Package picard.analysis
Class WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset>
- java.lang.Object
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- picard.analysis.WgsMetricsProcessorImpl<T>
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- All Implemented Interfaces:
WgsMetricsProcessor
public class WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset> extends Object implements WgsMetricsProcessor
Implementation ofWgsMetricsProcessor
that gets input data from a given iterator and processes it with a help of collector
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Constructor Summary
Constructors Constructor Description WgsMetricsProcessorImpl(htsjdk.samtools.util.AbstractLocusIterator<T,htsjdk.samtools.util.AbstractLocusInfo<T>> iterator, htsjdk.samtools.reference.ReferenceSequenceFileWalker refWalker, AbstractWgsMetricsCollector<T> collector, htsjdk.samtools.util.ProgressLogger progress)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
Adds result metric's data to input filevoid
processFile()
Method gets the data from iterator for each locus and processes it with the help of collector.
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Constructor Detail
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WgsMetricsProcessorImpl
public WgsMetricsProcessorImpl(htsjdk.samtools.util.AbstractLocusIterator<T,htsjdk.samtools.util.AbstractLocusInfo<T>> iterator, htsjdk.samtools.reference.ReferenceSequenceFileWalker refWalker, AbstractWgsMetricsCollector<T> collector, htsjdk.samtools.util.ProgressLogger progress)
- Parameters:
iterator
- inputAbstractLocusIterator
refWalker
- over processed reference filecollector
- inputAbstractWgsMetricsCollector
progress
- logger
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Method Detail
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processFile
public void processFile()
Method gets the data from iterator for each locus and processes it with the help of collector.- Specified by:
processFile
in interfaceWgsMetricsProcessor
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addToMetricsFile
public void addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
Adds result metric's data to input file- Specified by:
addToMetricsFile
in interfaceWgsMetricsProcessor
- Parameters:
file
- MetricsFile for result of collector's workincludeBQHistogram
- include base quality histogramdupeFilter
- counting filter for duplicate readsmapqFilter
- counting filter for mapping qualitypairFilter
- counting filter for reads without a mapped mate pair
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