def parseArguments():
output.add_argument('--BED',
action='store_true',
help='Instead of producing BAM files, write output in BEDPE format (as defined by MACS2). Note that only reads/fragments passing filtering criterion are written in BEDPE format.')
output.add_argument('--keepTags',
action='store_true',
help='If set, the original BAM tags will be kept in the output file.')

filtering = parser.add_argument_group('Optional arguments')

Expand Down Expand Up @@ -195,6 +198,10 @@ def shiftRead(b, chromDict, args):
b2.reference_start = start
b2.mapping_quality = b.mapping_quality
b2.cigar = ((0, end - start),) # Returned cigar is only matches

if args.keepTags:
b2.set_tags(b.get_tags(with_value_type=True))

if tLen < 0:
b2.template_length = tLen - deltaTLen
else:
Expand Down