/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/vcf/test/ |
H A D | VcfHeaderTest.cpp | 36 assert(header.getSampleName(2) == NULL); in testVcfHeader() 37 assert(header.getSampleName(0) == NULL); in testVcfHeader() 38 assert(header.getSampleName(1) == NULL); in testVcfHeader() 68 assert(header.getSampleName(2) == SAMPLES[2]); in testVcfHeader() 69 assert(header.getSampleName(0) == SAMPLES[0]); in testVcfHeader() 70 assert(header.getSampleName(1) == SAMPLES[1]); in testVcfHeader() 83 assert(header.getSampleName(2) == NULL); in testVcfHeader() 84 assert(header.getSampleName(0) == NULL); in testVcfHeader() 85 assert(header.getSampleName(1) == NULL); in testVcfHeader() 132 assert(newHeader.getSampleName(0) == NULL); in testVcfHeader() [all …]
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H A D | VcfFileTest.cpp | 138 assert(header.getSampleName(2) == NULL); in testVcfReadFile() 420 assert(header.getSampleName(2) == NULL); in testVcfReadFile() 574 assert(header.getSampleName(2) == NULL); in testVcfReadFile() 576 assert(header.getSampleName(1) == NULL); in testVcfReadFile() 728 assert(header.getSampleName(2) == NULL); in testVcfReadFile() 882 assert(header.getSampleName(2) == NULL); in testVcfReadFile() 1036 assert(header.getSampleName(2) == NULL); in testVcfReadFile() 1038 assert(header.getSampleName(1) == NULL); in testVcfReadFile() 1192 assert(header.getSampleName(2) == NULL); in testVcfReadFile() 1194 assert(header.getSampleName(1) == NULL); in testVcfReadFile() [all …]
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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 | 57 .map(Genotype::getSampleName) in deduplicateGenotypes() 65 if (!moreGenotypes.containsKey(g.getSampleName())) { in deduplicateGenotypes() 68 moreGenotypes.put(g.getSampleName(), newList); in deduplicateGenotypes() 70 (moreGenotypes.get(g.getSampleName())).add(g); in deduplicateGenotypes() 89 final String sampleName = genotypesForSameSample.get(0).getSampleName(); in defragmentGenotypes() 90 if (!genotypesForSameSample.stream().allMatch(g -> g.getSampleName().equals(sampleName))) { in defragmentGenotypes() 124 …ypes().size() == 1 && a.getGenotypes().get(0).getSampleName().equals(b.getGenotypes().get(0).getSa… in clusterTogether()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/metadata/ |
H A D | SimpleSampleLocatableMetadata.java | 25 public String getSampleName() { in getSampleName() method in SimpleSampleLocatableMetadata 26 return sampleMetadata.getSampleName(); in getSampleName()
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H A D | SampleMetadata.java | 12 String getSampleName(); in getSampleName() method
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H A D | SampleLocatableMetadata.java | 15 String getSampleName(); in getSampleName() method
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H A D | SimpleSampleMetadata.java | 25 public String getSampleName() { in getSampleName() method in SimpleSampleMetadata
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/formats/collections/ |
H A D | IntegerCopyNumberSegmentCollectionUnitTest.java | 59 Assert.assertEquals(collection.getMetadata().getSampleName(), EXPECTED_SAMPLE_NAME); in testIntegerCopyNumberSegmentCollectionReading() 72 Assert.assertEquals(readCollection.getMetadata().getSampleName(), EXPECTED_SAMPLE_NAME); in testWriteRead()
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H A D | BaselineCopyNumberCollectionUnitTest.java | 31 Assert.assertEquals(collection.getMetadata().getSampleName(), EXPECTED_SAMPLE_NAME); in testBaselineCopyNumberReading()
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/dports/graphics/alembic/alembic-1.8.3/lib/Alembic/AbcCoreHDF5/ |
H A D | SimplePrImpl.h | 352 std::string sample0Name = getSampleName( myName, 0 ); in getSample() 376 std::string sampleName = getSampleName( myName, iSampleIndex ); in getSample() 400 std::string sample0Name = getSampleName( myName, 0 ); in getKey() 423 std::string sampleName = getSampleName( myName, iSampleIndex ); in getKey()
