Package picard.analysis
Class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
java.lang.Object
picard.analysis.AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>
picard.analysis.CollectWgsMetrics.WgsMetricsCollector
picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
- Enclosing class:
CollectWgsMetricsWithNonZeroCoverage
protected class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
extends CollectWgsMetrics.WgsMetricsCollector
-
Field Summary
Fields inherited from class picard.analysis.AbstractWgsMetricsCollector
counter, coverageCap, highQualityDepthHistogramArray, intervals, unfilteredBaseQHistogramArray, unfilteredDepthHistogramArray
-
Constructor Summary
ConstructorsConstructorDescriptionWgsMetricsWithNonZeroCoverageCollector
(CollectWgsMetricsWithNonZeroCoverage metrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals) -
Method Summary
Modifier and TypeMethodDescriptionvoid
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 fileboolean
protected htsjdk.samtools.util.Histogram
<Integer> Methods inherited from class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
addInfo
Methods inherited from class picard.analysis.AbstractWgsMetricsCollector
addBaseQHistogram, getHighQualityDepthHistogram, getHistogram, getMetrics, getUnfilteredBaseQHistogram, getUnfilteredDepthHistogram, setCounter
-
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 classAbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>
- Parameters:
file
- MetricsFile for result of collector's workdupeFilter
- counting filter for duplicate readsadapterFilter
- counting filter for adapter readsmapqFilter
- counting filter for mapping qualitypairFilter
- counting filter for reads without a mapped mate pair
-
getDepthHistogram
-
areHistogramsEmpty
public boolean areHistogramsEmpty()
-