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Commit c46ecd9b authored by Venkat Malladi's avatar Venkat Malladi
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Fix call to check output.

parent d03b78fc
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workflow/scripts/convert_reads.py
+ 2
− 2
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...@@ -25,7 +25,7 @@ logger.setLevel(logging.INFO) ...@@ -25,7 +25,7 @@ logger.setLevel(logging.INFO)
def get_args(): def get_args():
'''Define arguments.''' '''Define arguments.'''
parser = argparse.ArgumentParser( parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG, description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter) formatter_class=argparse.RawDescriptionHelpFormatter)
...@@ -86,7 +86,7 @@ def convert_mapped_pe(bam, bam_basename): ...@@ -86,7 +86,7 @@ def convert_mapped_pe(bam, bam_basename):
% (cpu_count(), nmsrt_bam_filename, bam) % (cpu_count(), nmsrt_bam_filename, bam)
logger.info(samtools_sort_command) 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([ out, err = utils.run_pipe([
"bamToBed -bedpe -mate1 -i %s" % (nmsrt_bam_filename), "bamToBed -bedpe -mate1 -i %s" % (nmsrt_bam_filename),
......
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