# HG changeset patch
# User jeremie
# Date 1404310533 14400
# Node ID 62bf6aed1908f05cda8906cc017f948c69824f1a
# Parent  c220f4acef3f6479e5bab498a98b1316c6b0aa9f
Uploaded

diff -r c220f4acef3f -r 62bf6aed1908 breakdancer.py
--- a/breakdancer.py	Wed Jul 02 10:03:53 2014 -0400
+++ b/breakdancer.py	Wed Jul 02 10:15:33 2014 -0400
@@ -20,8 +20,8 @@
 parser.add_argument('-d', dest='prefix', required=False, help='prefix of fastq files that SV supporting reads will be saved by library')
 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='', action='store_true', help='print out Allele Frequency column', default=False)
+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('-y', dest='scoreFilter', type=int, required=False, help='output score filter', default=30)
 
 
@@ -152,6 +152,21 @@
 
 		# breakdancer
 		cmd = 'breakdancer-max %s' % (config)
+		cmd += ' -s %d -c %d -m %d -q %d -r %d -x %d -b %d -y %d' % (args.minLength, args.cutoff, args.maxSvSize, args.minMapQuality, args.minReadDepth, args.maxHaploidCov, args.bufferSize, args.scoreFilter)
+		if args.chromosome:
+			cmd += ' -o %s ' % (args.chromosome)
+		if args.onlyTrans:
+			cmd += ' -t '
+		if args.prefix:
+			cmd += ' -d %s ' % (args.prefix)
+		if args.bedFormat:
+			cmd += ' -g %s ' % (args.bedFormat)
+		if args.matePair:
+			cmd += ' -l '
+		if args.sortByLibrary:
+			cmd += ' -a '
+		if args.AFColumn:
+			cmd += ' -h '
 		execute(cmd, output=args.outputRawFile)
 
 		# breakdancer2vcf