GA4GHSchemeWithMissingAsHomRef (picard 2.18.2 API)

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java.lang.Object
- picard.vcf.GenotypeConcordanceScheme
- - picard.vcf.GA4GHSchemeWithMissingAsHomRef

```
public class GA4GHSchemeWithMissingAsHomRef
extends GenotypeConcordanceScheme
```
The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme. This scheme has been edited to count MISSING sites in the truth set differently for use with truth sets where the HOM_REF sites are not included in the data set. The MISSING truth sites are called like they are HOM_REF sites.

- Field Summary
  - Fields inherited from class picard.vcf.GenotypeConcordanceScheme
    EMPTY, FN_ONLY, FP_FN, FP_ONLY, FP_TN, FP_TN_FN, NA, scheme, TN_FN, TN_ONLY, TP_FN, TP_FP, TP_FP_FN, TP_ONLY, TP_TN
- Constructor Summary
  
  Constructors
  Constructor Description
  
  GA4GHSchemeWithMissingAsHomRef()
- Method Summary
  
  All Methods Instance Methods Concrete Methods
  Modifier and Type Method Description
  
  protected void initiateScheme()
  - Methods inherited from class picard.vcf.GenotypeConcordanceScheme
    addRow, getConcordanceStateArray, getConcordanceStateArray, getContingencyStateSet, getContingencyStateString, validateScheme
  - Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - GA4GHSchemeWithMissingAsHomRef
```
public GA4GHSchemeWithMissingAsHomRef()
```
- Method Detail
  - initiateScheme
```
protected void initiateScheme()
```
    Specified by:
    
    initiateScheme in class GenotypeConcordanceScheme

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