GvcfMetricAccumulator (picard 2.18.25 API)

java.lang.Object
- picard.vcf.CallingMetricAccumulator
- - picard.vcf.GvcfMetricAccumulator

All Implemented Interfaces:

VariantProcessor.Accumulator<CallingMetricAccumulator.Result>
```
public class GvcfMetricAccumulator
extends CallingMetricAccumulator
```
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 \ 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
Constructor Description

GvcfMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp)

Method Summary

All 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.
`void`	`setup(htsjdk.variant.vcf.VCFHeader vcfHeader)`

Methods inherited from class picard.vcf.CallingMetricAccumulator
getSingletonSample, result

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - GvcfMetricAccumulator
```
public GvcfMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp)
```
- Method Detail
  - setup
```
public void setup(htsjdk.variant.vcf.VCFHeader vcfHeader)
```
    Overrides:
    
    setup in class CallingMetricAccumulator
  - 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 interface VariantProcessor.Accumulator<CallingMetricAccumulator.Result>
    
    Overrides:
    
    accumulate in class CallingMetricAccumulator