From c46ecd9b90e3c8c014e0a9ffc6df753f272dab79 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 13 Jan 2018 08:22:51 -0600
Subject: [PATCH] Fix call to check output.
---
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 62faf72..b16964c 100644
--- a/workflow/scripts/convert_reads.py
+++ b/workflow/scripts/convert_reads.py
@@ -25,7 +25,7 @@ logger.setLevel(logging.INFO)
def get_args():
'''Define arguments.'''
-
+
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -86,7 +86,7 @@ def convert_mapped_pe(bam, bam_basename):
% (cpu_count(), nmsrt_bam_filename, bam)
logger.info(samtools_sort_command)
- utils.check_output(shlex.split(samtools_sort_command))
+ subprocess.check_output(shlex.split(samtools_sort_command))
out, err = utils.run_pipe([
"bamToBed -bedpe -mate1 -i %s" % (nmsrt_bam_filename),
--
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