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 java.lang.Object
implements WgsMetricsProcessor

Implementation of WgsMetricsProcessor that gets input data from a given iterator and processes it with a help of collector

Constructor Summary

Constructors

Constructor and 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)

Method Summary

Modifier and Type	Method and Description
void	addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<WgsMetrics,java.lang.Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter adapterFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter) Adds result metric's data to input file
void	processFile() Method gets the data from iterator for each locus and processes it with the help of collector.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

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 - input AbstractLocusIterator

refWalker - over processed reference file

collector - input AbstractWgsMetricsCollector

progress - logger

Method Detail

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 interface WgsMetricsProcessor

addToMetricsFile

public void addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<WgsMetrics,java.lang.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 interface WgsMetricsProcessor

Parameters:

file - MetricsFile for result of collector's work

includeBQHistogram - include base quality histogram

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