WgsMetricsProcessorImpl (picard 2.18.2 API)

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

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)`

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 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<CollectWgsMetrics.WgsMetrics,Integer> file,
                             boolean includeBQHistogram,
                             CountingFilter dupeFilter,
                             CountingFilter mapqFilter,
                             CountingPairedFilter pairFilter)
```
  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
  
  mapqFilter - counting filter for mapping quality
  
  pairFilter - counting filter for reads without a mapped mate pair

Class WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

WgsMetricsProcessorImpl

Method Detail

processFile

addToMetricsFile