| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ |
| H A D | CalculateGenotypePosteriorsIntegrationTest.java | 36 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false" + in testDefaultsWithPanel()
50 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false" + in testNumRefWithPanel()
67 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testUsingDiscoveredAF()
83 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testMissingPriors()
98 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testInputINDELs()
112 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testFamilyPriors()
125 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testSingleParentFamily()
148 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testNoDuplicatesForAdjacentInputs()
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| H A D | ReblockGVCFIntegrationTest.java | 36 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " false", in testJustOneSample()
80 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " false" + in testOneSampleAsForGnomAD()
92 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " false", in testNonRefADCorrection()
102 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " false", in testRawMQInput()
113 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " false", in testASAnnotationsAndSubsetting()
121 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " false", in testASAnnotationsAndSubsetting()
160 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " false" + in testNewCompressionScheme()
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| H A D | LeftAlignAndTrimVariantsIntegrationTest.java | 44 + " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " false" in testLeftAlignment()
62 + " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " false" in testLefAlignRequireReference()
80 + " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " false" in testSplitAllelesWithASFilters()
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| H A D | SelectVariantsIntegrationTest.java | 33 + " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false " in baseTestString()
47 + " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testSampleSelection()
63 … + " -O %s --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testExpressionSelection()
387 …iant " + testFile + " -O %s --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false… in testNoGTs()
966 , "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"}; in testSampleSelectionOnNio()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/ |
| H A D | VariantRecalibratorIntegrationTest.java | 45 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"
62 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"
81 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false",
101 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false",
117 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"
131 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"
145 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"
323 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testVariantRecalibratorIndel()
381 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testVariantRecalibratorSampling()
405 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testVariantRecalibratorModelInput()
[all …]
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| H A D | CNNScoreVariantsIntegrationTest.java | 62 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testAllDefaultArgs()
76 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testInferenceArchitecture()
99 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testInferenceWeights()
115 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testInferenceArchitectureAndWeights()
129 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testInferenceWithIntervals()
153 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testSmallBatchInference()
167 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testOnContigEdge()
192 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testInference2dResourceModel()
215 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testInferenceArchitecture2d()
244 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testInferenceWeights2d()
[all …]
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| H A D | ApplyVQSRIntegrationTest.java | 55 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testApplySNPRecalibration()
74 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testApplyIndelRecalibration()
88 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", in testApplyVQSRSnpAndIndelTogether()
133 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false"; in testApplyVQSRAlleleSpecificSNPmode()
151 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false"; in testApplyVQSRAlleleSpecificINDELmode()
188 " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false" + in testApplyVQSRAlleleSpecificINDELmodeGZIPIndex()
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| H A D | FilterVariantTranchesIntegrationTest.java | 107 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false") in runTrancheFiltering()
123 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in runTrancheFilteringOnBadInputs()
135 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in runTrancheFilteringOnGoodInputs()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
| H A D | HaplotypeCallerIntegrationTest.java | 92 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false" in testVCFModeIsConsistentWithPastResults()
122 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false" in testLinkedDebruijnModeIsConsistentWithPastResults()
158 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false" in testVCFModeIsConsistentWithPastResults_AlleleSpecificAnnotations()
221 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false", in testDRAGENDefaultArgIsConsistentWithPastResults()
260 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false", in testDRAGENGATKModeIsConsistentWithPastResults()
326 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false" in testGVCFModeIsConsistentWithPastResults()
363 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false" in testGVCFModeIsConsistentWithPastResultsUsingKmerGraphs()
399 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false" in testGVCFModeIsConsistentWithPastResults_AlleleSpecificAnnotations()
534 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false" in testGVCFModeGenotypePosteriors()
569 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, false) in testFloorGVCFBlocks()
[all …]
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/filters/ |
| H A D | VariantFiltrationIntegrationTest.java | 22 …+ hg19_chr1_1M_Reference + " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " fals… in baseTestString()
307 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testFilteredAndPassBecomeUnfiltered()
321 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testFilteredAndPassBecomeUnfiltered()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/ |
| H A D | MethylationTypeCallerIntegrationTest.java | 23 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false" in testBasicMethylationCoverage()
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| H A D | GnarlyGenotyperIntegrationTest.java | 118 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in runTool()
140 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in testOnHailOutput()
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| H A D | CombineGVCFsIntegrationTest.java | 183 args.add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, false); in runCombineGVCFSandAssertSomething()
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| H A D | GenotypeGVCFsIntegrationTest.java | 377 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, false) in runGenotypeGVCFSAndAssertSomething()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/ |
| H A D | HaplotypeCallerSparkIntegrationTest.java | 78 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false", in testVCFModeIsConsistentWithPastResults()
107 "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false" in testNonStrictVCFModeIsConsistentWithPastResults()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/spark/ |
| H A D | GATKSparkToolUnitTest.java | 34 … final String[] args = {"--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "true"}; in testGetDefaultToolVCFHeaderLines()
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| /dports/biology/gatk/gatk-4.2.0.0/src/testUtils/java/org/broadinstitute/hellbender/testutils/ |
| H A D | GenomicsDBTestUtils.java | 58 args.add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"); in createTempGenomicsDB()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/ |
| H A D | VariantWalkerGCSSupportIntegrationTest.java | 64 … " -O %s "+ " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE + " false", in testReadVCFOnGCS()
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| H A D | GATKToolUnitTest.java | 915 …vcfFile.getCanonicalPath(), "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "true"}; in testGetDefaultToolVCFHeaderLines()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/cmdline/ |
| H A D | StandardArgumentDefinitions.java | 37 public static final String ADD_OUTPUT_VCF_COMMANDLINE = "add-output-vcf-command-line"; field in StandardArgumentDefinitions
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/spark/ |
| H A D | GATKSparkTool.java | 112 … StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, shortName = StandardArgumentDefinitions.A…
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/ |
| H A D | GATKTool.java | 104 … StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, shortName = StandardArgumentDefinitions.A…
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/ |
| H A D | PostprocessGermlineCNVCallsIntegrationTest.java | 119 argumentsBuilder.add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, in getArgsForSingleSample()
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