Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryGenesFile
java.lang.Object
org.snpeff.snpEffect.factory.SnpEffPredictorFactory
org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenesFile
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
Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
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Constructor Summary
Constructors -
Method Summary
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, setCircularCorrectLargeGap, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
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Constructor Details
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SnpEffPredictorFactoryGenesFile
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Method Details
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create
- Specified by:
create
in classSnpEffPredictorFactory
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