| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/ |
| H A D | FeatureManager.java | 135 …nal int featureQueryLookahead, final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer) { in FeatureManager() argument
136 … this(toolInstance, featureQueryLookahead, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, null); in FeatureManager()
152 …featureQueryLookahead, final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer, final Ge… in FeatureManager() argument
156 …urces(featureQueryLookahead, toolInstance, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, gdbOptio… in FeatureManager()
180 …eatureSources(featureQueryLookahead, k, v, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, referenc… in FeatureManager()
195 …eProgram toolInstance, final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer, final Ge… in initializeFeatureSources() argument
209 …es(featureQueryLookahead, featureInput, featureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeFeatureSources()
224 final int cloudIndexPrefetchBuffer, final Path reference) { in addToFeatureSources() argument
226 …Input, featureQueryLookahead, featureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, new Geno… in addToFeatureSources()
244 … final int cloudIndexPrefetchBuffer, final GenomicsDBOptions genomicsDBOptions) { in addToFeatureSources() argument
[all …]
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| H A D | FeatureDataSource.java | 223 final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer) { in FeatureDataSource() argument
224 …aturePath), queryLookaheadBases, targetFeatureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer); in FeatureDataSource()
239 final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer) { in FeatureDataSource() argument
240 …eatureInput, queryLookaheadBases, targetFeatureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in FeatureDataSource()
257 … final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer, final Path reference) { in FeatureDataSource() argument
258 …eatureInput, queryLookaheadBases, targetFeatureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in FeatureDataSource()
275 …final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer, final GenomicsDBOptions genomic… in FeatureDataSource() argument
286 BucketUtils.getPrefetchingWrapper(cloudIndexPrefetchBuffer), in FeatureDataSource()
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| H A D | FeatureWalker.java | 36 …is, FeatureDataSource.DEFAULT_QUERY_LOOKAHEAD_BASES, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeFeatures()
60 …ource.DEFAULT_QUERY_LOOKAHEAD_BASES, null, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, referenc… in initializeDrivingFeatures()
63 …ces(0, drivingFeaturesInput, codec.getFeatureType(), cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeDrivingFeatures()
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| H A D | VariantWalker.java | 57 …gVariantCacheLookAheadBases(), VariantContext.class, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeDrivingVariants()
62 …, drivingVariantsFeatureInput, VariantContext.class, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeDrivingVariants()
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| H A D | GATKTool.java | 112 public int cloudIndexPrefetchBuffer = getDefaultCloudIndexPrefetchBufferSize(); field in GATKTool
405 return ConfigFactory.getInstance().getGATKConfig().cloudIndexPrefetchBuffer(); in getDefaultCloudIndexPrefetchBufferSize()
457 (cloudIndexPrefetchBuffer < 0 ? cloudPrefetchBuffer : cloudIndexPrefetchBuffer)); in initializeReads()
486 cloudIndexPrefetchBuffer, getGenomicsDBOptions()); in initializeFeatures()
981 cloudIndexPrefetchBuffer, in addFeatureInputsAfterInitialization()
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| H A D | MultiVariantWalker.java | 85 …eatureSources(0, featureInput, VariantContext.class, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeDrivingVariants()
98 …atureInputs, getDrivingVariantCacheLookAheadBases(), cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeDrivingVariants()
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| H A D | FeatureContext.java | 321 … final int cloudIndexPrefetchBuffer, final Path reference) { in createFeatureContextForTesting() argument
327 featureQueryLookahead, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, reference); in createFeatureContextForTesting()
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| H A D | VariantLocusWalker.java | 75 …gVariantCacheLookAheadBases(), VariantContext.class, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeDrivingVariants()
80 …, drivingVariantsFeatureInput, VariantContext.class, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeDrivingVariants()
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| H A D | IntervalWalker.java | 38 features = new FeatureManager(this, 0, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeFeatures()
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| H A D | AbstractConcordanceWalker.java | 80 …e, "truth"), CACHE_LOOKAHEAD, VariantContext.class, cloudPrefetchBuffer, cloudIndexPrefetchBuffer); in initializeTruthVariantsIfNecessary()
104 …le, "eval"), CACHE_LOOKAHEAD, VariantContext.class, cloudPrefetchBuffer, cloudIndexPrefetchBuffer); in onStartup()
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| H A D | ReadWalker.java | 67 … = new FeatureManager(this, FEATURE_CACHE_LOOKAHEAD, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeFeatures()
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| H A D | MultiVariantDataSource.java | 84 …t queryLookaheadBases, final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer, final Pa… in MultiVariantDataSource() argument
90 …ureInput, queryLookaheadBases, VariantContext.class, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in MultiVariantDataSource()
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| H A D | VariantWalkerBase.java | 65 …ager(this, DEFAULT_DRIVING_VARIANTS_LOOKAHEAD_BASES, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeFeatures()
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| H A D | ReadsPathDataSource.java | 180 int cloudPrefetchBuffer, int cloudIndexPrefetchBuffer) { in ReadsPathDataSource() argument
183 BucketUtils.getPrefetchingWrapper(cloudIndexPrefetchBuffer) ); in ReadsPathDataSource()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/spark/ |
| H A D | JoinReadsWithVariants.java | 62 …int cloudIndexPrefetchBuffer = ConfigFactory.getInstance().getGATKConfig().cloudIndexPrefetchBuffe… in openFeatureSource() local
63 …<>(path, null, DEFAULT_QUERY_LOOKAHEAD_BASES, null, cloudPrefetchBuffer, cloudIndexPrefetchBuffer); in openFeatureSource()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/ |
| H A D | DummyPlaceholderGatkTool.java | 31 …is, FeatureDataSource.DEFAULT_QUERY_LOOKAHEAD_BASES, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, in initializeFeatures()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/config/ |
| H A D | GATKConfig.java | 165 int cloudIndexPrefetchBuffer(); in cloudIndexPrefetchBuffer() method
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/resources/org/broadinstitute/hellbender/utils/config/ |
| H A D | GATKConfig.properties | 84 cloudIndexPrefetchBuffer = -1 key
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/test/ |
| H A D | FuncotatorTestUtils.java | 66 … final int cloudIndexPrefetchBuffer, final Path reference) { in createFeatureContext() argument
76 featureQueryLookahead, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, reference); in createFeatureContext()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/ |
| H A D | test_no_pair_orientation_info.vcf | 38 … true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disa…
39 … true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disa…
52 … true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disa…
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| H A D | test_no_pair_orientation_info_indels.vcf | 40 … true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disa…
41 … true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disa…
54 … true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disa…
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/ |
| H A D | synthetic.challenge.set1.tumor-vs-synthetic.challenge.set1.normal-filtered.vcf | 40 … true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disa…
41 … true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disa…
54 … true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disa…
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/collections/ |
| H A D | SimpleCountCollection.java | 162 ConfigFactory.getInstance().getGATKConfig().cloudIndexPrefetchBuffer()); in readOverlappingSubsetFromGCS()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/ |
| H A D | AnnotateIntervals.java | 171 cloudIndexPrefetchBuffer, in onTraversalStart()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/ |
| H A D | expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.noMD.noBQSR.md.bqsr.vcf | 8 … true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disa…
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