protected class CollectWgsMetrics.WgsMetricsCollector extends Object
Modifier and Type | Field and Description |
---|---|
protected int |
coverageCap |
protected long[] |
highQualityDepthHistogramArray |
protected htsjdk.samtools.util.IntervalList |
intervals |
protected long[] |
unfilteredBaseQHistogramArray |
protected long[] |
unfilteredDepthHistogramArray |
Constructor and Description |
---|
WgsMetricsCollector(int coverageCap,
htsjdk.samtools.util.IntervalList intervals) |
Modifier and Type | Method and Description |
---|---|
protected void |
addBaseQHistogram(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file) |
void |
addInfo(htsjdk.samtools.util.SamLocusIterator.LocusInfo info) |
void |
addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file,
boolean includeBQHistogram,
CountingFilter dupeFilter,
CountingFilter mapqFilter,
CountingPairedFilter pairFilter) |
protected htsjdk.samtools.util.Histogram<Integer> |
getHighQualityDepthHistogram() |
protected htsjdk.samtools.util.Histogram<Integer> |
getHistogram(long[] array,
String binLabel,
String valueLabel) |
protected CollectWgsMetrics.WgsMetrics |
getMetrics(CountingFilter dupeFilter,
CountingFilter mapqFilter,
CountingPairedFilter pairFilter) |
protected htsjdk.samtools.util.Histogram<Integer> |
getUnfilteredBaseQHistogram() |
protected htsjdk.samtools.util.Histogram<Integer> |
getUnfilteredDepthHistogram() |
protected final long[] unfilteredDepthHistogramArray
protected final long[] unfilteredBaseQHistogramArray
protected final long[] highQualityDepthHistogramArray
protected final htsjdk.samtools.util.IntervalList intervals
protected final int coverageCap
public WgsMetricsCollector(int coverageCap, htsjdk.samtools.util.IntervalList intervals)
public void addInfo(htsjdk.samtools.util.SamLocusIterator.LocusInfo info)
public void addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
protected void addBaseQHistogram(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file)
protected htsjdk.samtools.util.Histogram<Integer> getHighQualityDepthHistogram()
protected htsjdk.samtools.util.Histogram<Integer> getUnfilteredDepthHistogram()
protected htsjdk.samtools.util.Histogram<Integer> getUnfilteredBaseQHistogram()
protected htsjdk.samtools.util.Histogram<Integer> getHistogram(long[] array, String binLabel, String valueLabel)
protected CollectWgsMetrics.WgsMetrics getMetrics(CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)