From 2e6340838b9af6b88cf35ef4505013d1ee837f3d Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 7 Oct 2017 08:29:59 -0500
Subject: [PATCH] update samtools flagstat and name of outfile
---
workflow/scripts/map_reads.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index 6ccb5b9..ebce796 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -193,9 +193,9 @@ def main():
align_se(fastq, sai, reference, fastq_basename)
bam_mapstats_filename = '%s.raw.srt.bam.flagstat.qc' % (fastq_basename)
- with open(raw_bam_mapstats_filename, 'w') as fh:
+ with open(bam_mapstats_filename, 'w') as fh:
subprocess.check_call(
- shlex.split("%s flagstat %s" % (samtools, bam_mapstats_filename)),
+ shlex.split("samtools flagstat %s" % (bam_mapstats_filename)),
stdout=fh)
# Remove sai files
--
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