public RecordCountPerUnitCollector(
final String sample, final String library, final String readGroup) {
metric = new TotalNumberMetric();
metric.SAMPLE = sample;
metric.LIBRARY = library;
metric.READ_GROUP = readGroup;
unitsToMetrics.put(
noneOrStr(sample) + "_" + noneOrStr(library) + "_" + noneOrStr(readGroup), metric);
}
@Override
public void acceptRecord(final TestArg args) {
numProcessed += 1;
metric.TALLY += 1;
if (metric.SAMPLE != null) {
Assert.assertEquals(metric.SAMPLE, args.samRecord.getReadGroup().getSample());
}
if (metric.LIBRARY != null) {
Assert.assertEquals(metric.LIBRARY, args.samRecord.getReadGroup().getLibrary());
}
if (metric.READ_GROUP != null) {
Assert.assertEquals(metric.READ_GROUP, args.samRecord.getReadGroup().getPlatformUnit());
}
}
@Override
public void finish() {
metric.FINISHED = true;
}
