# HG changeset patch
# User jeremie
# Date 1404226296 14400
# Node ID 463a9ed9655b606b734e4c38a67e2a0fc4414d59
# Parent  acec6ba9884ad3de0e7d638ec3c953107e572db7
Uploaded

diff -r acec6ba9884a -r 463a9ed9655b breakdancer.py
--- a/breakdancer.py	Tue Jul 01 10:39:41 2014 -0400
+++ b/breakdancer.py	Tue Jul 01 10:51:36 2014 -0400
@@ -21,26 +21,26 @@
 binPath=binPath[:-1]
 print("--"+binPath+"--")
 
-bam2cfg = str(binPath)+"/bam2cfg.pl"
-breakdancer = binPath+"/breakdancer-max"
-breakdancer2vcf = binPath+"/breakdancer2vcf.py"
+bam2cfgPath = str(binPath)+"/bam2cfg.pl"
+breakdancerPath = binPath+"/breakdancer-max"
+breakdancer2vcfPath = binPath+"/breakdancer2vcf.py"
 
 
 def bam2cfg(args):
 	config = tmp_dir+"/breakdancer_config"
-	cmd = 'perl %s %s' % (bam2cfg, args.input_bam)
+	cmd = 'perl %s %s' % (bam2cfgPath, args.input_bam)
 	execute(cmd, output=config)
 	print ("\ncmd = %s  \n" ) %(cmd)
 	return config
 
 
 def breakdancer(args, config):
-	cmd = '%s %s' % (breakdancer, config)
+	cmd = '%s %s' % (breakdancerPath, config)
 	execute(cmd, output=args.output_raw)
 
 
 def breakdancer2vcf(args):
-	cmd = "python %s -i %s -o %s" % ( breakdancer2vcf, args.output_raw, args.output_vcf )
+	cmd = "python %s -i %s -o %s" % ( breakdancer2vcfPath, args.output_raw, args.output_vcf )
 	execute(cmd)