| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/ |
| H A D | AssemblyBasedSVDiscoveryTestDataProvider.java | 123 … delRange.getContig(), delRange.getStart(), delRange.getContig(), delRange.getEnd(), ""), in makeDeletionType()
134 ….SupportedType.INV.name(), invertedRegion.getContig(), invertedRegion.getStart() - 1, invertedRegi… in makeInversion()
142 invRange.getContig(), in makeInversionType()
146 … invRange.getContig(), invRange.getStart() - 1, invRange.getContig(), invRange.getEnd(), ""), in makeInversionType()
165 insertionPos.getContig(), in makeInsertionType()
169 …insertionPos.getContig(), insertionPos.getStart(), insertionPos.getContig(), insertionPos.getEnd()… in makeInsertionType()
179 …duplicatedRange.getContig(), duplicatedRange.getStart() , duplicatedRange.getContig(), duplicatedR… in makeTandemDuplication()
188 duplicatedRange.getContig(), in makeTandemDuplicationType()
192 …duplicatedRange.getContig(), duplicatedRange.getStart(), duplicatedRange.getContig(), duplicatedRa… in makeTandemDuplicationType()
221 …upstreamLoc.getContig(), upstreamLoc.getStart(), dnstreamLoc.getContig(), dnstreamLoc.getEnd(), "1… in makeBND()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/ |
| H A D | GenomeLoc.java | 78 public final String getContig() { in getContig() method in GenomeLoc
98 return getContig(); in toString()
100 return String.format("%s:%d", getContig(), getStart()); in toString()
102 return String.format("%s:%d-%d", getContig(), getStart(), getStop()); in toString()
151 return new GenomeLoc(getContig(), this.contigIndex, in merge()
165 …return new GenomeLoc[] { new GenomeLoc(getContig(),contigIndex,getStart(),splitPoint-1), new Genom… in split()
182 return new GenomeLoc(getContig(), this.contigIndex, in intersect()
252 … n = new GenomeLoc(this.getContig(), getContigIndex(), that.getStop() + 1, this.getStop()); in subtract()
536 return new GenomeLoc(loc.getContig(), loc.getContigIndex(), start, loc.getStop()); in setStart()
551 return new GenomeLoc(loc.getContig(), loc.getContigIndex(), loc.start, stop); in setStop()
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| H A D | SimpleInterval.java | 47 this(Utils.nonNull(locatable).getContig(), in SimpleInterval()
184 public String getContig(){ in getContig() method in SimpleInterval
243 if ( other == null || other.getContig() == null ) { in overlapsWithMargin()
247 …return this.contig.equals(other.getContig()) && this.start <= other.getEnd() + margin && other.get… in overlapsWithMargin()
259 if ( other == null || other.getContig() == null ) { in contains()
263 …return this.contig.equals(other.getContig()) && this.start <= other.getStart() && this.end >= othe… in contains()
273 return new SimpleInterval(getContig(), in intersect()
288 return new SimpleInterval(getContig(), in mergeWithContiguous()
303 …Utils.validateArg(this.getContig().equals(other.getContig()), "Cannot get span for intervals on di… in spanWith()
309 …return this.getContig().equals(that.getContig()) && this.getStart() <= that.getEnd() + 1 && that.g… in contiguous()
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| H A D | GenomeLocParser.java | 312 final String contig = locatable.getContig(); in parseGenomeLoc()
358 … allResolvedIntervals.stream().map(f -> f.getContig()).collect(Collectors.joining(" or ")) in getUnambiguousInterval()
386 …return createGenomeLoc(read.getContig(), getSequenceDictionary().getSequenceIndex(read.getContig()… in createGenomeLoc()
396 return createGenomeLoc(feature.getContig(), feature.getStart(), feature.getEnd()); in createGenomeLoc()
408 return createGenomeLoc(locatable.getContig(), locatable.getStart(), locatable.getEnd()); in createGenomeLoc()
430 final String contigName = loc.getContig(); in createGenomeLocAtStart()
455 …return createGenomeLocOnContig(loc.getContig(), loc.getContigIndex(), loc.getStart() - padding, lo… in createPaddedGenomeLoc()
