From 5435d541c0c75567ce5f91f465e68e587019cb33 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 23 Oct 2017 10:22:17 -0500
Subject: [PATCH] Fix output copu.
---
workflow/scripts/convert_reads.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py
index 8c090ae..e091296 100644
--- a/workflow/scripts/convert_reads.py
+++ b/workflow/scripts/convert_reads.py
@@ -30,7 +30,7 @@ def get_args():
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-b', '--bam',
- help="The bam file to run filtering and qc on.",
+ help="The bam file to convert.",
required=True)
parser.add_argument('-p', '--paired',
@@ -116,7 +116,7 @@ def main():
convert_mapped_pe(bam, bam_basename)
else:
bedse_filename = bam_basename + ".bedse.gz"
- shutil(tag_filename, bedse_filename)
+ shutil.copy(tag_filename, bedse_filename)
if __name__ == '__main__':
--
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