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Detects unmapped (no bai) bam files and doesn't blow up 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1725 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-09-25 12:56:28 +00:00
parent 7ffc1d97ef
commit de9f2b11da
1 changed files with 4 additions and 2 deletions
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6
python/Verify1KGArchiveBAMs.py
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@ -182,8 +182,10 @@ def readAlignmentIndex(file):
files = set()
if file <> None:
for line in open(file):
files.add(line.split()[0])
files.add(line.split()[4])
parts = line.split()
files.add(parts[0])
if len(parts) > 4: # we have an index, we're not unmapped
files.add(line.split()[4])
return files
def compareAlignmentIndices(remoteAlignmentIndex, alignmentIndex):