Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryGtf22
java.lang.Object
org.snpeff.snpEffect.factory.SnpEffPredictorFactory
org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22
This class creates a SnpEffectPredictor from a GTF 2.2 file
References: http://mblab.wustl.edu/GTF22.html
- Author:
- pcingola
-
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
-
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, 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
-
Constructor Details
-
SnpEffPredictorFactoryGtf22
-
-
Method Details
-
parse
Description copied from class:SnpEffPredictorFactoryGff
Parse a line- Overrides:
parse
in classSnpEffPredictorFactoryGff
- Returns:
- true if a line was parsed
-