# HG changeset patch
# User jeremie
# Date 1404310640 14400
# Node ID 2c3b8a1d8f4b7ef892bf642dd6e96501781ba08f
# Parent  62bf6aed1908f05cda8906cc017f948c69824f1a
Uploaded

diff -r 62bf6aed1908 -r 2c3b8a1d8f4b breakdancer.py
--- 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