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Merge pull request #1339 from broadinstitute/ldg_documentGenotypingCode 

Add some comments to AFCalculationResult
This commit is contained in:
ldgauthier 2016-04-08 16:02:21 -04:00
parent b4197f62f2 d573fc4adf
commit 2baa7a0b9e
3 changed files with 4 additions and 4 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
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@ -521,7 +521,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
@Ensures("MathUtils.goodLog10Probability(result)") @Ensures("MathUtils.goodLog10Probability(result)")
protected final double estimateLog10ReferenceConfidenceForOneSample(final int depth, final double log10OfTheta) { protected final double estimateLog10ReferenceConfidenceForOneSample(final int depth, final double log10OfTheta) {
final double log10PofNonRef = log10OfTheta + getRefBinomialProbLog10(depth); final double log10PofNonRef = log10OfTheta + getRefBinomialProbLog10(depth);
return MathUtils.log10OneMinusX(Math.pow(10.0, log10PofNonRef)); return MathUtils.log10OneMinusX(Math.pow(10.0, log10PofNonRef)); //TODO: this 10^log(PofNonRef) seems inefficient
} }
/** /**

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java
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@ -312,7 +312,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
* Compute genotypes at a given locus. * Compute genotypes at a given locus.
* *
* @param vc the GL-annotated variant context * @param vc the GL-annotated variant context
* @return the VariantCallContext object * @return the VariantCallContext object (can be null)
*/ */
public VariantCallContext calculateGenotypes(VariantContext vc) { public VariantCallContext calculateGenotypes(VariantContext vc) {
final VariantContext.Type type = vc.getType(); final VariantContext.Type type = vc.getType();

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationResult.java
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@ -69,8 +69,8 @@ import java.util.*;
* that users of this code can rely on the values coming out of these functions. * that users of this code can rely on the values coming out of these functions.
*/ */
public class AFCalculationResult { public class AFCalculationResult {
private final static int AF0 = 0; private final static int AF0 = 0; //index of the AC=0 entry in the log10 array (of priors, likelihoods, or posteriors listed below)
private final static int AF1p = 1; private final static int AF1p = 1; //index of the AC>0 entry in the log10 array
private final static int LOG_10_ARRAY_SIZES = 2; private final static int LOG_10_ARRAY_SIZES = 2;
private final double[] log10LikelihoodsOfAC; private final double[] log10LikelihoodsOfAC;