Package picard.analysis
Class WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset>
java.lang.Object
picard.analysis.WgsMetricsProcessorImpl<T>
- All Implemented Interfaces:
WgsMetricsProcessor
public class WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset>
extends Object
implements WgsMetricsProcessor
Implementation of
WgsMetricsProcessor
that gets input data from a given iterator
and processes it with a help of collector-
Constructor Summary
ConstructorsConstructorDescriptionWgsMetricsProcessorImpl
(htsjdk.samtools.util.AbstractLocusIterator<T, htsjdk.samtools.util.AbstractLocusInfo<T>> iterator, htsjdk.samtools.reference.ReferenceSequenceFileWalker refWalker, AbstractWgsMetricsCollector<T> collector, htsjdk.samtools.util.ProgressLogger progress) -
Method Summary
Modifier and TypeMethodDescriptionvoid
addToMetricsFile
(htsjdk.samtools.metrics.MetricsFile<WgsMetrics, Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter adapterFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter) Adds result metric's data to input filevoid
Method gets the data from iterator for each locus and processes it with the help of collector.
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Constructor Details
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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 Details
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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<WgsMetrics, Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter adapterFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter) Description copied from interface:WgsMetricsProcessor
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 readsadapterFilter
- counting filter for adapter readsmapqFilter
- counting filter for mapping qualitypairFilter
- counting filter for reads without a mapped mate pair
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