@Override
public void finish() {
// Let the collectors do any summary computations etc.
unpairedCollector.onComplete();
firstOfPairCollector.onComplete();
secondOfPairCollector.onComplete();
pairCollector.onComplete();
}
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);
}
}
@Override
public void addMetricsToFile(final MetricsFile<AlignmentSummaryMetrics, Comparable<?>> file) {
if (firstOfPairCollector.getMetrics().TOTAL_READS > 0) {
// override how bad cycle is determined for paired reads, it should be
// the sum of first and second reads
pairCollector.getMetrics().BAD_CYCLES =
firstOfPairCollector.getMetrics().BAD_CYCLES
+ secondOfPairCollector.getMetrics().BAD_CYCLES;
file.addMetric(firstOfPairCollector.getMetrics());
file.addMetric(secondOfPairCollector.getMetrics());
file.addMetric(pairCollector.getMetrics());
}
// if there are no reads in any category then we will returned an unpaired alignment summary
// metric with all zero values
if (unpairedCollector.getMetrics().TOTAL_READS > 0
|| firstOfPairCollector.getMetrics().TOTAL_READS == 0) {
file.addMetric(unpairedCollector.getMetrics());
}
}