Package picard.analysis
Class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
- java.lang.Object
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- picard.analysis.AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>
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- picard.analysis.CollectWgsMetrics.WgsMetricsCollector
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- picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
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- Enclosing class:
- CollectWgsMetricsWithNonZeroCoverage
protected class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector extends CollectWgsMetrics.WgsMetricsCollector
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Field Summary
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Fields inherited from class picard.analysis.AbstractWgsMetricsCollector
counter, coverageCap, highQualityDepthHistogramArray, intervals, unfilteredBaseQHistogramArray, unfilteredDepthHistogramArray
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Constructor Summary
Constructors Constructor Description WgsMetricsWithNonZeroCoverageCollector(CollectWgsMetricsWithNonZeroCoverage metrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)
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Method Summary
All Methods Instance Methods Concrete Methods 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 fileboolean
areHistogramsEmpty()
protected htsjdk.samtools.util.Histogram<Integer>
getDepthHistogram()
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Methods inherited from class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
addInfo
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Methods inherited from class picard.analysis.AbstractWgsMetricsCollector
addBaseQHistogram, getHighQualityDepthHistogram, getHistogram, getMetrics, getUnfilteredBaseQHistogram, getUnfilteredDepthHistogram, setCounter
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Constructor Detail
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WgsMetricsWithNonZeroCoverageCollector
public WgsMetricsWithNonZeroCoverageCollector(CollectWgsMetricsWithNonZeroCoverage metrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)
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Method Detail
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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
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getDepthHistogram
protected htsjdk.samtools.util.Histogram<Integer> getDepthHistogram()
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areHistogramsEmpty
public boolean areHistogramsEmpty()
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