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
-
Field Summary
Fields inherited from class SnpEffPredictorFactoryGff
FASTA_DELIMITERFields inherited from class SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT -
Constructor Summary
Constructors -
Method Summary
Methods inherited from class SnpEffPredictorFactoryGff
addExon, addExons, addGene, addGene, addIntergenicConserved, addInterval, addIntronConserved, addUtr3, addUtr5, create, findOrCreateExon, findOrCreateGene, findOrCreateTranscript, parse, readExonSequences, readExonSequencesGff, readGffMethods inherited from class 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
-
Constructor Details
-
SnpEffPredictorFactoryGff3
-