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Searched refs:vcfHeader (Results 1 – 25 of 47) sorted by relevance

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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/vcf_io/
H A Dtest_vcf_io.h54 seqan::VcfHeader vcfHeader; in SEQAN_DEFINE_TEST() local
115 seqan::VcfHeader vcfHeader; in SEQAN_DEFINE_TEST() local
296 seqan::VcfHeader vcfHeader; in SEQAN_DEFINE_TEST() local
302 resize(vcfHeader, 18); in SEQAN_DEFINE_TEST()
315 vcfHeader[6].key = "INFO"; in SEQAN_DEFINE_TEST()
317 vcfHeader[7].key = "INFO"; in SEQAN_DEFINE_TEST()
319 vcfHeader[8].key = "INFO"; in SEQAN_DEFINE_TEST()
321 vcfHeader[9].key = "INFO"; in SEQAN_DEFINE_TEST()
323 vcfHeader[10].key = "INFO"; in SEQAN_DEFINE_TEST()
325 vcfHeader[11].key = "INFO"; in SEQAN_DEFINE_TEST()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/funcotator/metadata/
H A DSamplePairExtractor.java40 public static List<TumorNormalPair> extractPossibleTumorNormalPairs(final VCFHeader vcfHeader) { in extractPossibleTumorNormalPairs() argument
41 Utils.nonNull(vcfHeader); in extractPossibleTumorNormalPairs()
43 if (vcfHeader.getMetaDataLine(Mutect2Engine.TUMOR_SAMPLE_KEY_IN_VCF_HEADER) != null) { in extractPossibleTumorNormalPairs()
44 …final VCFHeaderLine normalMetaDataLine = vcfHeader.getMetaDataLine(Mutect2Engine.NORMAL_SAMPLE_KEY… in extractPossibleTumorNormalPairs()
45 …return Collections.singletonList(new TumorNormalPair(vcfHeader.getMetaDataLine(Mutect2Engine.TUMOR… in extractPossibleTumorNormalPairs()
51 final List<String> sampleNames = vcfHeader.getSampleNamesInOrder(); in extractPossibleTumorNormalPairs()
/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/vcf/test/
H A DMakefile4 …vcfHeader.vcf expected/vcfHeader.vcf && diff results/vcfHeaderAddedFirst.vcf expected/vcfHeader.vc…
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/
H A Dcasbar.cpp874 seqan::VcfHeader vcfHeader; in detectSNPs() local
884 appendValue(vcfHeader, VcfHeaderRecord("phasing", "partial")); in detectSNPs()
897 writeHeader(vcfFileOut, vcfHeader); in detectSNPs()
910 seqan::VcfHeader vcfHeader; in detectSNPs() local
913 appendValue(vcfHeader, VcfHeaderRecord("fileformat", "VCFv4.1")); in detectSNPs()
914 appendValue(vcfHeader, VcfHeaderRecord("fileDate", "20090805")); in detectSNPs()
915 appendValue(vcfHeader, VcfHeaderRecord("source", "snp_meth_store")); in detectSNPs()
918 appendValue(vcfHeader, VcfHeaderRecord("phasing", "partial")); in detectSNPs()
931 writeHeader(vcfFileOut, vcfHeader); in detectSNPs()
952 seqan::VcfHeader vcfHeader; in detectSNPs() local
[all …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/gustaf/
H A Dmsplazer_out.h971 void _fillVcfHeader(seqan::VcfHeader & vcfHeader, in _fillVcfHeader() argument
983 appendValue(vcfHeader, seqan::VcfHeaderRecord( in _fillVcfHeader()
985 appendValue(vcfHeader, seqan::VcfHeaderRecord( in _fillVcfHeader()
987 appendValue(vcfHeader, seqan::VcfHeaderRecord( in _fillVcfHeader()
989 appendValue(vcfHeader, seqan::VcfHeaderRecord( in _fillVcfHeader()
993 appendValue(vcfHeader, seqan::VcfHeaderRecord( in _fillVcfHeader()
995 appendValue(vcfHeader, seqan::VcfHeaderRecord( in _fillVcfHeader()
997 appendValue(vcfHeader, VcfHeaderRecord( in _fillVcfHeader()
999 appendValue(vcfHeader, VcfHeaderRecord( in _fillVcfHeader()
1059 seqan::VcfHeader vcfHeader; in _writeGlobalBreakpoints() local
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/
H A DSVVCFWriterUnitTest.java76 final VCFHeader vcfHeader = SVVCFWriter.getVcfHeader(referenceSequenceDictionary); in testSetHeader() local
77 Assert.assertNotNull(vcfHeader.getSequenceDictionary()); in testSetHeader()
79 …final List<String> refContigs = vcfHeader.getContigLines().stream().map(VCFContigHeaderLine::getID… in testSetHeader()
