Mercurial > repos > jeremie > pindel_test
changeset 11:52d89fc2e7fe draft
Uploaded
| author | jeremie |
|---|---|
| date | Tue, 08 Jul 2014 05:27:52 -0400 |
| parents | accf671c1f3d |
| children | 4e22c03bff62 |
| files | pindel.py |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- 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: