Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryGff3
java.lang.Object
org.snpeff.snpEffect.factory.SnpEffPredictorFactory
org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff3
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
Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
FASTA_DELIMITER
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.SnpEffPredictorFactoryGff
addExon, addExons, addGene, addGene, addIntergenicConserved, addInterval, addIntronConserved, addUtr3, addUtr5, create, findOrCreateExon, findOrCreateGene, findOrCreateTranscript, parse, readExonSequences, readExonSequencesGff, readGff
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, setCircularCorrectLargeGap, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
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Constructor Details
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SnpEffPredictorFactoryGff3
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