convert standard analysis pipelines to use bam format natively

[erange.git] / siteintersects.py

diff --git a/siteintersects.py b/siteintersects.py
index 58d9e3059ad8a587c10badd3fb8c7cc820462047..9c0c38fa197cbd18669f65269c6f94672cc6e604 100755 (executable)
--- a/siteintersects.py
+++ b/siteintersects.py
@@ -127,7 +127,7 @@ def compareSites(siteFilename, rejectFilename, outfilename, siteDict, rejectSite
 
         siteNotCommon = True
         #TODO: as handed to me this is O(n^m) - probably could be better...
-        #TODO: QForAli - if there are multiple matches will count them but only write the first match to the file
+        #TODO: if there are multiple matches will count them but only write the first match to the file
         for (rstart, rstop, rline) in siteDict[chrom]:
             if regionsOverlap(start, stop, rstart, rstop):
                 commonSites += 1