Mercurial > repos > jeremie > breakdancer_bin
changeset 14:2c3b8a1d8f4b draft
Uploaded
author | jeremie |
---|---|
date | Wed, 02 Jul 2014 10:17:20 -0400 |
parents | 62bf6aed1908 |
children | 18d9c156ecd9 |
files | breakdancer.py |
diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/breakdancer.py Wed Jul 02 10:15:33 2014 -0400 +++ b/breakdancer.py Wed Jul 02 10:17:20 2014 -0400 @@ -21,7 +21,7 @@ parser.add_argument('-g', dest='bedFormat', required=False, help='dump SVs and supporting reads in BED format for GBrowse') parser.add_argument('-l', dest='matePair', required=False, help='analyze Illumina long insert (mate-pair) library') parser.add_argument('-a', dest='sortByLibrary', action='store_true', help='print out copy number and support reads per library rather than per bam', default=False) -parser.add_argument('-h', dest='AFColumn', action='store_true', help='print out Allele Frequency column', default=False) +# parser.add_argument('-h', dest='AFColumn', action='store_true', help='print out Allele Frequency column', default=False) parser.add_argument('-y', dest='scoreFilter', type=int, required=False, help='output score filter', default=30) @@ -165,8 +165,8 @@ cmd += ' -l ' if args.sortByLibrary: cmd += ' -a ' - if args.AFColumn: - cmd += ' -h ' + # if args.AFColumn: + # cmd += ' -h ' execute(cmd, output=args.outputRawFile) # breakdancer2vcf