467 String contigName = loc.getContig(); in createGenomeLocAtStop()
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| H A D | IntervalUtils.java | 570 lengths.put(loc.getContig(), loc.size()); in getContigSizes()
607 if(prevContig == null || !loc.getContig().equals(prevContig)) { in scatterContigIntervals()
610 prevContig = loc.getContig(); in scatterContigIntervals()
661 if(nextLoc == null || !nextLoc.getContig().equals(loc.getContig())) { in scatterContigIntervals()
839 if (left.getContig() == null || right.getContig() == null) { in overlaps()
841 } else if (!left.getContig().equals(right.getContig())) { in overlaps()
1003 currentContig = currentInterval.getContig(); in groupIntervalsByContig()
1024 splits.put(loc.getContig(), contigLocs); in splitByContig()
1162 resolvedIntervals.get(0).getContig(), in getResolvedIntervals()
1282 .collect(Collectors.groupingBy(Locatable::getContig)) in getSpanningIntervals()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/ |
| H A D | ReferenceContext.java | 140 this.window = new SimpleInterval(interval.getContig(), in ReferenceContext()
142 trimToContigLength(interval.getContig(), window.getEnd())); in ReferenceContext()
147 public String getContig() { return interval.getContig(); } in getContig() method in ReferenceContext
221 window.getContig(), in getBases()
223 trimToContigLength(window.getContig(), window.getEnd()) in getBases()
244 window.getContig(), in getBases()
246 trimToContigLength(window.getContig(), window.getEnd() + windowTrailingBases) in getBases()
315 window = new SimpleInterval(interval.getContig(), in setWindow()
377 return trimToContigLength(locus.getContig(), locus.getEnd() + windowTrailingBases); in calculateWindowStop()
424 final SimpleInterval newWindow = new SimpleInterval(window.getContig(), center, center) in getKmerAround()
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| H A D | VariantShard.java | 32 return getShardNumber() == that.getShardNumber() && getContig().equals(that.getContig()); in equals()
40 result = 5779 * result + getContig().hashCode(); in hashCode()
44 public String getContig() { in getContig() method in VariantShard
58 if (location.getContig()==null) { in getVariantShardsFromInterval()
67 shardList.add(new VariantShard(i, location.getContig())); in getVariantShardsFromInterval()
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| H A D | ReferenceShard.java | 34 return getContig().equals(that.getContig()); in equals()
42 result = 5779 * result + getContig().hashCode(); in hashCode()
46 public String getContig() { in getContig() method in ReferenceShard
68 return new ReferenceShard(location.getStart()/REFERENCE_SHARD_SIZE, location.getContig()); in getShardNumberFromInterval()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/ |
| H A D | BreakEndVariantType.java | 74 …WITCH) || !narl.getLeftJustifiedLeftRefLoc().getContig().equals(narl.getLeftJustifiedRightRefLoc()… in getIDString()
76 … String locationPartOfString = makeLocationString(narl.getLeftJustifiedLeftRefLoc().getContig(), in getIDString()
77 … narl.getLeftJustifiedLeftRefLoc().getStart(), narl.getLeftJustifiedRightRefLoc().getContig(), in getIDString()
141 …streamMate ? narl.getLeftJustifiedLeftRefLoc().getContig() : narl.getLeftJustifiedRightRefLoc().ge… in IntraChromosomalStrandSwitch55BreakEnd()
158 …return Allele.create(refBase + insertedSequence + "]" + novelAdjRefLoc.getContig() + ":" + novelAd… in constructAltAllele()
173 …streamMate ? narl.getLeftJustifiedLeftRefLoc().getContig() : narl.getLeftJustifiedRightRefLoc().ge… in IntraChromosomalStrandSwitch33BreakEnd()
190 …return Allele.create("[" + novelAdjRefLoc.getContig() + ":" + novelAdjRefLoc.getEnd() + "[" + inse… in constructAltAllele()
205 …streamMate ? narl.getLeftJustifiedLeftRefLoc().getContig() : narl.getLeftJustifiedRightRefLoc().ge… in IntraChromosomeRefOrderSwap()
