first pass cleanup of cistematic/genomes; change bamPreprocessing

[erange.git] / weighMultireads.py

diff --git a/weighMultireads.py b/weighMultireads.py
index 9fd041d4462abb552eef87ebd82430177106231f..f4b1691a07a08b15988539f75f1fbb2a62e148b2 100755 (executable)
--- a/weighMultireads.py
+++ b/weighMultireads.py
@@ -168,6 +168,7 @@ def reweighUsingPairs(RDS, pairDist, multiIDs, verbose=False):
                 chrom = "chr%s" % multiReadList[index][1]
                 reweighList.append((round(score,3), chrom, start, theID))
 
+            #TODO: Is this right? If match index is 0 are we doing nothing?
             if theMatch > 0:
                 RDS.reweighMultireads(reweighList)
                 fixedPair += 1
@@ -329,4 +330,4 @@ def reweighUsingRadius(RDS, radius, multiIDs, readsToSkip=[], verbose=False):
 
 
 if __name__ == "__main__":
-    main(sys.argv)
+    main(sys.argv)
\ No newline at end of file