Mercurial > repos > jeremie > pindel_test

changeset 10:accf671c1f3d draft

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Uploaded
author jeremie
date Mon, 07 Jul 2014 05:16:08 -0400
parents 844ad5ce74cc
children 52d89fc2e7fe
files pindel.py
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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)