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Commit adf18e06 authored by Venkat Malladi's avatar Venkat Malladi
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Update incorrect line break.

parent 7d54e3fe
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1 merge request!6Resolve "Bam Stats and Filter"
Pipeline #1055 failed with stage
in 54 minutes and 20 seconds
......@@ -194,7 +194,7 @@ def dedup_mapped(bam, bam_basename, paired):
# Generate mapping statistics
final_bam_file_mapstats_filename = final_bam_prefix + ".flagstat.qc"
with open(final_bam_file_mapstats_filename, 'w') as fh:
flagstat_command = "sambamba flagstat -t %d %s"
flagstat_command = "sambamba flagstat -t %d %s" \
% (cpu_count(), final_bam_filename)
logger.info(flagstat_command)
subprocess.check_call(shlex.split(flagstat_command), stdout=fh)
......
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