Package 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 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()
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Nested Class Summary
Nested Classes -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
accumulate
(htsjdk.variant.variantcontext.VariantContext vc) Incorporates the provided variant's data into the metric analysis.static String
getSingletonSample
(htsjdk.variant.variantcontext.VariantContext vc) result()
void
setup
(htsjdk.variant.vcf.VCFHeader vcfHeader)
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Constructor Details
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CallingMetricAccumulator
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Method Details
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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 interfaceVariantProcessor.Accumulator<CallingMetricAccumulator.Result>
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getSingletonSample
- 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.
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result
- Specified by:
result
in interfaceVariantProcessor.Accumulator<CallingMetricAccumulator.Result>
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