コード例 #1
0
 public IndividualAlignmentSummaryMetricsCollector(
     final AlignmentSummaryMetrics.Category pairingCategory,
     final String sample,
     final String library,
     final String readGroup) {
   metrics = new AlignmentSummaryMetrics();
   metrics.CATEGORY = pairingCategory;
   metrics.SAMPLE = sample;
   metrics.LIBRARY = library;
   metrics.READ_GROUP = readGroup;
 }
コード例 #2
0
      public void onComplete() {
        // summarize read data
        if (metrics.TOTAL_READS > 0) {
          metrics.PCT_PF_READS = (double) metrics.PF_READS / (double) metrics.TOTAL_READS;
          metrics.PCT_ADAPTER = this.adapterReads / (double) metrics.PF_READS;
          metrics.MEAN_READ_LENGTH = readLengthHistogram.getMean();

          // Calculate BAD_CYCLES
          metrics.BAD_CYCLES = 0;
          for (final Histogram<Integer>.Bin cycleBin : badCycleHistogram.values()) {
            final double badCyclePercentage = cycleBin.getValue() / metrics.TOTAL_READS;
            if (badCyclePercentage >= .8) {
              metrics.BAD_CYCLES++;
            }
          }

          if (doRefMetrics) {
            if (metrics.PF_READS > 0)
              metrics.PCT_PF_READS_ALIGNED =
                  (double) metrics.PF_READS_ALIGNED / (double) metrics.PF_READS;
            if (metrics.PF_READS_ALIGNED > 0)
              metrics.PCT_READS_ALIGNED_IN_PAIRS =
                  (double) metrics.READS_ALIGNED_IN_PAIRS / (double) metrics.PF_READS_ALIGNED;
            if (metrics.PF_READS_ALIGNED > 0)
              metrics.STRAND_BALANCE = numPositiveStrand / (double) metrics.PF_READS_ALIGNED;
            if (this.chimerasDenominator > 0)
              metrics.PCT_CHIMERAS = this.chimeras / (double) this.chimerasDenominator;

            if (nonBisulfiteAlignedBases > 0)
              metrics.PF_MISMATCH_RATE =
                  mismatchHistogram.getSum() / (double) nonBisulfiteAlignedBases;
            metrics.PF_HQ_MEDIAN_MISMATCHES = hqMismatchHistogram.getMedian();
            if (hqNonBisulfiteAlignedBases > 0)
              metrics.PF_HQ_ERROR_RATE =
                  hqMismatchHistogram.getSum() / (double) hqNonBisulfiteAlignedBases;
            if (metrics.PF_ALIGNED_BASES > 0)
              metrics.PF_INDEL_RATE = this.indels / (double) metrics.PF_ALIGNED_BASES;
          }
        }
      }