outputBuffer.setResultState(pair.getSamRecordIndex(), false); // you are not a duplicate! this.otherEndOfNonDuplicateReadEndsSet.remove(current); outputBuffer.setResultState(duplicate.getSamRecordIndex(), true); outputBuffer.setResultState(current.getSamRecordIndex(), false);
outputBuffer.setResultState(pair.getSamRecordIndex(), false); // you are not a duplicate! this.otherEndOfNonDuplicateReadEndsSet.remove(current); outputBuffer.setResultState(duplicate.getSamRecordIndex(), true); outputBuffer.setResultState(current.getSamRecordIndex(), false);
final ReadEndsForMateCigar pair = this.otherEndOfNonDuplicateReadEndsSet.subSet(current, true, current, true).first(); this.otherEndOfNonDuplicateReadEndsSet.remove(current); outputBuffer.setResultState(pair.getSamRecordIndex(), true); // track that this samRecordWithOrdinal has been through duplicate marking updateDuplicationMetrics(pair, metrics); outputBuffer.setResultState(duplicate.getSamRecordIndex(), true);
final ReadEndsForMateCigar pair = this.otherEndOfNonDuplicateReadEndsSet.subSet(current, true, current, true).first(); this.otherEndOfNonDuplicateReadEndsSet.remove(current); outputBuffer.setResultState(pair.getSamRecordIndex(), true); // track that this samRecordWithOrdinal has been through duplicate marking updateDuplicationMetrics(pair, metrics); outputBuffer.setResultState(duplicate.getSamRecordIndex(), true);
outputBuffer.setResultState(samRecordWithOrdinal, false); // indicate the present wrapped samRecordWithOrdinal is available for return numRecordsWithNoMateCigar++;
outputBuffer.setResultState(samRecordWithOrdinal, false); // indicate the present wrapped samRecordWithOrdinal is available for return numRecordsWithNoMateCigar++;
outputBuffer.setResultState(samRecordWithOrdinal, false); if(record.isSecondaryOrSupplementary()){ ++metrics.SECONDARY_OR_SUPPLEMENTARY_RDS;
outputBuffer.setResultState(samRecordWithOrdinal, false); if(record.isSecondaryOrSupplementary()){ ++metrics.SECONDARY_OR_SUPPLEMENTARY_RDS;