From de9f2b11daf28d9fc67604cdef23a6731c58bf7c Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 25 Sep 2009 12:56:28 +0000
Subject: [PATCH] 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
---
 python/Verify1KGArchiveBAMs.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/python/Verify1KGArchiveBAMs.py b/python/Verify1KGArchiveBAMs.py
index cc996e509..21e3c88a8 100644
--- a/python/Verify1KGArchiveBAMs.py
+++ b/python/Verify1KGArchiveBAMs.py
@@ -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):