/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/genotyper/ |
H A D | AlleleList.java | 32 int indexOfAllele(final A allele); in indexOfAllele() method 46 return indexOfAllele(allele) >= 0; in containsAllele() 57 public int indexOfAllele(final Allele allele) { 229 public int indexOfAllele(final A allele) { 230 return list.indexOfAllele(allele); 267 final int originalIndex = original.indexOfAllele(target.getAllele(i)); 291 return to.indexOfAllele(from.getAllele(fromIndex)); 330 public int indexOfAllele(final A allele) { 331 return to.indexOfAllele(allele);
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H A D | LikelihoodMatrix.java | 60 public int indexOfAllele(final A allele); in indexOfAllele() method
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H A D | IndexedAlleleList.java | 66 public int indexOfAllele(final A allele) { in indexOfAllele() method in IndexedAlleleList
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H A D | AlleleLikelihoods.java | 241 public int indexOfAllele(final A allele) { in indexOfAllele() method in AlleleLikelihoods 242 return alleles.indexOfAllele(allele); in indexOfAllele() 734 final int oldAlleleIndex = indexOfAllele(oldAllele); 859 final int nonRefAlleleIndex = indexOfAllele((A) Allele.NON_REF_ALLELE); 877 …&& !Double.isNaN(alleleLikelihood) && allelesToConsider.indexOfAllele(alleles.getAllele(i)) != MIS… 1289 public int indexOfAllele(final A allele) { 1291 return AlleleLikelihoods.this.indexOfAllele(allele);
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/genotyper/ |
H A D | AlleleListUnitTest.java | 51 al.indexOfAllele(null); in testEmptyListIndexOfNull() 52 Assert.assertEquals(al.indexOfAllele(null), -1); in testEmptyListIndexOfNull() 157 …Assert.assertEquals(subset.fromIndex(i), originalAlleleList.indexOfAllele(targetRandomAlleleList.g… in testSubsetPermutation() 162 Assert.assertEquals(subset.toIndex(j), targetRandomAlleleList.indexOfAllele(allele)); in testSubsetPermutation() 199 …Assert.assertEquals(permutation.toIndex(i), targetAlleleList.indexOfAllele(originalAlleleList.getA… in testShufflePermutation() 200 …Assert.assertEquals(permutation.fromIndex(i), originalAlleleList.indexOfAllele(targetAlleleList.ge… in testShufflePermutation()
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H A D | AlleleLikelihoodsUnitTest.java | 484 final int indexOfAllele = result.indexOfAllele(allele); 485 Assert.assertTrue(indexOfAllele >= 0); 486 Assert.assertFalse(alleleIndices.contains(indexOfAllele)); 487 alleleIndices.add(indexOfAllele); 488 Assert.assertSame(allele, alleles[indexOfAllele]); 696 return - Math.abs(31 * (indexOfSample + 1) + 101 * indexOfAllele + 1009 * readIndex); 723 final int indexOfAllele = result.indexOfAllele(allele); 724 Assert.assertTrue(indexOfAllele >= 0); 725 Assert.assertFalse(alleleIndices.contains(indexOfAllele)); 726 alleleIndices.add(indexOfAllele); [all …]
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H A D | AlleleListUnitTester.java | 55 Assert.assertEquals(actual.indexOfAllele(actualAllele), i, "allele index mismatch"); in assertAlleleList() 59 Assert.assertEquals(actual.indexOfAllele((A) NEVER_USE_ALLELE), -1); in assertAlleleList()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/ |
H A D | GenotypingData.java | 78 public int indexOfAllele(final A allele) { in indexOfAllele() method in GenotypingData 80 return likelihoods.indexOfAllele(allele); in indexOfAllele()
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H A D | GenotypingLikelihoods.java | 96 public int indexOfAllele(final A allele) { in indexOfAllele() method in GenotypingLikelihoods 98 return alleles.indexOfAllele(allele); in indexOfAllele()
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H A D | AlleleLikelihoodMatrixMapper.java | 61 public int indexOfAllele(final A allele) { in mapAlleles() method in AlleleLikelihoodMatrixMapper 63 return permutation.indexOfAllele(allele); in mapAlleles()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/ |
H A D | SubsettedLikelihoodMatrix.java | 31 final int[] oldIndices = alleles.stream().mapToInt(matrix::indexOfAllele).toArray(); in SubsettedLikelihoodMatrix() 60 public int indexOfAllele(final A allele) { return alleles.indexOf(allele); } in indexOfAllele() method in SubsettedLikelihoodMatrix
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/ |
H A D | GenotypingDataUnitTest.java | 33 Assert.assertEquals(data.indexOfAllele(data.getAllele(i)), i); in testInstantiation()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/pairhmm/ |
H A D | VectorPairHMMUnitTest.java | 142 public int indexOfAllele(Haplotype allele) {
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H A D | PairHMMUnitTest.java | 562 public int indexOfAllele(Haplotype allele) { in matrix() method in PairHMMUnitTest
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ |
H A D | VariantAnnotator.java | 274 … sampleMatrix.set(sampleMatrix.indexOfAllele(pileupAllele), readIndex.intValue(), 0); in makeLikelihoods()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
H A D | HaplotypeCallerGenotypingEngine.java | 208 …le.getKey()+" Haps: "+allele.getValue().stream().map(readLikelihoods::indexOfAllele).map(i -> Inte… in assignGenotypeLikelihoods()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
H A D | AssemblyBasedCallerUtilsUnitTest.java | 156 final int haplotypeIndex = sampleMatrix.indexOfAllele(haplotype); in testAnnotateReadLikelihoodsWithRegionsDataProvider() 304 final int alleleIndex = sampleMatrix.indexOfAllele(allele); in testAnnotateReadLikelihoodsWithSupportedAllelesDataProvider()
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