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H A D | AprImpl.cpp | 81 std::string sampleName = getSampleName( m_header->getName(), iSampleIndex ); in getDimensions() 128 std::string sampleName = getSampleName( m_header->getName(), iSampleIndex ); in getAs()
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H A D | Foundation.h | 86 inline std::string getSampleName( const std::string &iName, in getSampleName() function
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/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/vcf/ |
H A D | VcfSubsetSamples.cpp | 47 mySampleNames[i] = header.getSampleName(i); in init() 154 const char* sampleName = header.getSampleName(i); in init()
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H A D | VcfHeader.h | 73 const char* getSampleName(unsigned int index) const;
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/plotting/ |
H A D | PlotDenoisedCopyRatios.java | 157 final String sampleName = getSampleName(standardizedCopyRatios, denoisedCopyRatios); in doWork() 188 private static String getSampleName(final CopyRatioCollection standardizedCopyRatios, in getSampleName() method in PlotDenoisedCopyRatios 192 return standardizedCopyRatios.getMetadata().getSampleName(); in getSampleName()
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H A D | PlotModeledSegments.java | 204 final String sampleName = getSampleName(); in doWork() 255 private String getSampleName() { in getSampleName() method in PlotModeledSegments 264 return modeledSegments.getMetadata().getSampleName(); in getSampleName()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/ |
H A D | ModelSegmentsIntegrationTest.java | 118 …Assert.assertEquals(EXPECTED_METADATA.getSampleName(), copyRatioParameters.getMetadata().getSample… in assertOutputFiles() 122 …Assert.assertEquals(EXPECTED_METADATA.getSampleName(), alleleFractionParameters.getMetadata().getS… in assertOutputFiles()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/ |
H A D | VariantSummary.java | 214 countsPerSample.inc(type, g.getSampleName()); in update2() 217 if ( titvTable != null ) titvTable.inc(type, g.getSampleName()); in update2() 220 depthPerSample.inc(type, g.getSampleName()); in update2()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/ |
H A D | PostprocessGermlineCNVCalls.java | 494 .getMetadata().getSampleName(); in generateSegmentsVCFFileFromAllShards() 500 .getMetadata().getSampleName(); in generateSegmentsVCFFileFromAllShards() 534 .getMetadata().getSampleName(); in concatenateDenoisedCopyRatioFiles() 599 .getMetadata().getSampleName(); in getShardIntervalCopyNumberPosteriorData() 609 .getMetadata().getSampleName(); in getShardIntervalCopyNumberPosteriorData()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/ |
H A D | ReadOrientationFilter.java | 80 } else if (!artifactPriorCollections.containsKey(g.getSampleName())) { in artifactProbability() 119 …final Optional<ArtifactPrior> artifactPrior = artifactPriorCollections.get(g.getSampleName()).get(… in artifactProbability()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/records/ |
H A D | CoveragePerContig.java | 25 public String getSampleName() { in getSampleName() method in CoveragePerContig
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/dports/graphics/recastnavigation/recastnavigation-e75adf86f91eb3082220085e42dda62679f9a3ea/RecastDemo/Include/ |
H A D | TestCase.h | 100 const std::string& getSampleName() const { return m_sampleName; } in getSampleName() function
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/filters/ |
H A D | SampleReadFilter.java | 36 final String sample = ReadUtils.getSampleName(read, samHeader); in test()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ |
H A D | SampleList.java | 44 samples.append(genotype.getSampleName()); in annotate()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/collections/ |
H A D | CoveragePerContigCollection.java | 43 dataLine.append(coveragePerContig.getSampleName()); in CoveragePerContigCollection()
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