d412c5dc2fd685ff4cf35278a82538e55ec182b8,java/src/org/broadinstitute/sting/playground/piecemealannotator/TileAnnotator.java,TileAnnotator,callBases,#BasecallingReadModel#ArrayList#,63

Before Change


        for (RawRead rr : tileParser) {
            FourProbRead fpr = model.call(rr);

            for (int rangeIndex = 0; rangeIndex < cycleRanges.size(); rangeIndex++) {
                FourProbRead fprEnd = fpr.getSubset(cycleRanges.get(rangeIndex).getFirst(), cycleRanges.get(rangeIndex).getSecond());
                RawRead rrEnd = rr.getSubset(cycleRanges.get(rangeIndex).getFirst(), cycleRanges.get(rangeIndex).getSecond());

                SAMRecord sr = constructSAMRecord(rrEnd, fprEnd, sheader, cycleRanges.size() > 1, rangeIndex == 1);

                swriter.addAlignment(sr);
            }

            bstats.update(rr, fpr);

After Change



            SAMRecord sr = constructSAMRecord(rr, sqtag, sheader, false, false);

            swriter.addAlignment(sr);
        }

        bstats.notifyNow();