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Searched refs:getSampleName (Results 1 – 25 of 82) sorted by relevance

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/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/vcf/test/
H A DVcfHeaderTest.cpp36 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 …]
H A DVcfFileTest.cpp138 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 …]
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/sv/
H A DSVDepthOnlyCallDefragmenter.java57 .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()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/metadata/
H A DSimpleSampleLocatableMetadata.java25 public String getSampleName() { in getSampleName() method in SimpleSampleLocatableMetadata
26 return sampleMetadata.getSampleName(); in getSampleName()
H A DSampleMetadata.java12 String getSampleName(); in getSampleName() method
H A DSampleLocatableMetadata.java15 String getSampleName(); in getSampleName() method
H A DSimpleSampleMetadata.java25 public String getSampleName() { in getSampleName() method in SimpleSampleMetadata
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/formats/collections/
H A DIntegerCopyNumberSegmentCollectionUnitTest.java59 Assert.assertEquals(collection.getMetadata().getSampleName(), EXPECTED_SAMPLE_NAME); in testIntegerCopyNumberSegmentCollectionReading()
72 Assert.assertEquals(readCollection.getMetadata().getSampleName(), EXPECTED_SAMPLE_NAME); in testWriteRead()
H A DBaselineCopyNumberCollectionUnitTest.java31 Assert.assertEquals(collection.getMetadata().getSampleName(), EXPECTED_SAMPLE_NAME); in testBaselineCopyNumberReading()
/dports/graphics/alembic/alembic-1.8.3/lib/Alembic/AbcCoreHDF5/
H A DSimplePrImpl.h352 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()
H A DAprImpl.cpp81 std::string sampleName = getSampleName( m_header->getName(), iSampleIndex ); in getDimensions()
128 std::string sampleName = getSampleName( m_header->getName(), iSampleIndex ); in getAs()
H A DFoundation.h86 inline std::string getSampleName( const std::string &iName, in getSampleName() function
/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/vcf/
H A DVcfSubsetSamples.cpp47 mySampleNames[i] = header.getSampleName(i); in init()
154 const char* sampleName = header.getSampleName(i); in init()
H A DVcfHeader.h73 const char* getSampleName(unsigned int index) const;
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/plotting/
H A DPlotDenoisedCopyRatios.java157 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()
H A DPlotModeledSegments.java204 final String sampleName = getSampleName(); in doWork()
255 private String getSampleName() { in getSampleName() method in PlotModeledSegments
264 return modeledSegments.getMetadata().getSampleName(); in getSampleName()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/
H A DModelSegmentsIntegrationTest.java118 …Assert.assertEquals(EXPECTED_METADATA.getSampleName(), copyRatioParameters.getMetadata().getSample… in assertOutputFiles()
122 …Assert.assertEquals(EXPECTED_METADATA.getSampleName(), alleleFractionParameters.getMetadata().getS… in assertOutputFiles()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/
H A DVariantSummary.java214 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()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/
H A DPostprocessGermlineCNVCalls.java494 .getMetadata().getSampleName(); in generateSegmentsVCFFileFromAllShards()
500 .getMetadata().getSampleName(); in generateSegmentsVCFFileFromAllShards()
534 .getMetadata().getSampleName(); in concatenateDenoisedCopyRatioFiles()
599 .getMetadata().getSampleName(); in getShardIntervalCopyNumberPosteriorData()
609 .getMetadata().getSampleName(); in getShardIntervalCopyNumberPosteriorData()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/
H A DReadOrientationFilter.java80 } else if (!artifactPriorCollections.containsKey(g.getSampleName())) { in artifactProbability()
119 …final Optional<ArtifactPrior> artifactPrior = artifactPriorCollections.get(g.getSampleName()).get(… in artifactProbability()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/records/
H A DCoveragePerContig.java25 public String getSampleName() { in getSampleName() method in CoveragePerContig
/dports/graphics/recastnavigation/recastnavigation-e75adf86f91eb3082220085e42dda62679f9a3ea/RecastDemo/Include/
H A DTestCase.h100 const std::string& getSampleName() const { return m_sampleName; } in getSampleName() function
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/filters/
H A DSampleReadFilter.java36 final String sample = ReadUtils.getSampleName(read, samHeader); in test()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/
H A DSampleList.java44 samples.append(genotype.getSampleName()); in annotate()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/collections/
H A DCoveragePerContigCollection.java43 dataLine.append(coveragePerContig.getSampleName()); in CoveragePerContigCollection()

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