82 …final List<String> headerKeys = vcfHeader.getIDHeaderLines().stream().map(VCFIDHeaderLine::getID).… in testSetHeader()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/funcotator/
H A DFilterFuncotations.java124 final VCFHeader vcfHeader = getHeaderForVariants(); in onTraversalStart() local
126 …final VCFInfoHeaderLine funcotationHeaderLine = vcfHeader.getInfoHeaderLine(VcfOutputRenderer.FUNC… in onTraversalStart()
130 … vcfHeader.addMetaDataLine(new VCFFilterHeaderLine(FilterFuncotationsConstants.NOT_CLINSIG_FILTER, in onTraversalStart()
132 … vcfHeader.addMetaDataLine(new VCFInfoHeaderLine(FilterFuncotationsConstants.CLINSIG_INFO_KEY, 1, in onTraversalStart()
134 outputVcfWriter.writeHeader(vcfHeader); in onTraversalStart()
H A DFuncotator.java770 final VCFHeader vcfHeader = getHeaderForVariants(); in onTraversalStart() local
800 new ArrayList<>(vcfHeader.getInfoHeaderLines()) in onTraversalStart()
810 vcfHeader, in onTraversalStart()
/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/vcf/
H A DVcfHeader.h98 VcfHeader(const VcfHeader& vcfHeader);
99 VcfHeader& operator=(const VcfHeader& vcfHeader);
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/validation/
H A DRemoveNearbyIndels.java69 …final VCFHeader vcfHeader = new VCFHeader(inputHeader.getMetaDataInSortedOrder(), inputHeader.getG… in onTraversalStart() local
70 getDefaultToolVCFHeaderLines().forEach(vcfHeader::addMetaDataLine); in onTraversalStart()
72 vcfWriter.writeHeader(vcfHeader); in onTraversalStart()
H A DAnnotateVcfWithBamDepth.java71 final VCFHeader vcfHeader = new VCFHeader(headerLines, inputHeader.getGenotypeSamples()); in onTraversalStart() local
73 vcfWriter.writeHeader(vcfHeader); in onTraversalStart()
H A DAnnotateVcfWithExpectedAlleleFraction.java87 final VCFHeader vcfHeader = new VCFHeader(headerLines, inputHeader.getGenotypeSamples()); in onTraversalStart() local
90 vcfWriter.writeHeader(vcfHeader); in onTraversalStart()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/
H A DGenomicsDBUtils.java97 … final String vcfHeader, final GenomicsDBOptions genomicsDBOptions) { in createExportConfiguration() argument
104 .setVcfHeaderFilename(vcfHeader) in createExportConfiguration()
140 … final String vcfHeader) { in createExportConfiguration() argument
141 return createExportConfiguration(workspace, callsetJson, vidmapJson, vcfHeader, null); in createExportConfiguration()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/
H A DCpxVariantReInterpreterSpark.java103 final VCFHeader vcfHeader = VariantsSparkSource.getHeader(complexVCF); in runTool() local
104 …ract.getReInterpretZeroOrOneSegmentCalls(), derivedOneSegmentSimpleVCF, vcfHeader.getSequenceDicti… in runTool()
105 …tract.getReInterpretMultiSegmentsCalls(), derivedMultiSegmentSimpleVCF, vcfHeader.getSequenceDicti… in runTool()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/utils/
H A DSVVCFWriter.java91 final VCFHeader vcfHeader = getVcfHeader(referenceSequenceDictionary); in writeVariants() local
92 defaultToolVCFHeaderLines.forEach(vcfHeader::addMetaDataLine); in writeVariants()
93 vcfWriter.writeHeader(vcfHeader); in writeVariants()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/
H A DFilterMutectCalls.java132 final VCFHeader vcfHeader = new VCFHeader(headerLines, inputHeader.getGenotypeSamples()); in onTraversalStart() local
134 vcfWriter.writeHeader(vcfHeader); in onTraversalStart()
138 filteringEngine = new Mutect2FilteringEngine(MTFAC, vcfHeader, mutect2StatsTable); in onTraversalStart()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/
H A DLeftAlignAndTrimVariants.java179 private VCFHeader vcfHeader = null; field in LeftAlignAndTrimVariants
193 vcfHeader = new VCFHeader(actualLines, vcfSamples); in onTraversalStart()
194 vcfWriter.writeHeader(vcfHeader); in onTraversalStart()
