Searched refs:toolInstance (Results 1 – 3 of 3) sorted by relevance
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/ |
H A D | FeatureManagerUnitTest.java | 186 ValidFeatureArgumentSource toolInstance = new ValidFeatureArgumentSource(); in testHandleRequestForValidFeatureInputs() local 193 FeatureManager manager = new FeatureManager(toolInstance); in testHandleRequestForValidFeatureInputs() 204 ValidFeatureArgumentSource toolInstance = new ValidFeatureArgumentSource(); in testGetAllSequenceDictionaries() local 211 FeatureManager manager = new FeatureManager(toolInstance); in testGetAllSequenceDictionaries() 219 final ValidFeatureArgumentSource toolInstance = new ValidFeatureArgumentSource(); in testSequenceDictionary() local 225 final FeatureManager manager = new FeatureManager(toolInstance); in testSequenceDictionary() 233 final ValidFeatureArgumentSource toolInstance = new ValidFeatureArgumentSource(); in testTwoSequenceDictionaries() local 240 final FeatureManager manager = new FeatureManager(toolInstance); in testTwoSequenceDictionaries() 253 final FeatureManager manager = new FeatureManager(toolInstance); in testEmptySequenceDictionary() 267 final FeatureManager manager = new FeatureManager(toolInstance); in testHandleRequestForValidFeatureInputIterator() [all …]
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H A D | FeatureContextUnitTest.java | 48 …ArtificialFeatureContainingCommandLineProgram toolInstance = new ArtificialFeatureContainingComman… in testEmptyFeatureContext() local 52 …Assert.assertTrue(featureContext.getValues(toolInstance.featureArgument).isEmpty(), "Empty Feature… in testEmptyFeatureContext() 53 …Assert.assertTrue(featureContext.getValues(toolInstance.featureArgument, 1).isEmpty(), "Empty Feat… in testEmptyFeatureContext() 54 …ertTrue(featureContext.getValues(Arrays.<FeatureInput<Feature>>asList(toolInstance.featureArgument… in testEmptyFeatureContext() 55 …ertTrue(featureContext.getValues(Arrays.<FeatureInput<Feature>>asList(toolInstance.featureArgument… in testEmptyFeatureContext() 60 …final ArtificialFeatureContainingCommandLineProgram toolInstance = new ArtificialFeatureContaining… in testGetHeader() local 61 try (final FeatureManager featureManager = new FeatureManager(toolInstance)) { in testGetHeader() 63 final Object header = featureContext.getHeader(toolInstance.featureArgument); in testGetHeader() 64 …Assert.assertTrue(header instanceof VCFHeader, "Header for " + toolInstance.featureArgument.getFea… in testGetHeader()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/ |
H A D | FeatureManager.java | 103 public FeatureManager( final CommandLineProgram toolInstance ) { in FeatureManager() argument 104 this(toolInstance, FeatureDataSource.DEFAULT_QUERY_LOOKAHEAD_BASES); in FeatureManager() 117 … public FeatureManager( final CommandLineProgram toolInstance, final int featureQueryLookahead ) { in FeatureManager() argument 118 this(toolInstance, featureQueryLookahead, 0, 0); in FeatureManager() 135 …public FeatureManager(final CommandLineProgram toolInstance, final int featureQueryLookahead, fina… in FeatureManager() argument 136 … this(toolInstance, featureQueryLookahead, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, null); in FeatureManager() 152 …public FeatureManager(final CommandLineProgram toolInstance, final int featureQueryLookahead, fina… in FeatureManager() argument 153 this.toolInstanceSimpleClassName = toolInstance.getClass().getSimpleName(); in FeatureManager() 156 …initializeFeatureSources(featureQueryLookahead, toolInstance, cloudPrefetchBuffer, cloudIndexPrefe… in FeatureManager() 195 …ureSources( final int featureQueryLookahead, final CommandLineProgram toolInstance, final int clou… in initializeFeatureSources() argument [all …]
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