Update CollectWgsMetricsWithNonZeroCoverage.java

broadinstitute · Jul 31, 2024 · 6b17a85 · 6b17a85
1 parent b33b890
commit 6b17a85
Showing 1 changed file with 7 additions and 5 deletions.
diff --git a/src/main/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.java b/src/main/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.java
@@ -104,6 +104,7 @@ public WgsMetricsWithNonZeroCoverage() {
 
  public WgsMetricsWithNonZeroCoverage(final IntervalList intervals,
  final Histogram<Integer> highQualityDepthHistogram,
+ final Histogram<Integer> highQualitDepthHistogramNonZero,
  final Histogram<Integer> unfilteredDepthHistogram,
  final double pctExcludedByAdapter,
  final double pctExcludedByMapq,
@@ -116,7 +117,7 @@ public WgsMetricsWithNonZeroCoverage(final IntervalList intervals,
  final int coverageCap,
  final Histogram<Integer> unfilteredBaseQHistogram,
  final int sampleSize) {
- super(intervals, highQualityDepthHistogram, unfilteredDepthHistogram, pctExcludedByAdapter, pctExcludedByMapq, pctExcludedByDupes, pctExcludedByPairing, pctExcludedByBaseq,
+ super(intervals, highQualityDepthHistogram, highQualitDepthHistogramNonZero, unfilteredDepthHistogram, pctExcludedByAdapter, pctExcludedByMapq, pctExcludedByDupes, pctExcludedByPairing, pctExcludedByBaseq,
  pctExcludedByOverlap, pctExcludedByCapping, pctTotal, coverageCap, unfilteredBaseQHistogram, sampleSize);
  }
  }
@@ -170,6 +171,7 @@ protected int doWork() {
  @Override
  protected WgsMetrics generateWgsMetrics(final IntervalList intervals,
  final Histogram<Integer> highQualityDepthHistogram,
+ final Histogram<Integer> highQualitDepthHistogramNonZero,
  final Histogram<Integer> unfilteredDepthHistogram,
  final double pctExcludedByAdapter,
  final double pctExcludedByMapq,
@@ -207,7 +209,7 @@ protected WgsMetricsCollector getCollector(final int coverageCap, final Interval
 
  protected class WgsMetricsWithNonZeroCoverageCollector extends WgsMetricsCollector {
  Histogram<Integer> highQualityDepthHistogram;
- Histogram<Integer> highQualityDepthHistogramNonZero;
+ Histogram<Integer> highQualityDepthHistogramNonZeroFinal;
 
  public WgsMetricsWithNonZeroCoverageCollector(final CollectWgsMetricsWithNonZeroCoverage metrics,
  final int coverageCap, final IntervalList intervals) {
@@ -222,7 +224,7 @@ public void addToMetricsFile(final MetricsFile<WgsMetrics, Integer> file,
  final CountingFilter mapqFilter,
  final CountingPairedFilter pairFilter) {
  highQualityDepthHistogram = getDepthHistogram();
- highQualityDepthHistogramNonZero = getDepthHistogramNonZero();
+ highQualityDepthHistogramNonZeroFinal = getDepthHistogramNonZero();
 
  // calculate metrics the same way as in CollectWgsMetrics
  final WgsMetricsWithNonZeroCoverage metrics = (WgsMetricsWithNonZeroCoverage) getMetrics(dupeFilter, adapterFilter, mapqFilter, pairFilter);
@@ -239,7 +241,7 @@ public void addToMetricsFile(final MetricsFile<WgsMetrics, Integer> file,
  file.addMetric(metrics);
  file.addMetric(metricsNonZero);
  file.addHistogram(highQualityDepthHistogram);
- file.addHistogram(highQualityDepthHistogramNonZero);
+ file.addHistogram(highQualityDepthHistogramNonZeroFinal);
 
  if (includeBQHistogram) {
  addBaseQHistogram(file);
@@ -260,7 +262,7 @@ private Histogram<Integer> getDepthHistogramNonZero() {
  }
 
  public boolean areHistogramsEmpty() {
- return (highQualityDepthHistogram.isEmpty() || highQualityDepthHistogramNonZero.isEmpty());
+ return (highQualityDepthHistogram.isEmpty() || highQualityDepthHistogramNonZeroFinal.isEmpty());
  }
  }
 }