picard.analysis.AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>

picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector

protected class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector extends CollectWgsMetrics.WgsMetricsCollector

Field Summary

Fields inherited from class picard.analysis.AbstractWgsMetricsCollector
counter, coverageCap, highQualityDepthHistogramArray, intervals, unfilteredBaseQHistogramArray, unfilteredDepthHistogramArray
Constructor Summary

Constructors

Constructor

Description

WgsMetricsWithNonZeroCoverageCollector(CollectWgsMetricsWithNonZeroCoverage metrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)
Method Summary

Modifier and Type

Method

Description

void

addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<WgsMetrics,Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter adapterFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)

Adds collected metrics and depth histogram to file

boolean

areHistogramsEmpty()

protected htsjdk.samtools.util.Histogram<Integer>

getDepthHistogram()

Methods inherited from class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
addInfo

Methods inherited from class picard.analysis.AbstractWgsMetricsCollector
addBaseQHistogram, getHighQualityDepthHistogram, getHistogram, getMetrics, getUnfilteredBaseQHistogram, getUnfilteredDepthHistogram, setCounter

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- WgsMetricsWithNonZeroCoverageCollector
  
  public WgsMetricsWithNonZeroCoverageCollector(CollectWgsMetricsWithNonZeroCoverage metrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)
Method Details
- addToMetricsFile
  
  public void addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<WgsMetrics,Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter adapterFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
  
  Description copied from class: AbstractWgsMetricsCollector
  
  Adds collected metrics and depth histogram to file
  
  Overrides:
  
  addToMetricsFile in class AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>
  
  Parameters:
  
  file - MetricsFile for result of collector's work
  
  dupeFilter - counting filter for duplicate reads
  
  adapterFilter - counting filter for adapter reads
  
  mapqFilter - counting filter for mapping quality
  
  pairFilter - counting filter for reads without a mapped mate pair
- getDepthHistogram
  
  protected htsjdk.samtools.util.Histogram<Integer> getDepthHistogram()
- areHistogramsEmpty
  
  public boolean areHistogramsEmpty()

Class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector

Field Summary