@Override
  protected void finish() {
    multiCollector.finish();

    final MetricsFile<InsertSizeMetrics, Integer> file = getMetricsFile();
    multiCollector.addAllLevelsToFile(file);

    if (file.getNumHistograms() == 0) {
      // can happen if user sets MINIMUM_PCT = 0.5, etc.
      log.warn(
          "All data categories were discarded because they contained < "
              + MINIMUM_PCT
              + " of the total aligned paired data.");
      final InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector allReadsCollector =
          (InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector)
              multiCollector.getAllReadsCollector();
      log.warn(
          "Total mapped pairs in all categories: "
              + (allReadsCollector == null
                  ? allReadsCollector
                  : allReadsCollector.getTotalInserts()));
    } else {
      file.write(OUTPUT);

      final int rResult;
      if (HISTOGRAM_WIDTH == null) {
        rResult =
            RExecutor.executeFromClasspath(
                HISTOGRAM_R_SCRIPT,
                OUTPUT.getAbsolutePath(),
                HISTOGRAM_FILE.getAbsolutePath(),
                INPUT.getName());
      } else {
        rResult =
            RExecutor.executeFromClasspath(
                HISTOGRAM_R_SCRIPT,
                OUTPUT.getAbsolutePath(),
                HISTOGRAM_FILE.getAbsolutePath(),
                INPUT.getName(),
                String.valueOf(
                    HISTOGRAM_WIDTH)); // HISTOGRAM_WIDTH is passed because R automatically sets
                                       // histogram width to the last
        // bin that has data, which may be less than HISTOGRAM_WIDTH and confuse the user.
      }

      if (rResult != 0) {
        throw new PicardException(
            "R script " + HISTOGRAM_R_SCRIPT + " failed with return code " + rResult);
      }
    }
  }
 @Override
 protected void acceptRead(final SAMRecord record, final ReferenceSequence ref) {
   multiCollector.acceptRecord(record, ref);
 }