picard.analysis

Interface WgsMetricsProcessor

All Known Implementing Classes:

WgsMetricsProcessorImpl

public interface WgsMetricsProcessor

Interface for processing data and generate result for CollectWgsMetrics

Method Summary

Modifier and Type	Method and Description
void	addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,java.lang.Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter) Adds result metric's data to input file
void	processFile() Method processes the input data and accumulates result data

Method Detail

processFile

void processFile()

Method processes the input data and accumulates result data

addToMetricsFile

void addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,java.lang.Integer> file,
                      boolean includeBQHistogram,
                      CountingFilter dupeFilter,
                      CountingFilter mapqFilter,
                      CountingPairedFilter pairFilter)

Adds result metric's data to input file

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