# HG changeset patch
# User jeremie
# Date 1404221691 14400
# Node ID 87a6ec1e240066a399de7b7d780e3d9779fb787a
# Parent  d26b184866b4cd82355bf8ad03ddf3b7df814854
Uploaded

diff -r d26b184866b4 -r 87a6ec1e2400 breakdancer.py
--- a/breakdancer.py	Tue Jul 01 09:28:30 2014 -0400
+++ b/breakdancer.py	Tue Jul 01 09:34:51 2014 -0400
@@ -14,27 +14,27 @@
 errorFile = tmp_dir+"/errorLog"
 
 currentDir = os.path.dirname(os.path.abspath(__file__))
-bam2cfg_path = currentDir+"/bam2cfg.pl"
-# breakdancer_path = "/usr/bin/breakdancer-max"
-breakdancer_path = "breakdancer-max"
-breakdancer2vcf_path = currentDir+"/breakdancer2vcf.py"
+bam2cfg = "./bam2cfg.pl"
+# breakdancer = "/usr/bin/breakdancer-max"
+breakdancer = "breakdancer-max"
+breakdancer2vcf = "./breakdancer2vcf.py"
 
 
 def bam2cfg(args):
 	config = tmp_dir+"/breakdancer_config"
-	cmd = 'perl %s %s' % (bam2cfg_path, args.input_bam)
+	cmd = 'perl %s %s' % (bam2cfg, args.input_bam)
 	execute(cmd, output=config)
 	print ("\ncmd = %s  \n" ) %(cmd)
 	return config
 
 
 def breakdancer(args, config):
-	cmd = '%s %s' % (breakdancer_path, config)
+	cmd = '%s %s' % (breakdancer, config)
 	execute(cmd, output=args.output_raw)
 
 
 def breakdancer2vcf(args):
-	cmd = "python %s -i %s -o %s" % ( breakdancer2vcf_path, args.output_raw, args.output_vcf )
+	cmd = "python %s -i %s -o %s" % ( breakdancer2vcf, args.output_raw, args.output_vcf )
 	execute(cmd)