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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
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
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__":
if __name__ == "__main__":
- main(sys.argv)
+ main(sys.argv)
\ No newline at end of file