Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryGff3
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactory
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff3
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public class SnpEffPredictorFactoryGff3 extends SnpEffPredictorFactoryGff
This class creates a SnpEffectPredictor from a GFF3 file References: - http://www.sequenceontology.org/gff3.shtml - http://gmod.org/wiki/GFF3 - http://www.eu-sol.net/science/bioinformatics/standards-documents/gff3-format-description- Author:
- pcingola
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
FASTA_DELIMITER
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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 SnpEffPredictorFactoryGff3(Config config)
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Method Summary
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Methods inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
addExon, addExons, addGene, addIntergenicConserved, addInterval, addIntronConserved, addUtr3, addUtr5, create, findOrCreateExon, findOrCreateGene, findOrCreateTranscript, parse, readExonSequences, readExonSequencesGff, readGff
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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, replaceTranscript, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
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Constructor Detail
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SnpEffPredictorFactoryGff3
public SnpEffPredictorFactoryGff3(Config config)
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