Add option to recalculate the allele fraction based on AD instead of … #5118
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davidbenjamin
requested changes
Aug 15, 2018
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| /** | ||
| * Created by gauthier on 8/15/18. | ||
| * Bug Laura to fill this in |
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Might want to do something about this.
| Utils.nonNull(vc, "vc is null"); | ||
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| final GenotypesContext genotypes = vc.getGenotypes(); | ||
| if ( g == null || !g.isCalled() || g.hasExtendedAttribute(getKeyNames().get(0))) { //don't overwrite AF based on Bayesian estimate if it already exists |
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It should be clear in the class javadoc that this annotation does nothing if AF is already present.
| else if (likelihoods != null) { | ||
| DepthPerAlleleBySample adCalc = new DepthPerAlleleBySample(); | ||
| final int[] AD = adCalc.annotateWithLikelihoods(vc, g, new LinkedHashSet<>(vc.getAlleles()), likelihoods); | ||
| final double[] allAlleleFractions = MathUtils.normalizeFromRealSpace(Arrays.stream(AD).mapToDouble(x -> x*1.0).toArray()); |
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x -> x will work here without the *1.0
| @@ -235,10 +235,13 @@ private void addGenotypes(final LikelihoodMatrix<Allele> tumorLog10Matrix, | |||
| final Optional<LikelihoodMatrix<Allele>> normalLog10Matrix, | |||
| final VariantContextBuilder callVcb) { | |||
| final double[] tumorAlleleCounts = getEffectiveCounts(tumorLog10Matrix); | |||
| final Genotype tumorGenotype = new GenotypeBuilder(tumorSample, tumorLog10Matrix.alleles()) | |||
| .AD(Arrays.stream(tumorAlleleCounts).mapToInt(x -> (int) FastMath.round(x)).toArray()) | |||
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Is AD still getting added to the genotype in the new code below?
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Yes, the original code wrote out AD based on the Bayesian estimate, then overwrote it during annotation because DepthPerAlleleBySample is a StandardMutectAnnotation. So in theory, there didn't used to be a way to turn it off.
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I confirmed that the output without the arg does still have AD and added coverage in the tumor normal test.
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…the Bayesian estimate
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Codecov Report
@@ Coverage Diff @@
## master #5118 +/- ##
==============================================
+ Coverage 86.507% 86.577% +0.07%
- Complexity 29260 29716 +456
==============================================
Files 1814 1826 +12
Lines 135635 137753 +2118
Branches 15063 15313 +250
==============================================
+ Hits 117334 119262 +1928
- Misses 12833 13019 +186
- Partials 5468 5472 +4
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…the Bayesian estimate
For @meganshand until @davidbenjamin addresses #5096 in a more rigorous way