| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/readthreading/ |
| H A D | ReadThreadingAssembler.java | 128 final Haplotype refHaplotype, in runLocalAssembly() argument
136 Utils.nonNull(refHaplotype, "Reference haplotype cannot be null."); in runLocalAssembly()
156 refHaplotype.setGenomeLocation(activeRegionExtendedLocation); in runLocalAssembly()
157 resultSet.add(refHaplotype); in runLocalAssembly()
198 sanityCheckGraph(result.getSeqGraph(), refHaplotype); in assembleKmerGraphsAndHaplotypeCall() local
338 refHaplotype.setScore(kBestHaplotype.score()); in findBestPaths()
391 returnHaplotypes.add(refHaplotype); in findBestPaths()
504 sanityCheckReferenceGraph(graph, refHaplotype); in sanityCheckGraph()
602 final Haplotype refHaplotype, in createGraph() argument
608 if ( refHaplotype.length() < kmerSize ) { in createGraph()
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| H A D | JunctionTreeLinkedDeBruijnGraph.java | 398 …oid postProcessForHaplotypeFinding(final File debugGraphOutputPath, final Locatable refHaplotype) { in postProcessForHaplotypeFinding() argument
402 …printGraph(new File(debugGraphOutputPath, refHaplotype + "-sequenceGraph." + kmerSize + ".0.4.JT_u… in postProcessForHaplotypeFinding()
406 …printGraph(new File(debugGraphOutputPath, refHaplotype + "-sequenceGraph." + kmerSize + ".0.5.JT_p… in postProcessForHaplotypeFinding()
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| H A D | ReadThreadingGraph.java | 197 …oid postProcessForHaplotypeFinding(final File debugGraphOutputPath, final Locatable refHaplotype) { in postProcessForHaplotypeFinding() argument
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| H A D | AbstractReadThreadingGraph.java | 115 …ic abstract void postProcessForHaplotypeFinding(File debugGraphOutputPath, Locatable refHaplotype); in postProcessForHaplotypeFinding() argument
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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 | 240 refHaplotype.setCigar(refCigar); in testAnnotateReadLikelihoodsWithSupportedAllelesDataProvider()
329 return refHaplotype; in applyVariant()
1259 …refHaplotype.setCigar(new Cigar(Collections.singletonList(new CigarElement(refHaplotype.length(), … in testAddGivenAlleles()
1260 …refHaplotype.setGenomeLocation(new SimpleInterval("chr", assemblyRegionStart, assemblyRegionStart … in testAddGivenAlleles()
1262 assemblyResultSet.add(refHaplotype); in testAddGivenAlleles()
1335 …refHaplotype.setCigar(new Cigar(Collections.singletonList(new CigarElement(refHaplotype.length(), … in testAddMultiallelicGivenAlleles()
1336 …refHaplotype.setGenomeLocation(new SimpleInterval("chr", assemblyRegionStart, assemblyRegionStart … in testAddMultiallelicGivenAlleles()
1338 assemblyResultSet.add(refHaplotype); in testAddMultiallelicGivenAlleles()
1362 …refHaplotype.setCigar(new Cigar(Collections.singletonList(new CigarElement(refHaplotype.length(), … in testGivenAllelesHugeInsertion()
1363 …refHaplotype.setGenomeLocation(new SimpleInterval("chr", assemblyRegionStart, assemblyRegionStart … in testGivenAllelesHugeInsertion()
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| H A D | ReferenceConfidenceModelUnitTest.java | 595 …c AlleleLikelihoods<GATKRead, Haplotype> createDummyStratifiedReadMap(final Haplotype refHaplotype,
598 return new AlleleLikelihoods<>(samples, new IndexedAlleleList<>(refHaplotype),
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/readthreading/ |
| H A D | ReadThreadingAssemblerUnitTest.java | 120 final Haplotype refHaplotype = new Haplotype(refBases, true); in testAssembleRef() local
122 Assert.assertEquals(haplotypes, Collections.singletonList(refHaplotype)); in testAssembleRef()
173 final Haplotype refHaplotype = new Haplotype(refBases, true); in testAssemblyWithVariant() local
176 Assert.assertEquals(haplotypes, Arrays.asList(refHaplotype, altHaplotype)); in testAssemblyWithVariant()
181 final Haplotype refHaplotype = new Haplotype(refBases, true); in assemble() local
183 c.add(new CigarElement(refHaplotype.getBases().length, CigarOperator.M)); in assemble()
184 refHaplotype.setCigar(c); in assemble()
234 final Haplotype refHaplotype = new Haplotype(refBases, true); in testSimpleAssembly() local
238 Assert.assertEquals(haplotypes.get(0), refHaplotype); in testSimpleAssembly()
248 Haplotype refHaplotype; field in ReadThreadingAssemblerUnitTest.TestAssembler
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
| H A D | ReferenceConfidenceModel.java | 142 public List<VariantContext> calculateRefConfidence(final Haplotype refHaplotype, in calculateRefConfidence() argument
174 public List<VariantContext> calculateRefConfidence(final Haplotype refHaplotype, in calculateRefConfidence() argument
183 Utils.nonNull(refHaplotype, "refHaplotype cannot be null"); in calculateRefConfidence()
185 …Utils.validateArg(calledHaplotypes.contains(refHaplotype), "calledHaplotypes must contain the refH… in calculateRefConfidence()
