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Searched refs:indexOfAllele (Results 1 – 17 of 17) sorted by relevance

/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/genotyper/
H A DAlleleList.java32 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);
H A DLikelihoodMatrix.java60 public int indexOfAllele(final A allele); in indexOfAllele() method
H A DIndexedAlleleList.java66 public int indexOfAllele(final A allele) { in indexOfAllele() method in IndexedAlleleList
H A DAlleleLikelihoods.java241 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);
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/genotyper/
H A DAlleleListUnitTest.java51 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()
H A DAlleleLikelihoodsUnitTest.java484 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 …]
H A DAlleleListUnitTester.java55 Assert.assertEquals(actual.indexOfAllele(actualAllele), i, "allele index mismatch"); in assertAlleleList()
59 Assert.assertEquals(actual.indexOfAllele((A) NEVER_USE_ALLELE), -1); in assertAlleleList()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/
H A DGenotypingData.java78 public int indexOfAllele(final A allele) { in indexOfAllele() method in GenotypingData
80 return likelihoods.indexOfAllele(allele); in indexOfAllele()
H A DGenotypingLikelihoods.java96 public int indexOfAllele(final A allele) { in indexOfAllele() method in GenotypingLikelihoods
98 return alleles.indexOfAllele(allele); in indexOfAllele()
H A DAlleleLikelihoodMatrixMapper.java61 public int indexOfAllele(final A allele) { in mapAlleles() method in AlleleLikelihoodMatrixMapper
63 return permutation.indexOfAllele(allele); in mapAlleles()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/
H A DSubsettedLikelihoodMatrix.java31 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
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/
H A DGenotypingDataUnitTest.java33 Assert.assertEquals(data.indexOfAllele(data.getAllele(i)), i); in testInstantiation()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/pairhmm/
H A DVectorPairHMMUnitTest.java142 public int indexOfAllele(Haplotype allele) {
H A DPairHMMUnitTest.java562 public int indexOfAllele(Haplotype allele) { in matrix() method in PairHMMUnitTest
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/
H A DVariantAnnotator.java274 … sampleMatrix.set(sampleMatrix.indexOfAllele(pileupAllele), readIndex.intValue(), 0); in makeLikelihoods()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/
H A DHaplotypeCallerGenotypingEngine.java208 …le.getKey()+" Haps: "+allele.getValue().stream().map(readLikelihoods::indexOfAllele).map(i -> Inte… in assignGenotypeLikelihoods()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/
H A DAssemblyBasedCallerUtilsUnitTest.java156 final int haplotypeIndex = sampleMatrix.indexOfAllele(haplotype); in testAnnotateReadLikelihoodsWithRegionsDataProvider()
304 final int alleleIndex = sampleMatrix.indexOfAllele(allele); in testAnnotateReadLikelihoodsWithSupportedAllelesDataProvider()