Package picard.vcf
Class GvcfMetricAccumulator
java.lang.Object
picard.vcf.CallingMetricAccumulator
picard.vcf.GvcfMetricAccumulator
- All Implemented Interfaces:
VariantProcessor.Accumulator<CallingMetricAccumulator.Result>
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 \<NON_REF\> 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.-
Nested Class Summary
Nested classes/interfaces inherited from class picard.vcf.CallingMetricAccumulator
CallingMetricAccumulator.Result
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
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
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Constructor Details
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GvcfMetricAccumulator
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Method Details
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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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