Examples with BaseDistributionByCycleMetrics org.broadinstitute.hellbender.tools.picard.analysis.BaseDistributionByCycleMetrics used on opensource projects

Example 1 with BaseDistributionByCycleMetrics

use of org.broadinstitute.hellbender.tools.picard.analysis.BaseDistributionByCycleMetrics in project gatk by broadinstitute.

the class CollectBaseDistributionByCycleSpark method calculateBaseDistributionByCycle.

/**
     * Computes the MeanQualityByCycle. Creates a metrics file with relevant histograms.
     */
public MetricsFile<BaseDistributionByCycleMetrics, Integer> calculateBaseDistributionByCycle(final JavaRDD<GATKRead> reads) {
    final MetricsReadFilter metricsFilter = new MetricsReadFilter(this.pfReadsOnly, this.alignedReadsOnly);
    final JavaRDD<GATKRead> filteredReads = reads.filter(read -> metricsFilter.test(read));
    final HistogramGenerator hist = filteredReads.aggregate(new HistogramGenerator(), (hgp, read) -> hgp.addRead(read), (hgp1, hgp2) -> hgp1.merge(hgp2));
    final MetricsFile<BaseDistributionByCycleMetrics, Integer> metricsFile = getMetricsFile();
    hist.addToMetricsFile(metricsFile);
    return metricsFile;
}