CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollectorprotected static class CollectWgsMetrics.WgsMetricsCollector extends AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>
counter, coverageCap, highQualityDepthHistogramArray, intervals, unfilteredBaseQHistogramArray, unfilteredDepthHistogramArray| Constructor | Description |
|---|---|
WgsMetricsCollector(CollectWgsMetrics metrics,
int coverageCap,
htsjdk.samtools.util.IntervalList intervals) |
| Modifier and Type | Method | Description |
|---|---|---|
void |
addInfo(htsjdk.samtools.util.AbstractLocusInfo<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset> info,
htsjdk.samtools.reference.ReferenceSequence ref,
boolean referenceBaseN) |
Accumulates the data from AbstractLocusInfo in inner structures
|
addBaseQHistogram, addToMetricsFile, getHighQualityDepthHistogram, getHistogram, getMetrics, getUnfilteredBaseQHistogram, getUnfilteredDepthHistogram, setCounterpublic WgsMetricsCollector(CollectWgsMetrics metrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)
public void addInfo(htsjdk.samtools.util.AbstractLocusInfo<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset> info,
htsjdk.samtools.reference.ReferenceSequence ref,
boolean referenceBaseN)
AbstractWgsMetricsCollectoraddInfo in class AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>info - AbstractLocusInfo with aligned to reference position readsref - ReferenceSequencereferenceBaseN - true if current the value of reference base represents a no call