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Changed the intermediate files written during SplitBamByCellBarcodes from BAM to SAM #79

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merged 2 commits into from
Jul 28, 2020
Merged

Changed the intermediate files written during SplitBamByCellBarcodes from BAM to SAM #79

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changed the intermediate bam file writing of the SplitBam command to …
kishorikonwar Jul 20, 2020
200a032
changed the intermediate bam file writing of the SplitBam command to …
kishorikonwar Jul 20, 2020
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7 changes: 2 additions & 5 deletions src/sctools/bam.py
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Original file line number Diff line number Diff line change
Expand Up @@ -325,11 +325,8 @@ def write_barcodes_to_bins(
for i in range(len(bins)):
out_bam_name = os.path.join(f"{dirname}", f"{dirname}_{i}.bam")
filepaths.append(out_bam_name)
# For now, bam writing uses one thread for compression. Better logic could support more processes without
# starving the machine for resources
open_bam = pysam.AlignmentFile(
out_bam_name, "wb", template=input_alignments
)

open_bam = pysam.AlignmentFile(out_bam_name, "w", template=input_alignments)
files.append(open_bam)

# Loop over input; check each tag in priority order and partition barcodes into files based
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