avoid error due to finite precision error in M2 pon creation #5797
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Codecov Report
@@ Coverage Diff @@
## master #5797 +/- ##
===============================================
- Coverage 87.005% 86.997% -0.008%
- Complexity 32097 32112 +15
===============================================
Files 1974 1974
Lines 147213 147249 +36
Branches 16214 16218 +4
===============================================
+ Hits 128082 128102 +20
- Misses 13228 13239 +11
- Partials 5903 5908 +5
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LeeTL1220
approved these changes
Mar 15, 2019
| final double hetPrior = alleleFrequency * (1 - alleleFrequency) * 2; | ||
| final double homPrior = MathUtils.square(alleleFrequency); | ||
| final double hetLikelihood = MathUtils.binomialProbability(totalCount, altCount, 0.5); | ||
| final double homLikelihood = MathUtils.binomialProbability(totalCount, altCount, 0.98); | ||
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| final double artifactLikelihood = new BetaBinomialDistribution(null, ARTIFACT_ALPHA, ARTIFACT_BETA, totalCount).probability(altCount); | ||
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| return MathUtils.normalizeFromRealSpace(new double[] {hetPrior * hetLikelihood + homPrior * homLikelihood, ARTIFACT_PRIOR * artifactLikelihood})[0]; | ||
| final double[] relativeProbsOfHetHomArtifact = {hetPrior * hetLikelihood + homPrior * homLikelihood, ARTIFACT_PRIOR * artifactLikelihood}; | ||
| if (MathUtils.sum(relativeProbsOfHetHomArtifact) < 0) { |
| if (MathUtils.sum(relativeProbsOfHetHomArtifact) < 0) { | ||
| return 0; | ||
| } | ||
| return MathUtils.normalizeFromRealSpace(relativeProbsOfHetHomArtifact)[0]; |
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The indices look like they have special meaning. Can you describe, in a comment, the meaning of the values in [0] and [1]?
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@LeeTL1220 for the REBC pon.