- writeOutputFile(outfilename, genome, gidList, gidCount, searchGID)
- if markGID and doCache:
- hitRDS.saveCacheDB(hitfile)
+ writeOutputFile(outfilename, genome, gidCount, searchGID)
+
+
+def getCounts(bamfile, chrom, start, stop, uniqs=True, multi=False, splices=False, sense=''):
+ count = 0.0
+ for alignedread in bamfile.fetch(chrom, start, stop):
+ if countThisRead(alignedread, uniqs, multi, splices, sense):
+ count += 1.0/alignedread.opt('NH')
+
+ return count