Mercurial > repos > jeremie > breakdancer_test
changeset 21:199c0c7d3093 draft
Uploaded
author | jeremie |
---|---|
date | Tue, 01 Jul 2014 10:09:33 -0400 |
parents | b122ca66efc7 |
children | b4f641515363 |
files | breakdancer.py |
diffstat | 1 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/breakdancer.py Tue Jul 01 10:09:05 2014 -0400 +++ b/breakdancer.py Tue Jul 01 10:09:33 2014 -0400 @@ -5,6 +5,7 @@ parser = argparse.ArgumentParser(description='') +parser.add_argument('-x', dest='binPath') parser.add_argument ( '-i1', dest='input_bam', help='the bam input file' ) parser.add_argument ( '-o1', dest='output_raw', help='the output file' ) parser.add_argument ( '-o2', dest='output_vcf', help='the output file' ) @@ -14,10 +15,11 @@ errorFile = tmp_dir+"/errorLog" currentDir = os.path.dirname(os.path.abspath(__file__)) -bam2cfg = "./bam2cfg.pl" -# breakdancer = "/usr/bin/breakdancer-max" -breakdancer = "breakdancer-max" -breakdancer2vcf = "./breakdancer2vcf.py" + +binPath = args.binPath +bam2cfg = binPath+"/bam2cfg.pl" +breakdancer = binPath+"/breakdancer-max" +breakdancer2vcf = binPath+"/breakdancer2vcf.py" def bam2cfg(args):