From f665a9b04ba650ffa5163cf82e56872ba2dd0a06 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 27 Jun 2018 08:17:36 -0500
Subject: [PATCH] Fix extension.
---
workflow/scripts/convert_reads.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py
index eb805a8..400b916 100644
--- a/workflow/scripts/convert_reads.py
+++ b/workflow/scripts/convert_reads.py
@@ -119,7 +119,7 @@ def convert_mapped_pe(bam, bam_basename, tag_filename, chrm):
tag_steps = ["zcat -f %s" % (bedpe_filename)]
tag_steps.extend([r"""awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}'"""])
if chrm:
- tag_steps.extend["grep -v 'chrM'"]
+ tag_steps.extend(["grep -v 'chrM'"])
tag_steps.extend(['gzip -cn'])
out, err = utils.run_pipe(tag_steps, outfile=tag_filename)
os.remove(bedpe_filename)
--
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