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Static cache for binomial probability 

-- Very low level performance optimization
This commit is contained in:
Mark DePristo 2011-09-23 17:29:34 -04:00
parent 96ffc63caa
commit b66841f179
1 changed files with 16 additions and 1 deletions
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17
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -544,6 +544,21 @@ public class UnifiedGenotyperEngine {
AFs[i] = AlleleFrequencyCalculationModel.VALUE_NOT_CALCULATED; AFs[i] = AlleleFrequencyCalculationModel.VALUE_NOT_CALCULATED;
} }
private final static double[] binomialProbabilityDepthCache = new double[10000];
static {
for ( int i = 1; i < binomialProbabilityDepthCache.length; i++ ) {
binomialProbabilityDepthCache[i] = MathUtils.binomialProbability(0, i, 0.5);
}
}
private final double getRefBinomialProb(final int depth) {
if ( depth < binomialProbabilityDepthCache.length )
return binomialProbabilityDepthCache[depth];
else
return MathUtils.binomialProbability(0, depth, 0.5);
}
private VariantCallContext estimateReferenceConfidence(VariantContext vc, Map<String, AlignmentContext> contexts, double theta, boolean ignoreCoveredSamples, double initialPofRef) { private VariantCallContext estimateReferenceConfidence(VariantContext vc, Map<String, AlignmentContext> contexts, double theta, boolean ignoreCoveredSamples, double initialPofRef) {
if ( contexts == null ) if ( contexts == null )
return null; return null;
@ -567,7 +582,7 @@ public class UnifiedGenotyperEngine {
depth = context.getExtendedEventPileup().size(); depth = context.getExtendedEventPileup().size();
} }
P_of_ref *= 1.0 - (theta / 2.0) * MathUtils.binomialProbability(0, depth, 0.5); P_of_ref *= 1.0 - (theta / 2.0) * getRefBinomialProb(depth);
} }
return new VariantCallContext(vc, QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING, false); return new VariantCallContext(vc, QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING, false);