protected class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector extends CollectWgsMetrics.WgsMetricsCollector
counter, coverageCap, highQualityDepthHistogramArray, intervals, unfilteredBaseQHistogramArray, unfilteredDepthHistogramArray| Constructor | Description |
|---|---|
WgsMetricsWithNonZeroCoverageCollector(CollectWgsMetricsWithNonZeroCoverage metrics,
int coverageCap,
htsjdk.samtools.util.IntervalList intervals) |
| Modifier and Type | Method | Description |
|---|---|---|
void |
addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file,
boolean includeBQHistogram,
CountingFilter dupeFilter,
CountingFilter mapqFilter,
CountingPairedFilter pairFilter) |
Adds collected metrics and depth histogram to file
|
boolean |
areHistogramsEmpty() |
|
protected htsjdk.samtools.util.Histogram<Integer> |
getDepthHistogram() |
addBaseQHistogram, getHighQualityDepthHistogram, getHistogram, getMetrics, getUnfilteredBaseQHistogram, getUnfilteredDepthHistogram, setCounteraddInfopublic WgsMetricsWithNonZeroCoverageCollector(CollectWgsMetricsWithNonZeroCoverage metrics, 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)
AbstractWgsMetricsCollectoraddToMetricsFile in class AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>file - MetricsFile for result of collector's workdupeFilter - counting filter for duplicate readsmapqFilter - counting filter for mapping qualitypairFilter - counting filter for reads without a mapped mate pairprotected htsjdk.samtools.util.Histogram<Integer> getDepthHistogram()
public boolean areHistogramsEmpty()