Package picard.vcf
Class GvcfMetricAccumulator
- java.lang.Object
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- picard.vcf.CallingMetricAccumulator
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- picard.vcf.GvcfMetricAccumulator
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- 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 eachVariantContext
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.
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Nested Class Summary
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Nested classes/interfaces inherited from class picard.vcf.CallingMetricAccumulator
CallingMetricAccumulator.Result
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Constructor Summary
Constructors Constructor Description GvcfMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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)
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Methods inherited from class picard.vcf.CallingMetricAccumulator
getSingletonSample, result
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Constructor Detail
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GvcfMetricAccumulator
public GvcfMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp)
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Method Detail
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setup
public void setup(htsjdk.variant.vcf.VCFHeader vcfHeader)
- Overrides:
setup
in classCallingMetricAccumulator
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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 interfaceVariantProcessor.Accumulator<CallingMetricAccumulator.Result>
- Overrides:
accumulate
in classCallingMetricAccumulator
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