Package picard.vcf
Class CallingMetricAccumulator
- java.lang.Object
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- picard.vcf.CallingMetricAccumulator
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- 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, callsetup(VCFHeader)
once, thenaccumulate(htsjdk.variant.variantcontext.VariantContext)
as desired, then callresult()
.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CallingMetricAccumulator.Result
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Constructor Summary
Constructors Constructor Description CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp)
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Method Summary
All Methods Static 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.protected static String
getSingletonSample(htsjdk.variant.variantcontext.VariantContext vc)
CallingMetricAccumulator.Result
result()
void
setup(htsjdk.variant.vcf.VCFHeader vcfHeader)
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Constructor Detail
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CallingMetricAccumulator
public CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp)
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Method Detail
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setup
public void setup(htsjdk.variant.vcf.VCFHeader vcfHeader)
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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
protected static 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.
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result
public CallingMetricAccumulator.Result result()
- Specified by:
result
in interfaceVariantProcessor.Accumulator<CallingMetricAccumulator.Result>
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