Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryGenesFile
- java.lang.Object
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactory
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenesFile
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public class SnpEffPredictorFactoryGenesFile extends SnpEffPredictorFactory
This class creates a SnpEffectPredictor from a file (or a set of files) and a configuration The files used are: - genes.txt : Biomart query from Ensembl (see scripts/genes_dataset.xml) - Fasta files: One per chromosome (as described in the config file)- Author:
- pcingola
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
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Constructor Summary
Constructors Constructor Description SnpEffPredictorFactoryGenesFile(Config config)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description SnpEffectPredictor
create()
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Methods inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
add, add, add, add, add, add, addMarker, addSequences, adjustChromosomes, adjustTranscripts, beforeExonSequences, codingFromCds, collapseZeroLenIntrons, createRandSequences, deleteRedundant, exonsFromCds, exonsFromCds, findGene, findGene, findMarker, findTranscript, findTranscript, getOrCreateChromosome, getProteinByTrId, parsePosition, readExonSequences, replaceTranscript, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
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Constructor Detail
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SnpEffPredictorFactoryGenesFile
public SnpEffPredictorFactoryGenesFile(Config config)
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Method Detail
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create
public SnpEffectPredictor create()
- Specified by:
create
in classSnpEffPredictorFactory
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