protected class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector extends CollectWgsMetrics.WgsMetricsCollector
coverageCap, highQualityDepthHistogramArray, intervals, unfilteredBaseQHistogramArray, unfilteredDepthHistogramArray
Constructor and Description |
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WgsMetricsWithNonZeroCoverageCollector(int coverageCap,
htsjdk.samtools.util.IntervalList intervals) |
Modifier and Type | Method and Description |
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void |
addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file,
boolean includeBQHistogram,
CountingFilter dupeFilter,
CountingFilter mapqFilter,
CountingPairedFilter pairFilter) |
boolean |
areHistogramsEmpty() |
protected htsjdk.samtools.util.Histogram<Integer> |
getDepthHistogram() |
addBaseQHistogram, addInfo, getHighQualityDepthHistogram, getHistogram, getMetrics, getUnfilteredBaseQHistogram, getUnfilteredDepthHistogram
public WgsMetricsWithNonZeroCoverageCollector(int coverageCap, htsjdk.samtools.util.IntervalList intervals)
public void addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
addToMetricsFile
in class CollectWgsMetrics.WgsMetricsCollector
protected htsjdk.samtools.util.Histogram<Integer> getDepthHistogram()
public boolean areHistogramsEmpty()