picard.vcf

Class GA4GHSchemeWithMissingAsHomRef

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 and Description
GA4GHSchemeWithMissingAsHomRef()

Method Summary

Modifier and Type	Method and 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