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 \invalid input: '<'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 -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoidaccumulate(htsjdk.variant.variantcontext.VariantContext vc) Incorporates the provided variant's data into the metric analysis.voidsetup(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:
setupin classCallingMetricAccumulator
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accumulate
public void accumulate(htsjdk.variant.variantcontext.VariantContext vc) Description copied from class:CallingMetricAccumulatorIncorporates the provided variant's data into the metric analysis.- Specified by:
accumulatein interfaceVariantProcessor.Accumulator<CallingMetricAccumulator.Result>- Overrides:
accumulatein classCallingMetricAccumulator
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