- ignoreSense = True
- for read in hitDict[fullchrom]:
- tagStart = read["start"]
- tagReadID = read["readID"]
- if read.has_key("sense"):
- tagSense = read["sense"]
- ignoreSense = False
+ readlen = getHeaderComment(bamfile.header, "ReadLength")
+ for alignedread in bamfile.fetch(chromosome):
+ if doNotProcessRead(alignedread, doUniqs, doMulti):
+ continue
+
+ tagStart = alignedread.pos
+ tagReadID = addPairIDtoReadID(alignedread)
+ tagSense = ""
+ if not ignoreSense:
+ if alignedread.is_reverse:
+ tagSense = "-"
+ else:
+ tagSense = "+"