From d03b78fc6dc4b2d895a7b3be9610e06e52a95ede Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 12 Jan 2018 14:03:25 -0600
Subject: [PATCH] Fix map qc for paired-end data.
---
workflow/scripts/map_qc.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py
index 3f07068..4cc549f 100644
--- a/workflow/scripts/map_qc.py
+++ b/workflow/scripts/map_qc.py
@@ -34,7 +34,7 @@ STRIP_EXTENSIONS = ['.bam', '.srt']
def get_args():
'''Define arguments.'''
-
+
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -232,7 +232,7 @@ def compute_complexity(bam, paired, bam_basename):
if paired:
steps = [
- "sambamba sort -t %d -n %s" % (cpu_count(), bam),
+ "samtools sort -@%d -n %s" % (cpu_count(), bam),
"bamToBed -bedpe -i stdin",
r"""awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}'"""]
else:
--
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