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; }