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;
}
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;
}
}
}