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Searched refs:genomicsDBOptions (Results 1 – 7 of 7) sorted by relevance

/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/
H A DFeatureDataSource.java275 …oudPrefetchBuffer, final int cloudIndexPrefetchBuffer, final GenomicsDBOptions genomicsDBOptions) { in FeatureDataSource() argument
279 …Utils.nonNull(genomicsDBOptions, "GenomicsDBOptions must not be null. Calling tool may not read fr… in FeatureDataSource()
287 genomicsDBOptions); in FeatureDataSource()
319 … final GenomicsDBOptions genomicsDBOptions) { in getFeatureReader() argument
321 Utils.nonNull(genomicsDBOptions); in getFeatureReader()
323 if (genomicsDBOptions.getReference() == null) { in getFeatureReader()
327 final File referenceAsFile = genomicsDBOptions.getReference().toFile(); in getFeatureReader()
328 …urn (FeatureReader<T>)getGenomicsDBFeatureReader(featureInput, referenceAsFile, genomicsDBOptions); in getFeatureReader()
389 …atureReader(final GATKPath path, final File reference, final GenomicsDBOptions genomicsDBOptions) { in getGenomicsDBFeatureReader() argument
405 … createExportConfiguration(workspace, callsetJson, vidmapJson, vcfHeader, genomicsDBOptions); in getGenomicsDBFeatureReader()
[all …]
H A DVariantWalkerBase.java38 protected GenomicsDBOptions genomicsDBOptions; field in VariantWalkerBase
48 if (genomicsDBOptions == null) { in getGenomicsDBOptions()
49 genomicsDBOptions = new GenomicsDBOptions(referenceArguments.getReferencePath()); in getGenomicsDBOptions()
51 return genomicsDBOptions; in getGenomicsDBOptions()
H A DFeatureManager.java244 … final int cloudIndexPrefetchBuffer, final GenomicsDBOptions genomicsDBOptions) { in addToFeatureSources() argument
246 …ureQueryLookahead, featureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, genomicsDBOptions)); in addToFeatureSources()
/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
101 … .setReferenceGenome(genomicsDBOptions.getReference().toAbsolutePath().toString()) in createExportConfiguration()
105 .setProduceGTField(genomicsDBOptions.doCallGenotypes()) in createExportConfiguration()
108 ….setMaxDiploidAltAllelesThatCanBeGenotyped(genomicsDBOptions.getMaxDiploidAltAllelesThatCanBeGenot… in createExportConfiguration()
109 .setMaxGenotypeCount(genomicsDBOptions.getMaxGenotypeCount()) in createExportConfiguration()
110 … .setEnableSharedPosixfsOptimizations(genomicsDBOptions.sharedPosixFSOptimizations()); in createExportConfiguration()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/
H A DGenotypeGVCFs.java211 if (genomicsDBOptions == null) { in getGenomicsDBOptions()
212 …genomicsDBOptions = new GenomicsDBOptions(referenceArguments.getReferencePath(), genomicsdbArgs, g… in getGenomicsDBOptions()
214 return genomicsDBOptions; in getGenomicsDBOptions()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/
H A DGnarlyGenotyper.java174 if (genomicsDBOptions == null) { in getGenomicsDBOptions()
177 …genomicsDBOptions = new GenomicsDBOptions(referenceArguments.getReferencePath(), genomicsdbArgs, g… in getGenomicsDBOptions()
179 return genomicsDBOptions; in getGenomicsDBOptions()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/
H A DSelectVariants.java461 if (genomicsDBOptions == null) { in getGenomicsDBOptions()
462 … genomicsDBOptions = new GenomicsDBOptions(referenceArguments.getReferencePath(), genomicsdbArgs); in getGenomicsDBOptions()
464 return genomicsDBOptions; in getGenomicsDBOptions()