development release: conversion of ReadDataset to use BAM files

[erange.git] / siteintersects.py

diff --git a/siteintersects.py b/siteintersects.py
index e012bb49436c92f50a1d8722182d0cd72a754897..58d9e3059ad8a587c10badd3fb8c7cc820462047 100755 (executable)
--- a/siteintersects.py
+++ b/siteintersects.py
@@ -126,6 +126,8 @@ def compareSites(siteFilename, rejectFilename, outfilename, siteDict, rejectSite
             continue
 
         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
         for (rstart, rstop, rline) in siteDict[chrom]:
             if regionsOverlap(start, stop, rstart, rstop):
                 commonSites += 1
@@ -162,4 +164,4 @@ def writeRejectSiteFile(siteRejectFilename, rejectSiteDict):
     
 
 if __name__ == "__main__":
-    main(sys.argv)
+    main(sys.argv)
\ No newline at end of file