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fixing up docs from previous Pool Caller commit

This commit is contained in:
Eric Banks 2012-05-08 11:02:55 -04:00
parent b4999d14c1
commit 473d07b0c5
2 changed files with 33 additions and 25 deletions
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50
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
View File

@ -103,9 +103,34 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
return genotypeLikelihoods; return genotypeLikelihoods;
} }
/**
* Must be overridden by concrete subclasses
* @param vc variant context with alleles and genotype likelihoods
* @param log10AlleleFrequencyPriors priors
* @param result (pre-allocated) object to store likelihoods results
* @return the alleles used for genotyping
*/
protected abstract List<Allele> getLog10PNonRef(final VariantContext vc,
final double[] log10AlleleFrequencyPriors,
final AlleleFrequencyCalculationResult result);
/**
* Must be overridden by concrete subclasses
* @param vc variant context with alleles and genotype likelihoods
* @param allelesToUse alleles to subset
* @param assignGenotypes
* @param ploidy
* @return GenotypesContext object
*/
protected abstract GenotypesContext subsetAlleles(final VariantContext vc,
final List<Allele> allelesToUse,
final boolean assignGenotypes,
final int ploidy);
// ------------------------------------------------------------------------------------- // -------------------------------------------------------------------------------------
// //
// Multi-allelic implementation. // protected classes used to store exact model matrix columns
// //
// ------------------------------------------------------------------------------------- // -------------------------------------------------------------------------------------
@ -180,27 +205,4 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
return (obj instanceof ExactACset) && ACcounts.equals(((ExactACset)obj).ACcounts); return (obj instanceof ExactACset) && ACcounts.equals(((ExactACset)obj).ACcounts);
} }
} }
/**
* Must be overridden by concrete subclasses
* @param vc variant context with alleles and genotype likelihoods
* @param log10AlleleFrequencyPriors priors
* @param result (pre-allocated) object to store likelihoods results
* @return the alleles used for genotyping
*/
protected abstract List<Allele> getLog10PNonRef(final VariantContext vc,
final double[] log10AlleleFrequencyPriors,
final AlleleFrequencyCalculationResult result);
/**
* Must be overridden by concrete subclasses
* @param vc variant context with alleles and genotype likelihoods
* @param allelesToUse alleles to subset
* @param assignGenotypes
* @param ploidy
* @return GenotypesContext object
*/
protected abstract GenotypesContext subsetAlleles(final VariantContext vc,
final List<Allele> allelesToUse,
final boolean assignGenotypes,
final int ploidy);
} }

6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -102,6 +102,12 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
} }
// -------------------------------------------------------------------------------------
//
// Multi-allelic implementation.
//
// -------------------------------------------------------------------------------------
public static void linearExactMultiAllelic(final GenotypesContext GLs, public static void linearExactMultiAllelic(final GenotypesContext GLs,
final int numAlternateAlleles, final int numAlternateAlleles,
final double[] log10AlleleFrequencyPriors, final double[] log10AlleleFrequencyPriors,