From a3d75d8434ccc1ec41f549f1c92276854aac062a Mon Sep 17 00:00:00 2001
From: Holly Ruess <s185797@biohpcwsc012.biohpc.swmed.edu>
Date: Fri, 27 Dec 2019 08:17:40 -0600
Subject: [PATCH] fix pool and pseudo
---
workflow/scripts/convert_reads.py | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py
index 7191356..e8e5c2c 100644
--- a/workflow/scripts/convert_reads.py
+++ b/workflow/scripts/convert_reads.py
@@ -138,12 +138,11 @@ def main():
utils.strip_extensions(bam, ['.bam', '.dedup']))
tag_filename = bam_basename + '.tagAlign.gz'
+ convert_mapped(bam, tag_filename)
if paired: # paired-end data
- convert_mapped(bam, tag_filename)
convert_mapped_pe(bam, bam_basename, tag_filename)
else:
- convert_mapped(bam, tag_filename)
bedse_filename = bam_basename + ".bedse.gz"
shutil.copy(tag_filename, bedse_filename)
--
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