190 …Utils.validateArg( refHaplotype.length() == activeRegion.getPaddedSpan().size(), () -> "refHaploty… in calculateRefConfidence()
196 final byte[] ref = refHaplotype.getBases(); in calculateRefConfidence()
760 final Haplotype refHaplotype = new Haplotype(refBases, true); in createReferenceHaplotype() local
761 refHaplotype.setAlignmentStartHapwrtRef(alignmentStart); in createReferenceHaplotype()
763 c.add(new CigarElement(refHaplotype.getBases().length, CigarOperator.M)); in createReferenceHaplotype()
764 refHaplotype.setCigar(c); in createReferenceHaplotype()
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| H A D | AssemblyResultSet.java | 44 private Haplotype refHaplotype; field in AssemblyResultSet
75 if (refHaplotype == null) { in trimTo()
98 if (result.refHaplotype == null) { in trimTo()
170 return refHaplotype; in getReferenceHaplotype()
482 if (refHaplotype == null) { in updateReferenceHaplotype()
483 refHaplotype = newHaplotype; in updateReferenceHaplotype()
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| H A D | AssemblyBasedCallerUtils.java | 96 …lihoods<GATKRead, Haplotype> originalReadLikelihoods, final Haplotype refHaplotype, final Locatabl… in realignReadsToTheirBestHaplotype() argument
104 … = AlignmentUtils.createReadAlignedToRef(originalRead, bestHaplotype, refHaplotype, paddedReferenc… in realignReadsToTheirBestHaplotype()
277 …final Haplotype refHaplotype = createReferenceHaplotype(region, paddedReferenceLoc, referenceReade…
289 …ResultSet assemblyResultSet = assemblyEngine.runLocalAssembly(region, refHaplotype, fullReferenceW…
292 …getStart(), givenAlleles, argumentCollection.maxMnpDistance, aligner, refHaplotype, assemblyResult…
313 …final SmithWatermanAligner aligner, final Haplotype refHaplotype, final AssemblyResultSet assembly…
314 final int activeRegionStart = refHaplotype.getAlignmentStartHapwrtRef();
355 …final Cigar cigar = CigarUtils.calculateCigar(refHaplotype.getBases(), insertedHaplotype.getBases(…
357 insertedHaplotype.setGenomeLocation(refHaplotype.getGenomeLocation());
436 …c AlleleLikelihoods<GATKRead, Haplotype> createDummyStratifiedReadMap(final Haplotype refHaplotype, in createDummyStratifiedReadMap() argument
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| H A D | HaplotypeCallerEngine.java | 758 …final Haplotype refHaplotype = AssemblyBasedCallerUtils.createReferenceHaplotype(region, paddedLoc… in referenceModelForNoVariation() local
759 final List<Haplotype> haplotypes = Collections.singletonList(refHaplotype); in referenceModelForNoVariation()
760 return referenceConfidenceModel.calculateRefConfidence(refHaplotype, haplotypes, in referenceModelForNoVariation()
761 …dedLoc, region, AssemblyBasedCallerUtils.createDummyStratifiedReadMap(refHaplotype, samplesList, r… in referenceModelForNoVariation()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/ |
| H A D | SVContextUnitTest.java | 111 … final Haplotype refHaplotype = svc.composeHaplotypeBasedOnReference(0, paddingSize, reference); in testComposeReferenceHaplotype() local
112 Assert.assertNotNull(refHaplotype); in testComposeReferenceHaplotype()
113 Assert.assertTrue(refHaplotype.isReference()); in testComposeReferenceHaplotype()
115 …Assert.assertEquals(new SimpleInterval(refHaplotype.getGenomeLocation()), expectedInterval, svc.ge… in testComposeReferenceHaplotype()
116 …Assert.assertEquals(refHaplotype.getBases(), reference.getReferenceBases(expectedInterval).getBase… in testComposeReferenceHaplotype()
117 …Assert.assertEquals(refHaplotype.getCigar(), new Cigar(Collections.singletonList(new CigarElement(… in testComposeReferenceHaplotype()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/ |
| H A D | Mutect2Engine.java | 457 …final Haplotype refHaplotype = AssemblyBasedCallerUtils.createReferenceHaplotype(region, paddedLoc…
458 final List<Haplotype> haplotypes = Collections.singletonList(refHaplotype);
459 return referenceConfidenceModel.calculateRefConfidence(refHaplotype, haplotypes,
460 …dedLoc, region, AssemblyBasedCallerUtils.createDummyStratifiedReadMap(refHaplotype, samplesList, h…
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | AlignmentUtils.java | 52 final Haplotype refHaplotype, in createReadAlignedToRef() argument
58 Utils.nonNull(refHaplotype); in createReadAlignedToRef()
106 …ult leftAlignedReadToRefCigarResult = leftAlignIndels(readToRefCigar, refHaplotype.getBases(), rea… in createReadAlignedToRef()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | AlignmentUtilsUnitTest.java | 202 …ToRef(final GATKRead read, final Haplotype haplotype, final Haplotype refHaplotype, final int refS… in testReadAlignedToRef() argument
206 …Assert.assertNull(AlignmentUtils.createReadAlignedToRef(read, haplotype, refHaplotype, refStart, t… in testReadAlignedToRef()
210 … alignedRead = AlignmentUtils.createReadAlignedToRef(read, haplotype, refHaplotype, refStart, true… in testReadAlignedToRef()
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