Package picard.vcf
Class GA4GHSchemeWithMissingAsHomRef
- java.lang.Object
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- picard.vcf.GenotypeConcordanceScheme
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- picard.vcf.GA4GHSchemeWithMissingAsHomRef
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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.
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Constructor Summary
Constructors Constructor Description GA4GHSchemeWithMissingAsHomRef()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
initiateScheme()
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Methods inherited from class picard.vcf.GenotypeConcordanceScheme
addRow, getConcordanceStateArray, getConcordanceStateArray, getContingencyStateSet, getContingencyStateString, validateScheme
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Method Detail
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initiateScheme
protected void initiateScheme()
- Specified by:
initiateScheme
in classGenotypeConcordanceScheme
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