225 …return Allele.create("]" + novelAdjRefLoc.getContig() + ":" + novelAdjRefLoc.getEnd() + "]" + inse… in constructAltAllele()
227 …return Allele.create(refBase + insertedSequence + "[" + novelAdjRefLoc.getContig() + ":" + novelAd… in constructAltAllele()
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| H A D | SimpleSVType.java | 61 super(novelAdjacencyAndAltHaplotype.getLeftJustifiedLeftRefLoc().getContig(), in Inversion()
94 super(novelAdjacencyAndAltHaplotype.getLeftJustifiedLeftRefLoc().getContig(), in Deletion()
127 super(novelAdjacencyAndAltHaplotype.getLeftJustifiedLeftRefLoc().getContig(), in Insertion()
163 … + makeLocationString(novelAdjacencyAndAltHaplotype.getLeftJustifiedLeftRefLoc().getContig(), in getIDString()
165 … novelAdjacencyAndAltHaplotype.getLeftJustifiedLeftRefLoc().getContig(), in getIDString()
187 super(novelAdjacencyAndAltHaplotype.getLeftJustifiedLeftRefLoc().getContig(), in DuplicationTandem()
203 … + makeLocationString(dupSeqRepeatUnitRefSpan.getContig(), dupSeqRepeatUnitRefSpan.getStart(), in getIDString()
204 dupSeqRepeatUnitRefSpan.getContig(), dupSeqRepeatUnitRefSpan.getEnd()); in getIDString()
218 …getContigName(evidenceTargetLink.getPairedStrandedIntervals().getLeft().getInterval().getContig()), in ImpreciseDeletion()
244 + metadata.getContigName(leftInterval.getContig()) in getIDString()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/gcnv/ |
| H A D | GermlineCNVIntervalVariantComposerUnitTest.java | 131 {0, Collections.singleton(TEST_INTERVAL.getContig()), TEST_EXPECTED_MAP_CN - 1, in getAlleleDeterminationTestData()
133 {0, Collections.singleton(TEST_INTERVAL.getContig()), TEST_EXPECTED_MAP_CN + 1, in getAlleleDeterminationTestData()
135 {0, Collections.singleton(TEST_INTERVAL.getContig()), TEST_EXPECTED_MAP_CN, in getAlleleDeterminationTestData()
137 {1, Collections.singleton(TEST_INTERVAL.getContig()), TEST_EXPECTED_MAP_CN - 1, in getAlleleDeterminationTestData()
139 {1, Collections.singleton(TEST_INTERVAL.getContig()), TEST_EXPECTED_MAP_CN + 1, in getAlleleDeterminationTestData()
141 {1, Collections.singleton(TEST_INTERVAL.getContig()), TEST_EXPECTED_MAP_CN, in getAlleleDeterminationTestData()
143 {2, Collections.singleton(TEST_INTERVAL.getContig()), TEST_EXPECTED_MAP_CN - 1, in getAlleleDeterminationTestData()
145 {2, Collections.singleton(TEST_INTERVAL.getContig()), TEST_EXPECTED_MAP_CN + 1, in getAlleleDeterminationTestData()
147 {3, Collections.singleton(TEST_INTERVAL.getContig()), TEST_EXPECTED_MAP_CN, in getAlleleDeterminationTestData()
149 {3, Collections.singleton(TEST_INTERVAL.getContig()), TEST_EXPECTED_MAP_CN - 1, in getAlleleDeterminationTestData()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/variant/ |
| H A D | VariantContextVariantAdapter.java | 22 …return new MinimalVariant(new SimpleInterval(vc.getContig(),vc.getStart(),vc.getEnd()), vc.isSNP()… in sparkVariantAdapter()
26 public String getContig() { return variantContext.getContig(); } in getContig() method in VariantContextVariantAdapter
44 if (!getContig().equals(that.getContig())) { in equals()
67 getContig(), getStart(), getEnd(), isSnp(), isIndel()); in toString()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/sv/ |
| H A D | SVDepthOnlyCallDefragmenter.java | 49 …return new SVCallRecordWithEvidence(exampleCall.getContig(), newStart, exampleCall.getStartStrand(… in flattenCluster()
115 …Utils.validate(a.getContig().equals(a.getEndContig()), "Call A is depth-only but interchromosomal"… in clusterTogether()
116 …Utils.validate(b.getContig().equals(b.getEndContig()), "Call B is depth-only but interchromosomal"… in clusterTogether()
149 …final GenomeLoc callStart = parser.createGenomeLoc(call.getContig(), call.getStart(), call.getStar… in getClusteringInterval()
150 … final GenomeLoc callEnd = parser.createGenomeLoc(call.getContig(), call.getEnd(), call.getEnd()); in getClusteringInterval()
