Uses of Class
org.snpeff.snpEffect.SnpEffectPredictor
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Uses of SnpEffectPredictor in org.snpeff.coverage
Constructors in org.snpeff.coverage with parameters of type SnpEffectPredictor Constructor Description CountReads(java.lang.String fileName, SnpEffectPredictor snpEffectPredictor)
CountReadsOnMarkers(SnpEffectPredictor snpEffectPredictor)
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Uses of SnpEffectPredictor in org.snpeff.snpEffect
Methods in org.snpeff.snpEffect that return SnpEffectPredictor Modifier and Type Method Description SnpEffectPredictor
Config. getSnpEffectPredictor()
static SnpEffectPredictor
SnpEffectPredictor. load(Config config)
Load predictor from a binary fileSnpEffectPredictor
Config. loadSnpEffectPredictor()
Load a snpEff predictor WARNING: 'genome' object get replaced upon loading a snpEffectPredictor (this is a dangerous side effect)Methods in org.snpeff.snpEffect with parameters of type SnpEffectPredictor Modifier and Type Method Description void
Config. setSnpEffectPredictor(SnpEffectPredictor snpEffectPredictor)
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Uses of SnpEffectPredictor in org.snpeff.snpEffect.commandLine.eff
Constructors in org.snpeff.snpEffect.commandLine.eff with parameters of type SnpEffectPredictor Constructor Description MasterEff(int numWorkers, SnpEffCmdEff snpEffCmdEff, SnpEffectPredictor snpEffectPredictor, OutputFormatter outputFormatter, IntervalForest filterIntervals)
WorkerEff(SnpEffCmdEff snpEffCmdEff, SnpEffectPredictor snpEffectPredictor, OutputFormatter outputFormatter, IntervalForest filterIntervals)
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Uses of SnpEffectPredictor in org.snpeff.snpEffect.factory
Methods in org.snpeff.snpEffect.factory that return SnpEffectPredictor Modifier and Type Method Description abstract SnpEffectPredictor
SnpEffPredictorFactory. create()
SnpEffectPredictor
SnpEffPredictorFactoryFeatures. create()
SnpEffectPredictor
SnpEffPredictorFactoryGenesFile. create()
SnpEffectPredictor
SnpEffPredictorFactoryGff. create()
SnpEffectPredictor
SnpEffPredictorFactoryKnownGene. create()
SnpEffectPredictor
SnpEffPredictorFactoryRand. create()
SnpEffectPredictor
SnpEffPredictorFactoryRefSeq. create()
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Uses of SnpEffectPredictor in org.snpeff.snpEffect.testCases.integration
Methods in org.snpeff.snpEffect.testCases.integration that return SnpEffectPredictor Modifier and Type Method Description SnpEffectPredictor
TestCasesIntegrationBase. build(java.lang.String genome)
Build a genomeSnpEffectPredictor
TestCasesIntegrationBase. buildAndCompare(java.lang.String genome, java.lang.String refSeqFile, java.lang.String fastaFile, java.lang.String resultFile, boolean hideProtein)
Build a genome from a RefSeq file and compare results to 'expected' resultsSnpEffectPredictor
TestCasesIntegrationBase. buildEmbl(java.lang.String genome, java.lang.String emblFile)
Build a genome from a embl file and compare results to 'expected' resultsSnpEffectPredictor
TestCasesIntegrationBase. buildGeneBank(java.lang.String genome, java.lang.String genBankFile)
Build a genome from a genbank file and compare results to 'expected' resultsSnpEffectPredictor
TestCasesIntegrationBase. buildGff3AndCompare(java.lang.String genome, java.lang.String gff3File, java.lang.String resultFile, boolean readSeqs, boolean createRandSequences)
Build a genome from a GFF3 file and compare results to 'expected' resultsSnpEffectPredictor
TestCasesIntegrationBase. loadSnpEffectPredictor(java.lang.String genome, boolean build)
Load predictor and create interval forestConstructors in org.snpeff.snpEffect.testCases.integration with parameters of type SnpEffectPredictor Constructor Description CompareEffects(SnpEffectPredictor snpEffectPredictor, long randSeed, boolean verbose)
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Uses of SnpEffectPredictor in org.snpeff.snpEffect.testCases.unity
Fields in org.snpeff.snpEffect.testCases.unity declared as SnpEffectPredictor Modifier and Type Field Description protected SnpEffectPredictor
TestCasesBase. snpEffectPredictor
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Uses of SnpEffectPredictor in org.snpeff.stats
Methods in org.snpeff.stats with parameters of type SnpEffectPredictor Modifier and Type Method Description void
ReadsOnMarkersModel. setSnpEffectPredictor(SnpEffectPredictor snpEffectPredictor)
Constructors in org.snpeff.stats with parameters of type SnpEffectPredictor Constructor Description ReadsOnMarkersModel(SnpEffectPredictor snpEffectPredictor)
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Uses of SnpEffectPredictor in org.snpeff.svg
Constructors in org.snpeff.svg with parameters of type SnpEffectPredictor Constructor Description SvgTranslocation(Transcript tr1, Transcript tr2, VariantBnd varBnd, SnpEffectPredictor snpEffPredictor)
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