CallingMetricAccumulator (picard 2.18.2 API)

Skip navigation links

All Classes

SEARCH:

Summary:
Nested |
Field |
Constr |
Method

Detail:
Field |
Constr |
Method

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().

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class CallingMetricAccumulator.Result

Constructor Summary

Constructors
Constructor Description

CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp)

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)`

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

- Constructor Detail
  - CallingMetricAccumulator
```
public CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets dbsnp)
```
- Method Detail
  - 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 interface VariantProcessor.Accumulator<CallingMetricAccumulator.Result>
  - 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.
  - result
```
public CallingMetricAccumulator.Result result()
```
    Specified by:
    
    result in interface VariantProcessor.Accumulator<CallingMetricAccumulator.Result>

Skip navigation links

All Classes

Summary:
Nested |
Field |
Constr |
Method

Detail:
Field |
Constr |
Method