picard.vcf

Class GvcfMetricAccumulator

java.lang.Object

picard.vcf.CallingMetricAccumulator

picard.vcf.GvcfMetricAccumulator

All Implemented Interfaces:

VariantProcessor.Accumulator<CallingMetricAccumulator.Result>

public class GvcfMetricAccumulator
extends CallingMetricAccumulator

An accumulator for collecting metrics about a single-sample GVCF. The main point here is to subset the context of each VariantContext as it comes by to the alleles present in the genotype of the only sample. Since this is a GVCF we expect a symbolic \ allele to be present in each VC. If we do not subset the context this symbolic allele will cause the regular CallingMetricAccumulator to return only a small subset of the relevant metrics.

Author:

farjoun

Nested Class Summary

Nested classes/interfaces inherited from class picard.vcf.CallingMetricAccumulator

CallingMetricAccumulator.Result

Constructor Summary

Constructors

Constructor and Description
GvcfMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp)

Method Summary

Modifier and Type	Method and Description
void	accumulate(htsjdk.variant.variantcontext.VariantContext vc) Incorporates the provided variant's data into the metric analysis.
void	setup(htsjdk.variant.vcf.VCFHeader vcfHeader)

Methods inherited from class picard.vcf.CallingMetricAccumulator

getSingletonSample, result

Methods inherited from class java.lang.Object

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

Constructor Detail

GvcfMetricAccumulator

public GvcfMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp)

Method Detail

setup

public void setup(htsjdk.variant.vcf.VCFHeader vcfHeader)

Overrides:

setup in class CallingMetricAccumulator

accumulate

public void accumulate(htsjdk.variant.variantcontext.VariantContext vc)

Description copied from class: CallingMetricAccumulator

Incorporates the provided variant's data into the metric analysis.

Specified by:

accumulate in interface VariantProcessor.Accumulator<CallingMetricAccumulator.Result>

Overrides:

accumulate in class CallingMetricAccumulator