picard.vcf

Class CallingMetricAccumulator

java.lang.Object

picard.vcf.CallingMetricAccumulator

All Implemented Interfaces:

VariantProcessor.Accumulator<CallingMetricAccumulator.Result>

Direct Known Subclasses:

GvcfMetricAccumulator

public class CallingMetricAccumulator
extends java.lang.Object
implements VariantProcessor.Accumulator<CallingMetricAccumulator.Result>

Collects variants and generates metrics about them. To use, construct, call setup(VCFHeader) once, then accumulate(htsjdk.variant.variantcontext.VariantContext) as desired, then call result().

Author:

mccowan

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CallingMetricAccumulator.Result

Constructor Summary

Constructors

Constructor and Description
CallingMetricAccumulator(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.
protected static java.lang.String	getSingletonSample(htsjdk.variant.variantcontext.VariantContext vc)
CallingMetricAccumulator.Result	result()
void	setup(htsjdk.variant.vcf.VCFHeader vcfHeader)

Methods inherited from class java.lang.Object

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

Constructor Detail

CallingMetricAccumulator

public CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp)

Method Detail

setup

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

accumulate

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

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

Specified by:

accumulate in interface VariantProcessor.Accumulator<CallingMetricAccumulator.Result>

getSingletonSample

protected static java.lang.String getSingletonSample(htsjdk.variant.variantcontext.VariantContext vc)

Returns:

Sample name if there is only one sample that contains alternate allele(s), else null if either multiple samples that are not homref, or no samples that are not homref.

result

public CallingMetricAccumulator.Result result()

Specified by:

result in interface VariantProcessor.Accumulator<CallingMetricAccumulator.Result>