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bug fix for read duplication with nproc > 1 #80

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bug fix for read duplication with nproc > 1 #80

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bbce71d
bug fix for read duplication that occurs for reads spanning chunk bou…
blake-bowen Jun 18, 2026
85733b1
bug fix for read duplication - use `and` instead of chained comparison
blake-bowen Jun 18, 2026
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3 changes: 3 additions & 0 deletions sinto/filterbarcodes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,9 @@ def _iterate_reads(
bamlist = [pysam.AlignmentFile(x, filemode, header=newhead) for x in filelist]
for i in intervals:
for r in inputBam.fetch(i[0], i[1], i[2]):
# skip reads owned by the previous chunk (fetch returns overlaps); unmapped reads have reference_start < 0
if r.reference_start >= 0 and r.reference_start < i[1]:
continue
if readname_barcode is not None:
re_match = readname_barcode.search(r.qname)
cell_barcode = re_match.group()
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