225 … vcList = GATKVariantContextUtils.splitSomaticVariantContextToBiallelics(vc, false, vcfHeader); in apply()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/mason2/
H A Dmason_variator.cpp839 seqan::VcfHeader vcfHeader; in run() local
840 appendValue(vcfHeader, seqan::VcfHeaderRecord("fileformat", "VCFv4.1")); in run()
841 appendValue(vcfHeader, seqan::VcfHeaderRecord("source", "mason_variator")); in run()
843 appendValue(vcfHeader, seqan::VcfHeaderRecord( in run()
845 appendValue(vcfHeader, seqan::VcfHeaderRecord( in run()
847 appendValue(vcfHeader, seqan::VcfHeaderRecord( in run()
849 appendValue(vcfHeader, seqan::VcfHeaderRecord( in run()
851 appendValue(vcfHeader, seqan::VcfHeaderRecord( in run()
853 appendValue(vcfHeader, seqan::VcfHeaderRecord( in run()
871 appendValue(vcfHeader, seqan::VcfHeaderRecord("contig", contigStr)); in run()
[all …]
H A Dvcf_materialization.h111 seqan::VcfHeader vcfHeader; variable
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/
H A DFeatureDataSource.java399 …final String vcfHeader = IOUtils.appendPathToDir(workspace, GenomicsDBConstants.DEFAULT_VCFHEADER_… in getGenomicsDBFeatureReader() local
401 IOUtils.assertPathsAreReadable(callsetJson, vidmapJson, vcfHeader); in getGenomicsDBFeatureReader()
405 … createExportConfiguration(workspace, callsetJson, vidmapJson, vcfHeader, genomicsDBOptions); in getGenomicsDBFeatureReader()
/dports/biology/freebayes/freebayes-1.3.5/src/
H A DResultData.h72 void vcfHeader(ostream& out, string referenceFileName, vector<string>& samples, Parameters& paramet…
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/
H A DValidateBasicSomaticShortMutations.java153 … final VCFHeader vcfHeader = new VCFHeader(headerLines, inputHeader.getGenotypeSamples()); in onTraversalStart() local
155 vcfWriter.writeHeader(vcfHeader); in onTraversalStart()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/
H A DReferenceConfidenceVariantContextMergerUnitTest.java282 final VCFHeader vcfHeader = new VCFHeader(); in testMedianCalculationOnMixedSerializedTypes() local
283 vcfHeader.addMetaDataLine(GATKVCFHeaderLines.getInfoLine(MAP_QUAL_RANK_SUM_KEY)); in testMedianCalculationOnMixedSerializedTypes()
305 …ntextMerger merger = new ReferenceConfidenceVariantContextMerger(getAnnotationEngine(), vcfHeader); in testMedianCalculationOnMixedSerializedTypes()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/funcotator/
H A DFuncotatorIntegrationTest.java599 final VCFHeader vcfHeader = (VCFHeader)vcfReader.getHeader(); in largeDataValidationTest() local
601 …final VCFInfoHeaderLine funcotationHeaderLine = vcfHeader.getInfoHeaderLine(VcfOutputRenderer.FUNC… in largeDataValidationTest()
786 final VCFHeader vcfHeader = vcfInfo.getLeft(); in testManualAnnotationsCorrectness() local
787 …final VCFInfoHeaderLine funcotationHeaderLine = vcfHeader.getInfoHeaderLine(VcfOutputRenderer.FUNC… in testManualAnnotationsCorrectness()
1154 final VCFHeader vcfHeader = vcfInfo.getLeft(); in testVcfMafConcordance() local
1155 …final VCFInfoHeaderLine funcotationHeaderLine = vcfHeader.getInfoHeaderLine(VcfOutputRenderer.FUNC… in testVcfMafConcordance()
1316 final VCFHeader vcfHeader = vcfInfo.getLeft(); in testVcfDatasourceAccountsForAltAlleles() local
1317 …final VCFInfoHeaderLine funcotationHeaderLine = vcfHeader.getInfoHeaderLine(VcfOutputRenderer.FUNC… in testVcfDatasourceAccountsForAltAlleles()
1360 final VCFHeader vcfHeader = vcfInfo.getLeft(); in testCanAnnotateSpanningDeletions() local
1361 …final VCFInfoHeaderLine funcotationHeaderLine = vcfHeader.getInfoHeaderLine(VcfOutputRenderer.FUNC… in testCanAnnotateSpanningDeletions()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/
H A DFilterVariantTranches.java303 final VCFHeader vcfHeader = new VCFHeader(hInfo, samples); in writeVCFHeader() local
304 vcfWriter.writeHeader(vcfHeader); in writeVCFHeader()

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