169 if (coverageIntervals.get(paddedStartIndex).getContig().equals(callStart.getContig())) { in getClusteringInterval()
175 if (coverageIntervals.get(paddedEndIndex).getContig().equals(callEnd.getContig())) { in getClusteringInterval()
184 final int contigLength = dictionary.getSequence(call.getContig()).getSequenceLength(); in getClusteringInterval()
186 …return IntervalUtils.trimIntervalToContig(call.getContig(), paddedCallStart, paddedCallEnd, contig… in getClusteringInterval()
191 … return IntervalUtils.trimIntervalToContig(call.getContig(), newMinStart, newMaxEnd, contigLength); in getClusteringInterval()
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| H A D | SVClusterEngine.java | 118 …return new SVCallRecordWithEvidence(exampleCall.getContig(), newStart, exampleCall.getStartStrand(… in flattenCluster()
167 return a.getContig().equals(b.getContig()) in itemsAreIdentical()
197 example.getContig(), in deduplicateIdenticalItems()
213 if (!a.getContig().equals(a.getEndContig()) || !b.getContig().equals(b.getEndContig())) { in clusterTogetherBothDepthOnly()
216 … final SimpleInterval intervalA = new SimpleInterval(a.getContig(), a.getStart(), a.getEnd()); in clusterTogetherBothDepthOnly()
217 … final SimpleInterval intervalB = new SimpleInterval(b.getContig(), b.getStart(), b.getEnd()); in clusterTogetherBothDepthOnly()
223 final boolean intrachromosomalA = a.getContig().equals(a.getEndContig()); in clusterTogetherBothWithEvidence()
224 final boolean intrachromosomalB = b.getContig().equals(b.getEndContig()); in clusterTogetherBothWithEvidence()
236 final boolean intrachromosomalA = a.getContig().equals(a.getEndContig()); in clusterTogetherMixedEvidence()
237 final boolean intrachromosomalB = b.getContig().equals(b.getEndContig()); in clusterTogetherMixedEvidence()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/funcotator/ |
| H A D | AnnotatedIntervalToSegmentVariantContextConverterUnitTest.java | 34 .chr(interval.getContig()) in provideSegmentConversion()
44 .chr(interval.getContig()) in provideSegmentConversion()
54 .chr(interval.getContig()) in provideSegmentConversion()
64 .chr(interval.getContig()) in provideSegmentConversion()
81 Assert.assertEquals(new SimpleInterval(guess.getContig(), guess.getStart(), guess.getEnd()), in testConvert()
82 …new SimpleInterval(gtVariantContext.getContig(), gtVariantContext.getStart(), gtVariantContext.get… in testConvert()
83 Assert.assertEquals(new SimpleInterval(guess.getContig(), guess.getStart(), guess.getEnd()), in testConvert()
84 …new SimpleInterval(segment.getContig(), segment.getStart(), segment.getEnd()), "Guess variant cont… in testConvert()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/ |
| H A D | SegmentedCpxVariantSimpleVariantExtractor.java | 355 …final SimpleInterval deletedRange = new SimpleInterval(simple.getContig(), simple.getStart() + 1, …
389 interval = new SimpleInterval( vc.getContig(), vc.getStart(), vc.getEnd());
598 … SegmentedCpxVariantSimpleVariantExtractor.makeInsertion(refSegment.getContig(),
604 … SegmentedCpxVariantSimpleVariantExtractor.makeInsertion(refSegment.getContig(),
634 … result.add( makeInsertion(refSegment.getContig(), refSegment.getStart(), refSegment.getEnd() - 1,
653 …final SimpleInterval rearInsPos = SVUtils.makeOneBpInterval(refSegment.getContig(), refSegment.get…
752 final SimpleInterval insertionPos = new SimpleInterval(complexVC.getContig(),
818 … current = new SimpleInterval(current.getContig(), current.getStart(), next.getEnd());
842 …final SimpleInterval startAndStop = SVUtils.makeOneBpInterval(complexVC.getContig(), complexVC.get…
859 … final SimpleInterval insertionPos = SVUtils.makeOneBpInterval(complexVC.getContig(), pos);
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| H A D | CpxVariantInducingAssemblyContig.java | 249 output.writeString(segmentingLoc.getContig()); in serialize()
