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();