# HG changeset patch
# User jeremie
# Date 1404720253 14400
# Node ID b83483e9b1e8f716ae6e15c6ecf686e601eac259
# Parent  0e73928aa0ca147c4ec8c09c213fafb3436f36c6
Uploaded

diff -r 0e73928aa0ca -r b83483e9b1e8 breakdancer.py
--- a/breakdancer.py	Wed Jul 02 10:26:30 2014 -0400
+++ b/breakdancer.py	Mon Jul 07 04:04:13 2014 -0400
@@ -26,10 +26,10 @@
 
 
 
-binPath = os.environ['BREAKDANCER_BIN']
+# binPath = os.environ['BREAKDANCER_BIN']
 
-bam2cfgPath = binPath+"/bam2cfg.pl"
-breakdancer2vcfPath = binPath+"/breakdancer2vcf.py"
+# bam2cfgPath = binPath+"/bam2cfg.pl"
+# breakdancer2vcfPath = binPath+"/breakdancer2vcf.py"
 
 
 # def bam2cfg(args, tempDir):
@@ -147,7 +147,7 @@
 
 		# bam2cfg
 		config = tempDir+"/breakdancer_config"
-		cmd = 'perl %s %s' % (bam2cfgPath, args.inputBamFile)
+		cmd = 'bam2cfg.pl %s' % (args.inputBamFile)
 		execute(cmd, output=config)
 
 		# breakdancer
@@ -171,7 +171,7 @@
 
 		# breakdancer2vcf
 		if args.outputVcfFile:
-			cmd = "python %s -i %s -o %s" % (breakdancer2vcfPath, args.outputRawFile, args.outputVcfFile)
+			cmd = "breakdancer2vcf.py -i %s -o %s" % (args.outputRawFile, args.outputVcfFile)
 			execute(cmd)
 
 		#	quelques tests