# HG changeset patch
# User jeremie
# Date 1404724568 14400
# Node ID accf671c1f3d5662553af2d43f6a897156d66df2
# Parent  844ad5ce74cc730021c927f5fa98d7f90a8e089f
Uploaded

diff -r 844ad5ce74cc -r accf671c1f3d pindel.py
--- a/pindel.py	Mon Jul 07 05:12:51 2014 -0400
+++ b/pindel.py	Mon Jul 07 05:16:08 2014 -0400
@@ -76,7 +76,7 @@
 
 
 def indexBam(inputFastaFile, inputBamFile):
-	cmd = "samtools indexBam %s" %(inputBamFile)
+	cmd = "samtools index %s" %(inputBamFile)
 	execute(cmd)
 	cmd = "samtools faidx %s" %(inputFastaFile)
 	execute(cmd)
@@ -198,7 +198,7 @@
 	
 	try:
 		indexBam(args.inputFastaFile, args.inputBamFile)
-		meanInsertSize = int(getMeanInsertSize(args.inputBamFile))
+		meanInsertSize = int(getMeanInsertSize(args.inputBamFile, tempDir))
 		configFile = config(args.inputBamFile, meanInsertSize, args.name, tempDir)
 		pindelTempDir = pindel(args.inputFastaFile, configFile, args, tempDir)
 		pindel2vcf(args.outputVcfFile, args.inputFastaFile, args.name, pindelTempDir)