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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 DFeatureManagerUnitTest.java186 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()
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H A DFeatureContextUnitTest.java48 …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()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/
H A DFeatureManager.java103 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
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