313 eventPrimaryChromosome = head.referenceSpan.getContig(); in BasicInfo()
316 …alpha = new SimpleInterval(head.referenceSpan.getContig(), head.referenceSpan.getStart(), head.ref… in BasicInfo()
317 …omega = new SimpleInterval(tail.referenceSpan.getContig(), tail.referenceSpan.getEnd(), tail.refer… in BasicInfo()
320 …omega = new SimpleInterval(head.referenceSpan.getContig(), head.referenceSpan.getEnd(), head.refer… in BasicInfo()
350 output.writeString(alpha.getContig()); in serialize()
353 output.writeString(omega.getContig()); in serialize()
447 …start = new SimpleInterval(one.referenceSpan.getContig(), one.referenceSpan.getEnd(), one.referenc… in Jump()
448 …landing = new SimpleInterval(two.referenceSpan.getContig(), two.referenceSpan.getEnd(), two.refere… in Jump()
486 output.writeString(start.getContig()); in serialize()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ |
| H A D | ReviseAssemblyUnitTest.java | 69 Assert.assertEquals(noUnbranchedAssembly.getContig(0), tigA); in testRemoveUnbranched()
70 Assert.assertEquals(noUnbranchedAssembly.getContig(1), tigB); in testRemoveUnbranched()
71 … Assert.assertEquals(new String(noUnbranchedAssembly.getContig(2).getSequence()), "TTTTAAAAGCGC"); in testRemoveUnbranched()
113 … Assert.assertEquals(new String(expandedAssembly.getContig(2).getSequence()), "ACACTTTTAAAA"); in testNoCrossingUnphasedContigs()
114 … Assert.assertEquals(new String(expandedAssembly.getContig(3).getSequence()), "TGTGTTTTAAAA"); in testNoCrossingUnphasedContigs()
115 … Assert.assertEquals(new String(expandedAssembly.getContig(0).getSequence()), "TTTTAAAAGCGC"); in testNoCrossingUnphasedContigs()
116 … Assert.assertEquals(new String(expandedAssembly.getContig(1).getSequence()), "TTTTAAAATATA"); in testNoCrossingUnphasedContigs()
136 … Assert.assertEquals(new String(expandedAssembly.getContig(0).getSequence()), "ACACTTTTTTTTTTTT"); in testCycleResolution()
160 … Assert.assertEquals(new String(expandedAssembly.getContig(0).getSequence()), "TTTTTTTTTTTT"); in testCycleResolutionAcrossPhasing()
161 … Assert.assertEquals(new String(expandedAssembly.getContig(1).getSequence()), "TTTTTTTTGTGT"); in testCycleResolutionAcrossPhasing()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ |
| H A D | EvidenceTargetLink.java | 83 …return readMetadata.getContigName(sourceInterval.getContig()) + "\t" + (sourceInterval.getStart() … in toBedpeString()
84 …"\t" + readMetadata.getContigName(targetInterval.getContig()) + "\t" + (targetInterval.getStart() … in toBedpeString()
94 …return readMetadata.getContigName(sourceInterval.getContig()) + "_" + (sourceInterval.getStart() -… in getId()
95 …"_" + readMetadata.getContigName(targetInterval.getContig()) + "_" + (targetInterval.getStart() - … in getId()
112 …dIntervals().getLeft().getInterval().getContig() == getPairedStrandedIntervals().getRight().getInt… in isImpreciseDeletion()
121 …dIntervals().getLeft().getInterval().getContig() != getPairedStrandedIntervals().getRight().getInt… in getDistance()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/ |
| H A D | GenomeLocParserUnitTest.java | 153 assertEquals("1", loc.getContig()); in testCreateGenomeLoc2()
161 assertEquals("1", loc.getContig()); in testCreateGenomeLoc3()
376 Assert.assertEquals(loc.getContig(), contig); in testParsingPositions()
385 Assert.assertEquals(loc.getContig(), read.getContig()); in testCreationFromSAMRecord()
405 Assert.assertEquals(loc.getContig(), read.getContig()); in testCreationFromSAMRecordUnmappedButOnGenome()
415 Assert.assertEquals(loc.getContig(), feature.getContig()); in testCreationFromFeature()
424 Assert.assertEquals(loc.getContig(), locatable.getContig()); in testCreationFromLocatable()
438 Assert.assertEquals(loc.getContig(), feature.getContig()); in testCreationFromVariantContext()
