VariantProcessor.Accumulator<CallingMetricAccumulator.Result>
GvcfMetricAccumulator
public class CallingMetricAccumulator extends Object implements VariantProcessor.Accumulator<CallingMetricAccumulator.Result>
setup(VCFHeader)
once, then
accumulate(htsjdk.variant.variantcontext.VariantContext)
as desired, then call result()
.Modifier and Type | Class | Description |
---|---|---|
static class |
CallingMetricAccumulator.Result |
Constructor | Description |
---|---|
CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp) |
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) |
public CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp)
public void setup(htsjdk.variant.vcf.VCFHeader vcfHeader)
public void accumulate(htsjdk.variant.variantcontext.VariantContext vc)
accumulate
in interface VariantProcessor.Accumulator<CallingMetricAccumulator.Result>
protected static String getSingletonSample(htsjdk.variant.variantcontext.VariantContext vc)
public CallingMetricAccumulator.Result result()
result
in interface VariantProcessor.Accumulator<CallingMetricAccumulator.Result>