| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/ |
| H A D | GenotypingDataUnitTest.java | 20 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = ReadLikelihoodsUnitTester.readLikelihoods(… in testInstantiation() local
26 Assert.assertEquals(data.readLikelihoods(), likelihoods); in testInstantiation() local
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| H A D | IndependentSampleGenotypesModelUnitTest.java | 23 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = ReadLikelihoodsUnitTester.readLikelihoods(… in testCalculateLikelihoods() local
45 …private AlleleList<Allele> discardAllelesAtRandom(final AlleleList<Allele> likelihoods, final int … in discardAllelesAtRandom()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ |
| H A D | StrandBiasTest.java | 29 final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in annotate()
52 …, Object> calculateAnnotationFromLikelihoods(final AlleleLikelihoods<GATKRead, Allele> likelihoods, in calculateAnnotationFromLikelihoods()
121 … public static int[][] getContingencyTable( final AlleleLikelihoods<GATKRead, Allele> likelihoods, in getContingencyTable()
134 … public static int[][] getContingencyTable( final AlleleLikelihoods<GATKRead, Allele> likelihoods, in getContingencyTable()
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| H A D | DepthPerAlleleBySample.java | 47 final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in annotate()
62 …ntext vc, Genotype g, Set<Allele> alleles, final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in annotateWithLikelihoods()
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| H A D | QualByDepth.java | 58 final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in annotate()
101 …getDepth(final GenotypesContext genotypes, final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in getDepth()
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| H A D | RankSumTest.java | 26 final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in annotate()
59 …QualsFromLikelihood(VariantContext vc, AlleleLikelihoods<GATKRead, Allele> likelihoods, List<Doubl… in fillQualsFromLikelihood()
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| H A D | RMSMappingQuality.java | 110 … final AlleleLikelihoods<GATKRead, Allele> likelihoods){ in annotateRawData()
216 final AlleleLikelihoods<GATKRead, Allele> likelihoods, in calculateRawData()
236 final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in annotate()
390 final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in getNumOfReads()
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| H A D | SampleList.java | 32 final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in annotate()
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| H A D | InfoFieldAnnotation.java | 30 … final AlleleLikelihoods<GATKRead, Allele> likelihoods); in annotate()
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| H A D | AS_StrandBiasMutectAnnotation.java | 29 …nnotate(ReferenceContext ref, VariantContext vc, AlleleLikelihoods<GATKRead, Allele> likelihoods) { in annotate()
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| H A D | Coverage.java | 43 final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in annotate()
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| H A D | GenotypeAnnotation.java | 33 final AlleleLikelihoods<GATKRead, Allele> likelihoods); in annotate()
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| H A D | GenotypeSummaries.java | 37 final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in annotate()
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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 | 17 private final AlleleLikelihoods<GATKRead, A> likelihoods; field in GenotypingData
30 …c GenotypingData(final PloidyModel ploidyModel, final AlleleLikelihoods<GATKRead, A> likelihoods) { in GenotypingData()
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| H A D | GenotypingLikelihoods.java | 16 private final GenotypeLikelihoods[] likelihoods; field in GenotypingLikelihoods
37 … AlleleList<A> alleles, final PloidyModel ploidyModel, final List<GenotypeLikelihoods> likelihoods… in GenotypingLikelihoods()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ |
| H A D | VariantAnnotatorEngineUnitTest.java | 53 final AlleleLikelihoods<GATKRead, Allele> likelihoods = in testCombineAnnotations() local
140 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = new AlleleLikelihoods<>(sampleList, allele… in makeReadLikelihoods() local
176 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = makeReadLikelihoods(ref, alt, refAllele, a… in testAllAnnotations() local
203 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = makeReadLikelihoods(ref, alt, refAllele, a… in testMultipleAnnotations() local
239 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = makeReadLikelihoods(ref, alt, refAllele, a… in testCoverageAnnotationOnDbSnpSite() local
274 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = makeReadLikelihoods(ref, alt, refAllele, a… in testCoverageAnnotationOnOverlapSite() local
317 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = makeReadLikelihoods(ref, alt, refAllele, a… in testCoverageAnnotationOnDBSNPAndOverlapSite() local
361 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = makeReadLikelihoods(ref, alt, refAllele, a… in testCoverageAnnotationViaEngine() local
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| H A D | RMSMappingQualityUnitTest.java | 90 final AlleleLikelihoods<GATKRead, Allele> likelihoods = in testLikelihoods() local
110 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = new AlleleLikelihoods<>(sampleList, allele… in testEmptyLikelihoods() local
163 final AlleleLikelihoods<GATKRead, Allele> likelihoods = in testLikelihoods_AS() local
184 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = new AlleleLikelihoods<>(sampleList, allele… in testLikelihoodsEmpty_AS() local
341 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = ArtificialAnnotationUtils.makeLikelihoods(… in testGetNumReadsFallbackBehavior() local
360 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = ArtificialAnnotationUtils.makeLikelihoods(… in testGetNumReadsFallbackReturnsNegativeOneWhenDataIsBad() local
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| H A D | DepthPerAlleleBySampleUnitTest.java | 57 final AlleleLikelihoods<GATKRead, Allele> likelihoods = in testUsingReads() local
84 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = new AlleleLikelihoods<>(sampleList, allele… in testBlowUp() local
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| H A D | CoverageUnitTest.java | 50 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = new AlleleLikelihoods<>(sampleList, allele… in testLikelihoodsEmpty() local
76 final AlleleLikelihoods<GATKRead, Allele> likelihoods = in testLikelihoods() local
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| H A D | BaseQualityRankSumTestUnitTest.java | 60 final AlleleLikelihoods<GATKRead, Allele> likelihoods = in testBaseQual() local
86 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = new AlleleLikelihoods<>(sampleList, allele… in testEmptyIfNoGenotypes() local
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| H A D | MappingQualityZeroUnitTest.java | 70 final AlleleLikelihoods<GATKRead, Allele> likelihoods = in testLikelihoods() local
88 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = new AlleleLikelihoods<>(sampleList, allele… in testEmptyLikelihoods() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ |
| H A D | AS_RMSMappingQuality.java | 78 final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in annotate()
95 … final AlleleLikelihoods<GATKRead, Allele> likelihoods ) { in annotateRawData()
111 final AlleleLikelihoods<GATKRead, Allele> likelihoods, in calculateRawData()
203 …private void getRMSDataFromLikelihoods(final AlleleLikelihoods<GATKRead, Allele> likelihoods, Redu… in getRMSDataFromLikelihoods()
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| H A D | AS_QualByDepth.java | 78 final AlleleLikelihoods<GATKRead, Allele> likelihoods ) { in annotate()
94 … final AlleleLikelihoods<GATKRead, Allele> likelihoods) { in annotateRawData()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/testutils/ |
| H A D | ArtificialAnnotationUtils.java | 74 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = initializeReadLikelihoods(sample, new Inde… in makeLikelihoods() local
112 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = initializeReadLikelihoods(sample, new Inde… in makeTriAllelicLikelihoods() local
164 final AlleleLikelihoods<GATKRead, Allele> likelihoods = in makeHetAlleleVariantContext() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/ |
| H A D | UniqueAltReadCountUnitTest.java | 32 … final AlleleLikelihoods<GATKRead, Allele> likelihoods = createTestLikelihoods(Optional.empty()); in testSingleDuplicate() local
99 …final AlleleLikelihoods<GATKRead, Allele> likelihoods = new AlleleLikelihoods<>(sampleList, allele… in createTestLikelihoods() local
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