452 Assert.assertEquals(loc.getContig(), rec.getSequenceName()); in testCreateGenomeLocOnContig()
482 Assert.assertEquals(loc.getContig(), contig); in testGenomeLocOnContig()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/ |
| H A D | CombineGVCFs.java | 154 ctx.getSource(), ctx.getContig(), ctx.getStart())); in apply()
160 …atable last = prevPos!=null && prevPos.getContig().equals(variantContextsOverlappingCurrentMerge.g… in apply()
162 int end = last.getContig().equals(referenceContext.getWindow().getContig()) in apply()
166 createIntermediateVariants( new SimpleInterval(last.getContig(), last.getStart(), end)); in apply()
218 … SimpleInterval loc = new SimpleInterval(intervalToClose.getContig(), stoppedLoc, stoppedLoc); in createIntermediateVariants()
330 … endPreviousStates(new SimpleInterval(loc.getContig(), loc.getStart() - 1, loc.getStart() - 1), in mergeWithNewVCs()
402 …final SimpleInterval closingSpot = new SimpleInterval(stoppedVCs.get(0).getContig(), pos.getStart(… in endPreviousStates()
433 …if ( prevPos == null || !prevPos.getContig().equals(first.getContig()) || first.getStart() >= prev… in referenceBlockMerge()
454 …return new VariantContextBuilder("", first.getContig(), start, end, Arrays.asList(refAllele, Allel… in referenceBlockMerge()
484 variantContextsOverlappingCurrentMerge.get(0).getContig(), in onTraversalSuccess()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/codecs/table/ |
| H A D | TableCodecUnitTest.java | 57 Assert.assertEquals(tc.decode("1:1 1 2 3").getContig(), "1"); in testChrs()
58 Assert.assertEquals(tc.decode("chr1:1 1 2 3").getContig(), "chr1"); in testChrs()
59 Assert.assertEquals(tc.decode("1:1+ 1 2 3").getContig(), "1"); in testChrs()
60 Assert.assertEquals(tc.decode("1 1 2 3").getContig(), "1"); in testChrs()
61 Assert.assertEquals(tc.decode("fred 1 2 3").getContig(), "fred"); in testChrs()
62 Assert.assertEquals(tc.decode("2:1,000 1 2 3").getContig(), "2"); in testChrs()
79 Assert.assertEquals(decode.getContig(), contig, "contig"); in testDecode1()
112 Assert.assertEquals(decode.getLocation().getContig(), "1"); in testDecodeHeader2()
113 Assert.assertEquals(decode.getContig(), "1"); in testDecodeHeader2()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/activityprofile/ |
| H A D | ActivityProfileStateRange.java | 37 … Utils.validate(next.getLoc().getContig().equals(prev.getLoc().getContig()), "Contigs differ"); in ActivityProfileStateRange()
50 public String getContig() { in getContig() method in ActivityProfileStateRange
51 return interval.getContig(); in getContig()
64 …ofileState state = new ActivityProfileState(new SimpleInterval(interval.getContig(), pos, pos), ac… in toIteratorActivityProfileState()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/spark/ |
| H A D | SparkSharder.java | 290 if (locatable.getContig() != null) {
351 public String getContig() {
352 return interval.getContig();
374 int intervalContigIndex = sequenceDictionary.getSequenceIndex(interval.getContig());
375 int locatableContigIndex = sequenceDictionary.getSequenceIndex(locatable.getContig());
401 int intervalContigIndex = sequenceDictionary.getSequenceIndex(current.getContig());
407 nextContigIndex = sequenceDictionary.getSequenceIndex(next.getContig());
417 SAMSequenceRecord seq = sequenceDictionary.getSequence(current.getContig());
418 … Utils.validate(seq != null, "Contig not found in sequence dictionary: " + current.getContig());
522 public String getContig() {
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/consensus/ |
| H A D | ReadsWithSameUMI.java | 68 … from another contig: set contig = %s, read contig = %s", interval.getContig(), read.getContig())); in addRead()
93 public String getContig() { in getContig() method in ReadsWithSameUMI
94 return interval.getContig(); in getContig()
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