public void acceptRecord(final SAMRecordAndReference args) { final SAMRecord rec = args.getSamRecord(); final ReferenceSequence ref = args.getReferenceSequence(); if (rec.getReadPairedFlag()) { if (rec.getFirstOfPairFlag()) { firstOfPairCollector.addRecord(rec, ref); } else { secondOfPairCollector.addRecord(rec, ref); } pairCollector.addRecord(rec, ref); } else { unpairedCollector.addRecord(rec, ref); } }