# HG changeset patch
# User jeremie
# Date 1404811672 14400
# Node ID 52d89fc2e7fe728af46edc03f1a6a8058aaf05b6
# Parent  accf671c1f3d5662553af2d43f6a897156d66df2
Uploaded

diff -r accf671c1f3d -r 52d89fc2e7fe pindel.py
--- a/pindel.py	Mon Jul 07 05:16:08 2014 -0400
+++ b/pindel.py	Tue Jul 08 05:27:52 2014 -0400
@@ -165,8 +165,8 @@
 	samFile = tempDir+"/sam"
 	histogramFile = tempDir+"/histogram"
 	outputFile = tempDir+"/output"
-	cmd = "samtools view -h %s %s" % (bamFile, samFile)
-	execute(cmd)
+	cmd = "samtools view -h -o %s %s" % (bamFile, samFile)
+	execute(cmd, )
 	cmd = "picard-tools CollectInsertSizeMetrics H=%s O=%s I=%s" % (histogramFile, outputFile, samFile)
 	execute(cmd)
 	try: