Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
A
- aa(String) - Method in class org.snpeff.codons.CodonTable
-
Translate codons to an amino acid sequence
- aa(String, boolean) - Method in class org.snpeff.codons.CodonTable
- aa(String, Genome, String) - Method in class org.snpeff.codons.CodonTables
-
Translate a codon into an amino acid for a given genome+chromosome
- AA_TO_CODE - Static variable in class org.snpeff.util.GprSeq
- aa1 - Variable in class org.snpeff.pdb.DistanceResult
- aa2 - Variable in class org.snpeff.pdb.DistanceResult
- aa2Code(char) - Static method in class org.snpeff.util.GprSeq
-
Convert from AA char to code
- aa2Code(String) - Static method in class org.snpeff.util.GprSeq
-
Convert from AA sequence to codes
- aaAlt - Variable in class org.snpeff.snpEffect.VariantEffect
- aaCode(char) - Method in class org.snpeff.snpEffect.HgvsProtein
- aaCode(String) - Method in class org.snpeff.snpEffect.HgvsProtein
-
Use one letter / three letter AA codes Most times we want to vonvert to 3 letter code HGVS: the three-letter amino acid code is prefered (see Discussion), with "*" designating a translation termination codon; for clarity we this page describes changes using the three-letter amino acid
- aaNumber2Pos() - Method in class org.snpeff.interval.Transcript
-
Calculate chromosome position as function of Amino Acid number Note that returns the chromosomal position of the first base for each Amino Acid
- aaNumber2Pos(int) - Method in class org.snpeff.interval.Transcript
-
Find a genomic position of the first base in a Amino Acid 'aaNum'
- aaPairCode(byte, byte) - Static method in class org.snpeff.util.GprSeq
-
Code an AA-pair
- aaPairCode(char, char) - Static method in class org.snpeff.util.GprSeq
-
Code an AA-pair
- aaPos1 - Variable in class org.snpeff.pdb.DistanceResult
- aaPos2 - Variable in class org.snpeff.pdb.DistanceResult
- aaRef - Variable in class org.snpeff.snpEffect.VariantEffect
- aasAroundNew - Variable in class org.snpeff.snpEffect.VariantEffect
- aasAroundOld - Variable in class org.snpeff.snpEffect.VariantEffect
- aaThreeLetterCode(char) - Method in class org.snpeff.codons.CodonTable
- aaThreeLetterCode(String) - Method in class org.snpeff.codons.CodonTable
-
Convert 1-letter code to 3-letter code (amino acids) Reference: http://www.hgvs.org/mutnomen/standards.html#aalist
- ACAT - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
- accession - Variable in class org.snpeff.nextProt.CvTerm
- accession - Variable in class org.snpeff.nextProt.LocationTargetIsoform
- AcgtTree - Class in org.snpeff.spliceSites
-
ACGT tree
- AcgtTree() - Constructor for class org.snpeff.spliceSites.AcgtTree
- AcgtTree(String, AcgtTree) - Constructor for class org.snpeff.spliceSites.AcgtTree
- add(double) - Method in class org.snpeff.gsa.PvaluesList
-
Add a p-value to the list
- add(double) - Method in class org.snpeff.gsa.ScoreList
-
Add a p-value to the list
- add(double) - Method in class org.snpeff.gtex.GtexExperiment
- add(double) - Method in class org.snpeff.stats.Average
- add(double) - Method in class org.snpeff.stats.AverageInt
- add(double) - Method in class org.snpeff.stats.CounterDouble
- add(long) - Method in class org.snpeff.stats.Counter
- add(long) - Method in class org.snpeff.stats.CounterDouble
- add(String) - Method in class org.snpeff.geneSets.GeneSets
-
Add a gene and aliases
- add(String) - Method in class org.snpeff.spliceSites.AcgtTree
- add(String, int) - Method in class org.snpeff.geneSets.GeneSetsRanked
-
Add a 'ranked' gene (to every corresponding GeneSet in this collection)
- add(String, String) - Method in class org.snpeff.gtex.IdMap
-
Add a mapping id invalid input: '<'-> name
- add(String, String) - Method in class org.snpeff.interval.GffMarker
-
Add key value pair
- add(String, String) - Method in class org.snpeff.logStatsServer.LogStats
-
Add a 'name=value' pair
- add(String, String) - Method in class org.snpeff.nextProt.NextProtSequenceConservation
- add(String, String) - Method in class org.snpeff.vcf.VcfGenotype
-
Add a name=value pair WARNING: This method does NOT change the FORMAT field.
- add(String, GeneSet) - Method in class org.snpeff.geneSets.GeneSets
-
Add a gene and it's corresponding gene set
- add(Collection<? extends Marker>) - Method in class org.snpeff.interval.tree.IntervalForest
-
Add all intervals
- add(Collection<T>) - Method in class org.snpeff.binseq.indexer.SequenceIndexer
-
Add a collection of sequences
- add(K, Collection<V>) - Method in class org.snpeff.collections.MultivalueHashMap
-
Add multiple values
- add(K, V) - Method in class org.snpeff.collections.MultivalueHashMap
-
Add a single value
- add(CodonTable) - Method in class org.snpeff.codons.CodonTables
-
Add a codon table
- add(FeatureCoordinates) - Method in class org.snpeff.genBank.Feature
- add(GoTerm) - Method in class org.snpeff.geneOntology.GoTerms
-
Add a GOTerm (if not already in this GOTerms) WARNING: Creates 'fake' symbolNames based on symbolIds.
- add(GeneSet) - Method in class org.snpeff.geneSets.GeneSets
-
Add a gene set
- add(Cds) - Method in class org.snpeff.interval.Transcript
-
Add a CDS
- add(Cds) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- add(Chromosome) - Method in class org.snpeff.interval.Genome
-
Add a chromosome
- add(Chromosome) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- add(Chromosome, int, int, double) - Method in class org.snpeff.gsa.ChrPosScoreList
- add(Exon) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Add an exon
- add(Gene) - Method in class org.snpeff.geneSets.GeneStats
- add(Gene) - Method in class org.snpeff.interval.Genes
-
Add a gene interval to this collection
- add(Gene) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Add a Gene
- add(Gene) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Add a gene interval
- add(Gene, boolean) - Method in class org.snpeff.geneSets.GeneStats
-
Add a gene, update statistics
- add(Intron) - Method in class org.snpeff.interval.Transcript
-
Add an intron
- add(Marker) - Method in class org.snpeff.interval.CytoBands
- add(Marker) - Method in class org.snpeff.interval.Markers
-
Add an interval to the collection
- add(Marker) - Method in class org.snpeff.interval.tree.IntervalForest
-
Add an interval
- add(Marker) - Method in class org.snpeff.interval.tree.IntervalTree
-
Add an interval object to the interval tree's list Note: Marks the tree as 'not inSync', but will not rebuild the tree until the next query or call to build
- add(Marker) - Method in class org.snpeff.interval.tree.IntervalTreeArray
- add(Marker) - Method in class org.snpeff.interval.tree.IntervalTreeOri
-
Add an interval object to the interval tree's list Note: Marks the tree as 'not inSync', but will not rebuild the tree until the next query or call to build
- add(Marker) - Method in interface org.snpeff.interval.tree.Itree
-
Add an interval object to the interval tree's list
- add(Marker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Add a generic Marker
- add(Marker) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Add a marker
- add(Markers) - Method in class org.snpeff.interval.Markers
-
Add all intervals
- add(Markers) - Method in class org.snpeff.interval.tree.IntervalForest
-
Add all intervals
- add(Markers) - Method in class org.snpeff.interval.tree.IntervalTree
-
Add all intervals to interval tree's list Note: Marks the tree as 'not inSync', but will not rebuild the tree until the next query or call to build
- add(Markers) - Method in class org.snpeff.interval.tree.IntervalTreeArray
- add(Markers) - Method in class org.snpeff.interval.tree.IntervalTreeOri
-
Add all intervals to interval tree's list Note: Marks the tree as 'not inSync', but will not rebuild the tree until the next query or call to build
- add(Markers) - Method in interface org.snpeff.interval.tree.Itree
-
Add all intervals to interval tree's list
- add(SpliceSite) - Method in class org.snpeff.interval.Exon
-
Add a splice site to the collection
- add(SpliceSite) - Method in class org.snpeff.interval.Intron
-
Add a splice site to the collection
- add(SpliceSite) - Method in class org.snpeff.interval.Transcript
-
Add a SpliceSite
- add(Transcript) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Add a transcript
- add(Utr) - Method in class org.snpeff.interval.Transcript
-
Add a UTR
- add(Variant, Marker, EffectType, String) - Method in class org.snpeff.snpEffect.VariantEffects
-
Add an effect
- add(Variant, Marker, EffectType, VariantEffect.EffectImpact, String) - Method in class org.snpeff.snpEffect.VariantEffects
-
Add an effect
- add(NextProtXmlAnnotation) - Method in class org.snpeff.nextProt.NextProtXmlEntry
-
Add an annotation
- add(OsCmdRunner) - Method in class org.snpeff.osCmd.OsCmdQueue
-
Add command to be executed
- add(OsCmdRunner, String) - Method in class org.snpeff.osCmd.OsCmdQueue
-
Add command to be executed, only if 'outputFile' does not exist
- add(IdMapperEntry) - Method in class org.snpeff.pdb.IdMapper
- add(TfamEntry) - Method in class org.snpeff.ped.PedFamily
-
Add an entry t this family
- add(TfamEntry) - Method in class org.snpeff.ped.PedPedigree
-
Add an entry to this pedigree
- add(Entity) - Method in class org.snpeff.reactome.events.Complex
- add(Entity) - Method in class org.snpeff.reactome.Monitor
- add(Entity, String) - Method in class org.snpeff.reactome.Reactome
-
Add an entity invalid input: '<'-> geneId
- add(Event) - Method in class org.snpeff.reactome.events.Pathway
- add(SamHeaderRecord) - Method in class org.snpeff.sam.SamHeader
-
Add a record to the header
- add(EffectType) - Method in class org.snpeff.filter.VariantEffectFilter
- add(VariantEffect) - Method in class org.snpeff.outputFormatter.OutputFormatter
-
Add effects to list
- add(VariantEffect) - Method in class org.snpeff.snpEffect.VariantEffects
-
Add an effect
- add(VcfAnnotator) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
-
Add a new annotator
- add(VcfHeader) - Method in class org.snpeff.vcf.VcfHeader
-
Add all missing lines from 'vcfHeader'
- add(VcfHeaderEntry) - Method in class org.snpeff.vcf.VcfHeader
-
Add header line
- add(T) - Method in class org.snpeff.binseq.indexer.SequenceIndexer
-
Add a sequence to this index
- add(T) - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
-
Add a sequence to this index
- add(T) - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Add a subinterval
- addAll(Iterable<T>) - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Add all intervals
- addAll(Collection<? extends Marker>) - Method in class org.snpeff.interval.Markers
-
Add all markers in this collection
- addAll(Collection<IdMapperEntry>) - Method in class org.snpeff.pdb.IdMapper
- addAll(Markers) - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Add all markers
- addAll(Markers) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Add a set of markers
- addBestU12Score(Transcript, String, String, int, int) - Method in class org.snpeff.spliceSites.SpliceTypes
-
Calculate the best U12 score.
- addCatalyst(Entity) - Method in class org.snpeff.reactome.events.Reaction
- addChild(GoTerm) - Method in class org.snpeff.geneOntology.GoTerm
-
Add a goTermId as a child of this GOTerm Also adds 'this' as parent of 'goTerm'
- addChromosomeSequence(String, String) - Method in class org.snpeff.binseq.GenomicSequences
-
Create a sequence for the whole chromsome (mostly used in test cases)
- addColumn(String, int[]) - Method in class org.snpeff.stats.plot.GoogleLineChart
- addColumn(String, ArrayList<String>) - Method in class org.snpeff.stats.plot.GoogleLineChart
- addEffect(EffectType) - Method in class org.snpeff.snpEffect.VariantEffect
- addEffectImpact(VariantEffect.EffectImpact) - Method in class org.snpeff.snpEffect.VariantEffect
- addEffectType(Variant, Marker, EffectType) - Method in class org.snpeff.snpEffect.VariantEffects
-
Add: If possible, only add an effect type (otherwise add the full effect)
- addEffectType(EffectType) - Method in class org.snpeff.snpEffect.VariantEffect
- addEffectType(EffectType) - Method in class org.snpeff.vcf.VcfEffect
- addErrorMessage(ErrorWarningType) - Method in class org.snpeff.snpEffect.VariantEffect
- addErrorWarning(Variant, ErrorWarningType) - Method in class org.snpeff.snpEffect.VariantEffects
- addErrorWarningInfo(ErrorWarningType) - Method in class org.snpeff.snpEffect.VariantEffect
-
Add an error or warning
- addExon(Transcript, GffMarker, String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Create a new exon
- addExons(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Create and add a new exon
- addFeatures(Features) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
-
Add all features
- addFile(String) - Method in class org.snpeff.coverage.CountReadsOnMarkers
-
Add a SAM/BAM file to be processed
- addFilter(String) - Method in class org.snpeff.vcf.VcfEntry
-
Add string to FILTER field
- addFormat(String) - Method in class org.snpeff.vcf.VcfEntry
-
Add a 'FORMAT' field
- addFormat(VcfHeaderFormat) - Method in class org.snpeff.vcf.VcfHeader
-
Add a 'FORMAT' meta info
- addGene(String) - Method in class org.snpeff.geneSets.GeneSet
-
Add one gene to genesSet
- addGene(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
- addGene(GffMarker, boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Create and add a gene based on GffMarker
- addGeneId(String) - Method in class org.snpeff.reactome.Entity
-
Add a geneId
- addGeneSequences(String, String) - Method in class org.snpeff.binseq.GenomicSequences
-
Add sequences for each gene in the genome
- addGeneSetCount(int) - Method in class org.snpeff.geneSets.Result
-
Add an item to the list of counts
- addGenotype(String) - Method in class org.snpeff.vcf.VcfEntry
-
Add a genotype as a string
- addHeader() - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
-
Add header
- addHeaderRecord(String) - Method in class org.snpeff.sam.SamHeader
- addHeaders(VcfFileIterator) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- addHeaders(VcfFileIterator) - Method in interface org.snpeff.snpEffect.VcfAnnotator
-
Add annotation headers to VCF file
- addHeaders(VcfFileIterator) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
- addInfo(String, String) - Method in class org.snpeff.vcf.VcfEntry
-
Add a "key=value" tuple the info field
- addInfo(VcfEntry) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
-
Add effects to INFO field
- addInfo(VcfHeaderInfo) - Method in class org.snpeff.vcf.VcfHeader
-
Add a VCF INFO header definition
- addInfoMessage(ErrorWarningType) - Method in class org.snpeff.snpEffect.VariantEffect
- addInput(Entity) - Method in class org.snpeff.reactome.events.Reaction
- addInteresting(String) - Method in class org.snpeff.geneSets.GeneSets
-
Add a symbol as 'interesting' gene (to every corresponding GeneSet in this collection)
- addInterestingSymbol(String, int, HashSet<String>) - Method in class org.snpeff.geneOntology.GoTerms
-
Add a symbol as 'interesting' symbol (to every corresponding GOTerm in this set)
- addInterestingSymbolId(String) - Method in class org.snpeff.geneOntology.GoTerm
-
Add one gene to interestingGenesSet
- addIntergenicConserved(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Add an intergenic conserved region
- addInterval(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Add interval based on GffMarker data
- addIntronConserved(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Add an intron conserved region
- addIsoformSequence(String, String) - Method in class org.snpeff.nextProt.NextProtXmlEntry
-
Add an Isoform sequence
- additionalEffect(String, String, int, int, String, String) - Method in class org.snpeff.interval.codonChange.CodonChange
-
Calculate additional effect due to codon changes E.g.
- addLine(String) - Method in class org.snpeff.vcf.VcfHeader
-
Add line to header (can add many lines)
- addMarker(Marker, boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Add a marker to the collection
- addMarkers(NextProtMarkerFactory) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
-
Create all markers for this annotation
- addMarkers(NextProtMarkerFactory) - Method in class org.snpeff.nextProt.NextProtXmlEntry
-
Create all Markers for this entry
- addMarkers(NextProtXmlEntry, NextProtXmlIsoform, NextProtXmlAnnotation, Location, String) - Method in class org.snpeff.nextProt.NextProtMarkerFactory
-
Create markers and add them
- addMarkerType(Marker, String) - Method in class org.snpeff.coverage.CountReads
- addMarkerType(Marker, String) - Method in class org.snpeff.coverage.CountReadsOnMarkers
- addOutput(Entity) - Method in class org.snpeff.reactome.events.Reaction
- addPerGene(Marker) - Method in class org.snpeff.interval.Gene
-
Add a gene dependent marker
- addProteinMapping(Attributes) - Method in class org.snpeff.nextProt.NextProtXmlIsoform
-
Add a transcript mapping
- addRegulationTrack(String) - Method in class org.snpeff.SnpEff
- addRegulator(Entity, String) - Method in class org.snpeff.reactome.events.Reaction
- addRegulator(Entity, Reaction.RegulationType) - Method in class org.snpeff.reactome.events.Reaction
- addResults(String) - Method in class org.snpeff.reactome.Monitor
- addScore(String, double) - Method in class org.snpeff.stats.CountByType
-
Add score for a type
- addSequences(String, String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Add genomic reference sequences
- addSymbolId(String) - Method in class org.snpeff.geneOntology.GoTerm
-
Add one gene to genesSet
- addSymbolId(GoTerm, String) - Method in class org.snpeff.geneOntology.GoTerms
-
Add a symbolId (as well as all needed mappings)
- addSymbolsFromChilds() - Method in class org.snpeff.geneOntology.GoTerms
-
Use symbols for chids in DAG For every GOTerm, each child's symbols are added to the term so that root term contains every symbol and every interestingSymbol
- addSymbolsFromChilds(GoTerm) - Method in class org.snpeff.geneOntology.GoTerm
-
Add all symbols from childs to goTerm
- addTranscriptMapping(Attributes) - Method in class org.snpeff.nextProt.NextProtXmlIsoform
-
Add a protein mapping
- addType(Marker, String) - Method in class org.snpeff.coverage.MarkerTypes
- addUtr3(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Create new UTR3primes
- addUtr5(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Create UTR5primes
- addWarningMessge(ErrorWarningType) - Method in class org.snpeff.snpEffect.VariantEffect
- adjust() - Method in class org.snpeff.interval.Gene
-
Adjust start, end and strand values
- adjust() - Method in class org.snpeff.interval.Transcript
-
Adjust transcript coordinates
- adjust(Marker) - Method in class org.snpeff.interval.Marker
-
Adjust [start,end] to include child
- adjustChromosomes() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Adjust chromosome length using gene information This is used when the sequence is not available (which makes sense on test-cases and debugging only)
- adjustedPvalue - Variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- adjustTranscripts() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Adjust transcripts: recalculate start, end, strand, etc.
- align() - Method in class org.snpeff.align.NeedlemanWunsch
- align() - Method in class org.snpeff.align.NeedlemanWunschOverlap
- align() - Method in class org.snpeff.align.VcfRefAltAlign
- ALL_ALLELES - Enum constant in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
- ALLELE - Enum constant in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
- ALLELE_FEQUENCY_COMMON - Static variable in class org.snpeff.vcf.VcfEntry
- ALLELE_FEQUENCY_LOW - Static variable in class org.snpeff.vcf.VcfEntry
- AlleleCountStats - Class in org.snpeff.stats
-
Count singletons and other allele counts per sample
- AlleleCountStats() - Constructor for class org.snpeff.stats.AlleleCountStats
- alleleFrequencyType() - Method in class org.snpeff.vcf.VcfEntry
-
Categorization by allele frequency
- allSymbols() - Method in class org.snpeff.geneOntology.GoTerms
-
Create a set with all the symbols
- alt - Variable in class org.snpeff.fileIterator.MatrixEntry
- alt - Variable in class org.snpeff.interval.Variant
- alt() - Method in class org.snpeff.snpEffect.HgvsDna
- alts - Variable in class org.snpeff.vcf.VcfEntry
- altStr - Variable in class org.snpeff.vcf.VcfEntry
- ALTTENATIVE_3SS - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
- ALTTENATIVE_5SS - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
- ALTTENATIVE_POLY_A - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
- ALTTENATIVE_PROMOMOTER - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
- AMINO_ACIDS - Static variable in class org.snpeff.util.GprSeq
- aminoAcids(Chain) - Static method in class org.snpeff.pdb.PdbUtil
-
Get all AAs in a chain
- analyzeAndCreate() - Method in class org.snpeff.spliceSites.SpliceTypes
-
Analyze and create conserved splice sites donor-acceptor pairs.
- and(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
- andNot(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
- andNotCount(OpenBitSet, OpenBitSet) - Static method in class org.snpeff.collections.OpenBitSet
-
Returns the popcount or cardinality of "a and not b" or "intersection(a, not(b))".
- ANN_FIELD_NAMES - Static variable in class org.snpeff.vcf.VcfEffect
- annotate(String, String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
-
Annotate: Calculate the effect of variants and show results
- annotate(VcfEntry) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
-
Annotate a VCF entry
- annotate(VcfEntry) - Method in interface org.snpeff.snpEffect.VcfAnnotator
-
Annotate a VCF file entry
- annotate(VcfEntry) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
- annotateFinish(VcfFileIterator) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
-
Finish annotations and create reports
- annotateFinish(VcfFileIterator) - Method in interface org.snpeff.snpEffect.VcfAnnotator
-
This method is called after all annotations have been performed.
- annotateFinish(VcfFileIterator) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
- annotateInit(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
-
Calculate the effect of variants and show results
- annotateInit(VcfFileIterator) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- annotateInit(VcfFileIterator) - Method in interface org.snpeff.snpEffect.VcfAnnotator
-
Initialize annotator: This method is called after vcfFile is opened, but before the header is output.
- annotateInit(VcfFileIterator) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
- antisense - Enum constant in enum class org.snpeff.interval.BioType
- anyBackToRef(VcfEntry) - Method in class org.snpeff.vcf.Pedigree
-
Are there any "back to reference" cancer variant
- anyDerived() - Method in class org.snpeff.vcf.Pedigree
-
Is there any derived sample?
- anythingSet() - Method in interface org.snpeff.filter.Filter
-
Has any of the paremeters been set?
- anythingSet() - Method in class org.snpeff.filter.VariantEffectFilter
-
Is any of the options set?
- apply(Variant) - Method in class org.snpeff.interval.Exon
-
Apply variant to exon WARNING: There might be conditions which change the exon type (e.g.
- apply(Variant) - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Apply a variant.
- apply(Variant) - Method in class org.snpeff.interval.Intron
- apply(Variant) - Method in class org.snpeff.interval.Marker
-
Apply a variant to a marker.
- apply(Variant) - Method in class org.snpeff.interval.MarkerSeq
-
Apply variant
- apply(Variant) - Method in class org.snpeff.interval.Transcript
-
Create a new transcript after applying changes in variant
- applyDel(Variant) - Method in class org.snpeff.interval.Marker
-
Apply a Variant to a marker.
- applyDel(Variant, MarkerSeq) - Method in class org.snpeff.interval.MarkerSeq
-
Apply a change type deletion (update sequence)
- applyDup(Variant) - Method in class org.snpeff.interval.Marker
-
Apply a Variant to a marker.
- applyDup(Variant, MarkerSeq) - Method in class org.snpeff.interval.MarkerSeq
-
Apply a change type duplication (update sequence)
- applyIns(Variant) - Method in class org.snpeff.interval.Marker
-
Apply a Variant to a marker.
- applyIns(Variant, MarkerSeq) - Method in class org.snpeff.interval.MarkerSeq
-
Apply a change type insertion (update sequence)
- applyMixed(Variant) - Method in class org.snpeff.interval.Marker
-
Apply a mixed variant Note: MIXED variant is interpreted as "MNP + InDel"
- applyMnp(Variant, MarkerSeq) - Method in class org.snpeff.interval.MarkerSeq
-
Apply a change type MNP (update sequence)
- applySnp(Variant, MarkerSeq) - Method in class org.snpeff.interval.MarkerSeq
-
Apply a change type SNP (update sequence)
- args - Variable in class org.snpeff.SnpEff
- ArrayUtil - Class in org.snpeff.collections
-
Methods for manipulating arrays.
- ArrayUtil() - Constructor for class org.snpeff.collections.ArrayUtil
- assign(String, int) - Method in class org.snpeff.fileIterator.TableFile
-
Assign values parse from 'line' into array elements indexed by 'idx'
- autoClose - Variable in class org.snpeff.fileIterator.FileIterator
- AutoHashMap<K,
V> - Class in org.snpeff.collections -
A Hash that creates new elements if they don't exists
- AutoHashMap(V) - Constructor for class org.snpeff.collections.AutoHashMap
- Average - Class in org.snpeff.stats
-
A simple class that calculates averages
- Average() - Constructor for class org.snpeff.stats.Average
- AverageInt - Class in org.snpeff.stats
-
A simple class that calculates average of integer numbers
- AverageInt() - Constructor for class org.snpeff.stats.AverageInt
- avg() - Method in class org.snpeff.gsa.ScoreList
-
Get average
- avg() - Method in class org.snpeff.nmer.NmerCount
-
Average number of nmers
- avg() - Method in class org.snpeff.stats.FloatStats
- AVG - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
- AVG_MAX_10 - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
- AVG_MIN_10 - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
- avgCoverage(int, int) - Method in class org.snpeff.coverage.CoverageChr
-
Calculate Coverage per base
- avgCoverage(Marker) - Method in class org.snpeff.coverage.CountFragments
-
Calculate Fragments Per Kilobase of exon per Million fragments mapped (FPKM)
- avgCoverage(Marker) - Method in class org.snpeff.coverage.Coverage
-
Calculate average coverage per base
- avgLargestTop(int) - Method in class org.snpeff.gsa.ScoreList
-
Get average pvalue (largest N)
- avgSmallestTop(int) - Method in class org.snpeff.gsa.ScoreList
-
Get average score (smallest N)
B
- BAD - Static variable in class org.snpeff.probablility.RankSumPdf
- BASE2CODE - Static variable in class org.snpeff.binseq.DnaSequenceByte
- base2index(char) - Static method in class org.snpeff.spliceSites.AcgtTree
- baseAt(int) - Method in class org.snpeff.interval.Transcript
-
Find base at genomic coordinate 'pos'
- baseName(String) - Static method in class org.snpeff.util.Gpr
-
Return file's name (without the path)
- baseName(String, String) - Static method in class org.snpeff.util.Gpr
-
Return file's name (without the path)
- baseNumber2MRnaPos(int) - Method in class org.snpeff.interval.Transcript
-
Calculate distance from transcript start to a position mRNA is roughly the same than cDNA.
- baseNumberCds(int, boolean) - Method in class org.snpeff.interval.Transcript
-
Calculate base number in a CDS where 'pos' maps
- baseNumberCds2Codon(int) - Method in class org.snpeff.interval.Transcript
-
Return a codon that includes 'cdsBaseNumber'
- baseNumberCds2Pos() - Method in class org.snpeff.interval.Transcript
-
Calculate chromosome position as function of CDS number
- baseNumberCds2Pos(int) - Method in class org.snpeff.interval.Transcript
- BASES - Static variable in class org.snpeff.binseq.DnaSequenceByte
- BASES - Static variable in class org.snpeff.motif.Pwm
- BASES - Static variable in class org.snpeff.spliceSites.AcgtTree
- BASES - Static variable in class org.snpeff.util.GprSeq
- BASES_PER_BYTE - Static variable in class org.snpeff.binseq.DnaSequenceByte
- BASES_PER_LONGWORD - Static variable in class org.snpeff.binseq.coder.DnaCoder
- basesAt(int, int) - Method in class org.snpeff.interval.MarkerSeq
-
Base in this marker at position 'index' (relative to marker start)
- basesAtPos(int, int) - Method in class org.snpeff.interval.MarkerSeq
-
Base at position 'pos' (genomic coordinates)
- BasesChangeCounter - Class in org.snpeff.overlap
-
Counts how many bases changed, given an XOR between two longs
- BasesChangeCounter(Coder) - Constructor for class org.snpeff.overlap.BasesChangeCounter
- basesPerWord() - Method in class org.snpeff.binseq.coder.Coder
-
How many bases can we pack in a word
- basesPerWord() - Method in class org.snpeff.binseq.coder.DnaCoder
- basesPerWord() - Method in class org.snpeff.binseq.coder.DnaQualityCoder
- baseToBits(char) - Method in class org.snpeff.binseq.coder.Coder
-
Encode a base using a binary representation
- baseToBits(char) - Method in class org.snpeff.binseq.coder.DnaCoder
-
Encode a base using 2 bits
- baseToBits(char, boolean) - Method in class org.snpeff.binseq.coder.DnaCoder
- baseToBits(char, int) - Method in class org.snpeff.binseq.coder.DnaQualityCoder
- BED - Enum constant in enum class org.snpeff.SnpEff.InputFormat
- BED - Enum constant in enum class org.snpeff.SnpEff.OutputFormat
- BED - Enum constant in enum class org.snpeff.snpEffect.commandLine.SnpEffCmdDump.DumpFormat
- BED_OFFSET - Static variable in class org.snpeff.fileIterator.RegulationBedFileIterator
- BEDANN - Enum constant in enum class org.snpeff.SnpEff.OutputFormat
- BedAnnotationOutputFormatter - Class in org.snpeff.outputFormatter
-
Formats: Show all annotations that intersect the BED input file.
- BedAnnotationOutputFormatter() - Constructor for class org.snpeff.outputFormatter.BedAnnotationOutputFormatter
- BedFileIterator - Class in org.snpeff.fileIterator
-
Opens a sequence change file and iterates over all intervals in BED format.
- BedFileIterator(String) - Constructor for class org.snpeff.fileIterator.BedFileIterator
- BedFileIterator(String, Genome) - Constructor for class org.snpeff.fileIterator.BedFileIterator
- BedOutputFormatter - Class in org.snpeff.outputFormatter
-
Formats output as BED file Referneces: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
- BedOutputFormatter() - Constructor for class org.snpeff.outputFormatter.BedOutputFormatter
- beforeExonSequences() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Perform some actions before reading sequences
- begin - Variable in class org.snpeff.nextProt.Location
- bestId - Variable in class org.snpeff.binseq.indexer.OverlapRessult
- bestReference - Variable in class org.snpeff.binseq.indexer.OverlapRessult
- bestScore - Variable in class org.snpeff.binseq.indexer.OverlapRessult
- bestSequence - Variable in class org.snpeff.binseq.indexer.OverlapRessult
- bestU12Score(String) - Method in class org.snpeff.spliceSites.SpliceTypes
-
Find the best score for PWM matrix in U12 branch points
- BETA - Static variable in class org.snpeff.reactome.Entity
- BigBedFileIterator - Class in org.snpeff.fileIterator
-
FileIterator for BigBed features WARNING: Removed in 2022-01 due to dependency on IGV's code (which depends on Log4j, which has a major security issue) Note: I use Broad's IGV code to do all the work, this is just a wrapper
- BigBedFileIterator(String) - Constructor for class org.snpeff.fileIterator.BigBedFileIterator
- bin64(long) - Static method in class org.snpeff.util.Gpr
-
Show a long as a 64 bit binary number
- BinarySequence - Class in org.snpeff.binseq
-
Base class for a binary 'read'.
- BinarySequence() - Constructor for class org.snpeff.binseq.BinarySequence
- Binomial - Class in org.snpeff.probablility
-
Calculate binomial distribution References http://en.wikipedia.org/wiki/Binomial_distribution
- Binomial() - Constructor for class org.snpeff.probablility.Binomial
- BinSeqFileIterator<T> - Class in org.snpeff.fileIterator
-
Reads all sequences from a file Warning: You should always call "close()" at the end of the iteration.
- BinSeqFileIterator(String) - Constructor for class org.snpeff.fileIterator.BinSeqFileIterator
- BIOMART - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
- BioType - Enum Class in org.snpeff.interval
-
BioTypes: Gene or transcript bioType annotation References: http://www.ensembl.org/info/genome/genebuild/biotypes.html Biotypes classifies genes and transcripts into groups including: protein coding, pseudogene , processed pseudogene, miRNA, rRNA, scRNA, snoRNA, snRNA.
- bits - Variable in class org.snpeff.collections.OpenBitSet
- BITS_PER_BASE - Static variable in class org.snpeff.binseq.coder.DnaCoder
- BITS_PER_BASE - Static variable in class org.snpeff.binseq.DnaSequenceByte
- BITS_PER_LONGWORD - Static variable in class org.snpeff.binseq.coder.Coder
- bits2words(long) - Static method in class org.snpeff.collections.OpenBitSet
-
returns the number of 64 bit words it would take to hold numBits
- bitscore - Variable in class org.snpeff.fileIterator.BlastResultEntry
- bitsPerBase() - Method in class org.snpeff.binseq.coder.Coder
-
How many bits do we need for each base
- bitsPerBase() - Method in class org.snpeff.binseq.coder.DnaCoder
- BitUtil - Class in org.snpeff.collections
-
A variety of high efficiency bit twiddling routines.
- BitUtil() - Constructor for class org.snpeff.collections.BitUtil
- BlackBoxEvent - Class in org.snpeff.reactome.events
-
A black box event
- BlackBoxEvent(int, String) - Constructor for class org.snpeff.reactome.events.BlackBoxEvent
- BlastResultEntry - Class in org.snpeff.fileIterator
- BlastResultEntry() - Constructor for class org.snpeff.fileIterator.BlastResultEntry
- BlastResultFileIterator - Class in org.snpeff.fileIterator
-
Iterate on each line of a GWAS catalog (TXT format)
- BlastResultFileIterator(String) - Constructor for class org.snpeff.fileIterator.BlastResultFileIterator
- BND - Enum constant in enum class org.snpeff.interval.Variant.VariantType
- BND_CURL_SIZE - Static variable in class org.snpeff.svg.SvgBnd
- body - Variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
- BONFERRONI - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
- BooleanMutable - Class in org.snpeff.stats
-
A mutable boolean
- BooleanMutable() - Constructor for class org.snpeff.stats.BooleanMutable
- BooleanMutable(boolean) - Constructor for class org.snpeff.stats.BooleanMutable
- branchU12Threshold(double) - Method in class org.snpeff.spliceSites.SpliceTypes
-
Calculate threshold of U12 PWM scores Pick the score that gives a 'thresholdU12Percentile'.
- BUFFER_SIZE - Static variable in class org.snpeff.fastq.FastqSplit
- BUFFER_SIZE - Static variable in class org.snpeff.osCmd.StreamGobbler
- build() - Method in class org.snpeff.binseq.GenomicSequences
-
Build interval forest
- build() - Method in class org.snpeff.interval.CytoBands
- build() - Method in class org.snpeff.interval.tree.IntervalForest
-
Build all trees
- build() - Method in class org.snpeff.interval.tree.IntervalTree
-
Build the interval tree to reflect the list of intervals, Will not run if this is currently in sync
- build() - Method in class org.snpeff.interval.tree.IntervalTreeArray
- build() - Method in class org.snpeff.interval.tree.IntervalTreeOri
-
Build the interval tree to reflect the list of intervals, Will not run if this is currently in sync
- build() - Method in interface org.snpeff.interval.tree.Itree
-
Build the interval tree to reflect the list of intervals.
- build(Markers) - Method in class org.snpeff.interval.tree.IntervalNode
-
Build interval tree
- build(Markers) - Method in class org.snpeff.interval.tree.IntervalTreeArray
-
Index intervals from 'start' to 'end' (index in 'markers')
- BUILD - Static variable in class org.snpeff.SnpEff
- BUILD_DATE - Static variable in class org.snpeff.SnpEff
- buildForest() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Create interval trees (forest)
- buildPerGene() - Method in class org.snpeff.interval.Gene
-
Build gene dependent interval tree
- BY - Static variable in class org.snpeff.Pcingola
- BYTES_PER_LONGWORD - Static variable in class org.snpeff.binseq.coder.Coder
C
- CACHE_MAX_N - Static variable in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Cache size roughly (N * NT)^2
- CACHE_MAX_N - Static variable in class org.snpeff.probablility.RankSumPdf
-
Cache size roughly (N * NT)^2
- CACHE_MAX_NT - Static variable in class org.snpeff.probablility.RankSumPdf
- cacheSetPdf(int, int, long, double) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
- calc() - Method in class org.snpeff.reactome.Entity
- calc(HashSet<Entity>) - Method in class org.snpeff.reactome.Entity
-
Calculate entities.
- calc(HashSet<Entity>) - Method in class org.snpeff.reactome.events.Reaction
-
Calculate entities.
- calcAlignment() - Method in class org.snpeff.align.NeedlemanWunschOverlap
- calcAlignmentScore() - Method in class org.snpeff.align.NeedlemanWunschOverlap
-
Calculate score matrix
- calcHetero() - Method in class org.snpeff.vcf.VcfEntry
-
Is this entry heterozygous? Infer Hom/Her if there is only one sample in the file.
- calcLogOddsWeight() - Method in class org.snpeff.motif.Pwm
-
Calculate log odds matrix from counts Reference: http://en.wikipedia.org/wiki/Position-specific_scoring_matrix
- calcRor(int) - Method in class org.snpeff.overlap.SequenceRotator
- calculateFromSam(String, boolean) - Static method in class org.snpeff.coverage.CountFragments
-
Calculate coverage from a SAM file
- calculateFromSam(String, boolean) - Static method in class org.snpeff.coverage.Coverage
-
Calculate coverage from a SAM file
- canBeCached(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Is the number in the cache
- canBeCached(int, int) - Static method in class org.snpeff.probablility.RankSumPdf
-
Is the number in the cache
- canonical - Variable in class org.snpeff.SnpEff
- canonical() - Method in class org.snpeff.interval.Gene
-
Get canonical transcript Canonical transcripts are defined as the longest CDS of amongst the protein coding transcripts.
- canonical() - Method in class org.snpeff.SnpEff
-
Filter canonical transcripts
- canonicalFile - Variable in class org.snpeff.SnpEff
- canParseLine(String) - Static method in class org.snpeff.interval.GffMarker
-
Can this line (form a GFF file) be parsed? Note: Returns false for headers, empty lines and lines having less number of fields than expected
- canRead(String) - Static method in class org.snpeff.util.Gpr
-
Can we read this file (either exact name or append a '.gz'
- canUseChiSquareApproximation(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
-
Can ChiSquare approximation be used? A rule of the thumb says it can be used if every expected frequency is more than 10
- capacity() - Method in class org.snpeff.collections.OpenBitSet
-
Returns the current capacity in bits (1 greater than the index of the last bit)
- cardinality() - Method in class org.snpeff.collections.OpenBitSet
- catalyst - Variable in class org.snpeff.reactome.events.Reaction
- CatalystActivity - Class in org.snpeff.reactome.events
-
A catalyst activity event
- CatalystActivity(int, String) - Constructor for class org.snpeff.reactome.events.CatalystActivity
- cdf(double) - Method in class org.snpeff.gsa.ScoreList
-
Cumulative distribution function of p-values: P[ pValues invalid input: '<'= p ] (i.e.
- cdf(double, double, double) - Static method in class org.snpeff.probablility.NormalDistribution
-
DESCRIPTION The main computation evaluates near-minimax approximations derived from those in "Rational Chebyshev approximations for the error function" by W.
- cdf(double, int, int) - Method in class org.snpeff.probablility.Binomial
-
Cumulative probability function P( K invalid input: '<'= k )
- cdf(int) - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
-
Cummulative distribution for this number
- cdf(int, int, int) - Static method in class org.snpeff.probablility.RankSumPdf
-
Cumulative density function (cdf)
- cdf(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Probability of getting a rank sum less or equal to 'r' when adding the ranks of 'nt' selected items.
- cdfApfloat(double, double, double[], double[]) - Static method in class org.snpeff.probablility.NormalDistribution
-
CDF using apfloat
- cdfExact(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Cumulative density function (cdf)
- cdfNormal(int, int, int) - Static method in class org.snpeff.probablility.RankSumPdf
-
Normal approximation to rankSum CDF
- cdfNormal(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Normal approximation to rankSum CDF
- cdfTriangle(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Uniform 'approximation' to rank sum statistic
- cdfUniform(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Uniform 'approximation' to rank sum statistic
- cdfUp(double, int, int) - Method in class org.snpeff.probablility.Binomial
-
Cumulative probability function, upper tail P( K > k )
- cdfUpEq(double, int, int) - Method in class org.snpeff.probablility.Binomial
-
Cumulative probability function, upper tail P( K >= k )
- cdfUpper(double) - Method in class org.snpeff.gsa.ScoreList
-
Cumulative distribution function of p-values: P[ pValues > p ] (i.e.
- cDnaPos - Variable in class org.snpeff.snpEffect.VariantEffect
- cds() - Method in class org.snpeff.interval.Transcript
-
Retrieve coding sequence
- Cds - Class in org.snpeff.interval
-
CDS: The coding region of a gene, also known as the coding sequence or CDS (from Coding DNA Sequence), is that portion of a gene's DNA or RNA, composed of exons, that codes for protein.
- Cds() - Constructor for class org.snpeff.interval.Cds
- Cds(Transcript, int, int, boolean, String) - Constructor for class org.snpeff.interval.Cds
- CDS - Enum constant in enum class org.snpeff.genBank.Feature.Type
- CDS - Enum constant in enum class org.snpeff.interval.GffType
- CDS - Enum constant in enum class org.snpeff.snpEffect.EffectType
- CDS_STAT_COMPLETE - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene
- CDS_STAT_COMPLETE - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRefSeq
- cdsAlt - Variable in class org.snpeff.interval.codonChange.CodonChangeStructural
- cdsBaseNumber(int) - Method in class org.snpeff.interval.codonChange.CodonChange
-
Calculate base number in a cds where 'pos' is
- cdsDiff() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
-
Differences between two CDSs after removing equal codons from the beginning and from the end of both strings
- cdsMarker() - Method in class org.snpeff.interval.Transcript
-
Create a marker of the coding region in this transcript
- cdsRef - Variable in class org.snpeff.interval.codonChange.CodonChangeStructural
- center - Variable in class org.snpeff.interval.tree.IntervalNode
- CHANGE_SEPARATOR - Static variable in class org.snpeff.stats.VariantEffectStats
- CHANGE_SEPARATOR - Static variable in class org.snpeff.stats.VariantStats
- changeQuality(String, FastqVariant, FastqVariant) - Static method in class org.snpeff.util.GprSeq
-
Change a fastQ encoding in a quality sequence
- Character - Enum constant in enum class org.snpeff.vcf.VcfInfoType
- characterize() - Method in class org.snpeff.interval.ExonSpliceCharacterizer
-
Characterize all exons
- characters(char[], int, int) - Method in class org.snpeff.nextProt.NextProtHandler
- check() - Method in class org.snpeff.vcf.VcfEntry
-
Perform several simple checks and report problems (if any).
- checkHypergeometricParams(int, int, int, int) - Method in class org.snpeff.probablility.Hypergeometric
-
Check if hypergeometric paramters are correct
- checkInterestingGenes(Set<String>) - Method in class org.snpeff.geneSets.GeneSets
-
Checks that every symboolID is in the set (as 'interesting' genes)
- checkInterestingGenes(Set<String>) - Method in class org.snpeff.geneSets.GeneSetsRanked
-
Checks that every symboolID is in the set (as 'interesting' genes)
- checkInterestingSymbolIds(Set<String>) - Method in class org.snpeff.geneOntology.GoTerms
-
Checks that every symboolID is in the set (as 'interesting' symbols)
- checkParams() - Method in class org.snpeff.pdb.ProteinInteractions
- child - Variable in class org.snpeff.vcf.PedigreeEntry
- childNum - Variable in class org.snpeff.vcf.PedigreeEntry
- chiSquareApproximation(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
-
Chi-Square approximation for Fisher's exact test
- chiSquareCDF(double, int) - Method in class org.snpeff.probablility.FisherExactTest
-
Chi-Square Cumulative Distribution Function probability that an observed chi-square value for a correct model should be less than chiSquare nu = the degrees of freedom
- chiSquareCDFComplementary(double, int) - Static method in class org.snpeff.gsa.ScoreList
-
Upper tail 1 - ChiSquareCDF(p)
- chiSquareCDFComplementary(double, int) - Method in class org.snpeff.probablility.FisherExactTest
-
Chi-Square Complementary of Cumulative Distribution Function: 1 - chiSquareCDF(x, nu) probability that an observed chi-square value for a correct model should be greater than chiSquare nu = the degrees of freedom
- chr - Variable in class org.snpeff.fileIterator.MatrixEntry
- chr - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- CHR_LEN_SEPARATE_FILE - Static variable in class org.snpeff.binseq.GenomicSequences
- chr1 - Variable in class org.snpeff.pdb.DistanceResult
- chr2 - Variable in class org.snpeff.pdb.DistanceResult
- CHROM_PREFIX - Static variable in class org.snpeff.vcf.VcfHeader
- CHROMO_PREFIX - Static variable in class org.snpeff.interval.ChromosomeSimpleName
- Chromosome - Class in org.snpeff.interval
-
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
- Chromosome() - Constructor for class org.snpeff.interval.Chromosome
- Chromosome(Genome, int, int, String) - Constructor for class org.snpeff.interval.Chromosome
- CHROMOSOME - Enum constant in enum class org.snpeff.snpEffect.EffectType
- CHROMOSOME_ELONGATION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- CHROMOSOME_END - Static variable in class org.snpeff.interval.Intergenic
- CHROMOSOME_LARGE_DELETION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- CHROMOSOME_LARGE_DUPLICATION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- CHROMOSOME_LARGE_INVERSION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- CHROMOSOME_START - Static variable in class org.snpeff.interval.Intergenic
- chromosomeName - Variable in class org.snpeff.vcf.VcfEntry
- chromosomeNameOri - Variable in class org.snpeff.interval.Interval
- chromosomeNamesSorted() - Method in class org.snpeff.interval.Genome
-
Get a sorted list of chromosomes
- ChromosomeSimpleName - Class in org.snpeff.interval
-
Convert chromosome names to simple names
- ChrPosScoreList - Class in org.snpeff.gsa
-
A list of invalid input: '<'chromosome, position, scores>
- ChrPosScoreList() - Constructor for class org.snpeff.gsa.ChrPosScoreList
- ChrPosStats - Class in org.snpeff.stats
-
How many changes per position do we have in a chromosome.
- ChrPosStats(String, int) - Constructor for class org.snpeff.stats.ChrPosStats
- CIRCULAR_GENE_ID - Static variable in class org.snpeff.interval.Gene
- circularClone() - Method in class org.snpeff.interval.Gene
-
In a circular genome, a gene can have negative coordinates or crosses over chromosome end.
- CircularCorrection - Class in org.snpeff.interval
-
Correct circular genomic coordinates Nomenclature: We use coordinates at the beginning of the chromosme and negative coordinates
- CircularCorrection(Transcript) - Constructor for class org.snpeff.interval.CircularCorrection
- CircularCorrection(Transcript, int) - Constructor for class org.snpeff.interval.CircularCorrection
- clazz - Variable in class org.snpeff.fileIterator.LineClassFileIterator
- cleanUnderscores(String) - Static method in class org.snpeff.vcf.VcfEntry
-
Return a string without leading, trailing and duplicated underscores
- clear() - Method in class org.snpeff.binseq.GenomicSequences
- clear() - Method in class org.snpeff.interval.Markers
- clear(int, int) - Method in class org.snpeff.collections.OpenBitSet
-
Clears a range of bits.
- clear(long) - Method in class org.snpeff.collections.OpenBitSet
-
clears a bit, allowing access beyond the current set size without changing the size.
- clear(long, long) - Method in class org.snpeff.collections.OpenBitSet
-
Clears a range of bits.
- clearStats() - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
-
Clear previous statistics
- clone() - Method in class org.snpeff.binseq.BinarySequence
- clone() - Method in class org.snpeff.binseq.DnaSequence
- clone() - Method in class org.snpeff.collections.OpenBitSet
- clone() - Method in class org.snpeff.interval.Interval
- clone() - Method in class org.snpeff.interval.IntervalAndSubIntervals
- clone() - Method in class org.snpeff.interval.Marker
- clone() - Method in class org.snpeff.interval.Variant
- clone() - Method in class org.snpeff.outputFormatter.OutputFormatter
- clone() - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
- clone() - Method in class org.snpeff.snpEffect.VariantEffect
- cloneAndSet(String, int, int) - Method in class org.snpeff.pdb.IdMapperEntry
-
Clone the object and return a copy having a different chain ID
- cloneShallow() - Method in class org.snpeff.interval.Cds
- cloneShallow() - Method in class org.snpeff.interval.Chromosome
- cloneShallow() - Method in class org.snpeff.interval.Custom
- cloneShallow() - Method in class org.snpeff.interval.Exon
- cloneShallow() - Method in class org.snpeff.interval.Gene
- cloneShallow() - Method in class org.snpeff.interval.GenericMarker
- cloneShallow() - Method in class org.snpeff.interval.Intergenic
- cloneShallow() - Method in class org.snpeff.interval.IntervalAndSubIntervals
- cloneShallow() - Method in class org.snpeff.interval.Intron
- cloneShallow() - Method in class org.snpeff.interval.Marker
-
Perform a shallow clone
- cloneShallow() - Method in class org.snpeff.interval.MarkerSeq
- cloneShallow() - Method in class org.snpeff.interval.MicroRnaBindingSite
- cloneShallow() - Method in class org.snpeff.interval.Motif
- cloneShallow() - Method in class org.snpeff.interval.NextProt
- cloneShallow() - Method in class org.snpeff.interval.ProteinInteractionLocus
- cloneShallow() - Method in class org.snpeff.interval.ProteinProteinInteractionLocus
- cloneShallow() - Method in class org.snpeff.interval.Regulation
- cloneShallow() - Method in class org.snpeff.interval.Transcript
- cloneShallow() - Method in class org.snpeff.interval.Variant
- cloneShallow() - Method in class org.snpeff.interval.VariantWithScore
- cloneShallow() - Method in class org.snpeff.vcf.VcfEntry
- close() - Method in class org.snpeff.fileIterator.BinSeqFileIterator
-
Close file (if not already done)
- close() - Method in class org.snpeff.fileIterator.FastqFileIterator
-
Close file
- close() - Method in class org.snpeff.fileIterator.FileIterator
-
Close file
- close() - Method in class org.snpeff.fileIterator.NullReader
- close() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- close() - Method in class org.snpeff.osCmd.OsCmdRunner
-
Close (kill) command
- close() - Method in class org.snpeff.outputFormatter.OutputFormatter
-
CLose output files, if any
- close() - Method in class org.snpeff.svg.Svg
- close() - Method in class org.snpeff.vcf.FileIndexChrPos
-
Close file
- CLOSEST - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
- cmd() - Method in class org.snpeff.SnpEff
-
Create an appropriate SnpEffCmd* object
- CochranArmitageTest - Class in org.snpeff.probablility
-
Calculate a Cochran-Armitage test Reference: http://en.wikipedia.org/wiki/Cochran-Armitage_test_for_trend The trend test is applied when the data take the form of a 2 x k contingency table.
- CODE_TO_AA - Static variable in class org.snpeff.util.GprSeq
- CODE_TO_DNA - Static variable in class org.snpeff.util.GprSeq
- code2aa(byte) - Static method in class org.snpeff.util.GprSeq
-
Convert from AA_code to AA letter
- code2aa(byte[]) - Static method in class org.snpeff.util.GprSeq
-
Convert from AA_code to AA letter
- code2aa(int[]) - Static method in class org.snpeff.util.GprSeq
-
Convert from AA_code to AA letter
- code2aaPair(int) - Static method in class org.snpeff.util.GprSeq
- code2dna(byte) - Static method in class org.snpeff.util.GprSeq
-
Convert from DNA_code to DNA letter
- coder - Static variable in class org.snpeff.binseq.DnaSequencePe
- Coder - Class in org.snpeff.binseq.coder
-
Class used to encode invalid input: '&' decode sequences into binary and vice-versa They are usually stored in 'long' words
- Coder() - Constructor for class org.snpeff.binseq.coder.Coder
- coding - Variable in class org.snpeff.interval.codonChange.CodonChangeStructural
- coding(boolean) - Static method in enum class org.snpeff.interval.BioType
-
Basic bioTypes for coding / non-coding genes
- CODING - Enum constant in enum class org.snpeff.interval.Gene.GeneType
- CODING - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.Coding
- codingFromCds() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Only coding transcripts have CDS: Make sure that transcripts having CDS are protein coding It might not be always "precise" though: $ grep CDS genes.gtf | cut -f 2 | ~/snpEff/scripts/uniqCount.pl 113 IG_C_gene 64 IG_D_gene 24 IG_J_gene 366 IG_V_gene 21 TR_C_gene 3 TR_D_gene 82 TR_J_gene 296 TR_V_gene 461 non_stop_decay 63322 nonsense_mediated_decay 905 polymorphic_pseudogene 34 processed_transcript 1340112 protein_coding
- codon(String) - Method in class org.snpeff.codons.CodonTable
-
Translate an amino acid into a codon
- codon(String, Genome, String) - Method in class org.snpeff.codons.CodonTables
-
Translate an amino acid into a codon for a given genome+chromosome
- CODON_CHANGE - Enum constant in enum class org.snpeff.snpEffect.EffectType
- CODON_CHANGE_PLUS_CODON_DELETION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- CODON_CHANGE_PLUS_CODON_INSERTION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- CODON_DELETION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- CODON_INSERTION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- CODON_SIZE - Static variable in class org.snpeff.interval.codonChange.CodonChange
- codonChange() - Method in class org.snpeff.interval.codonChange.CodonChange
-
Calculate a list of codon changes
- codonChange() - Method in class org.snpeff.interval.codonChange.CodonChangeInv
- codonChange() - Method in class org.snpeff.interval.codonChange.CodonChangeMixed
- codonChange() - Method in class org.snpeff.interval.codonChange.CodonChangeMnp
-
Calculate a list of codon changes
- codonChange() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
- codonChange(Exon) - Method in class org.snpeff.interval.codonChange.CodonChange
-
Calculate the effect on an exon
- codonChange(Exon) - Method in class org.snpeff.interval.codonChange.CodonChangeDel
-
Analyze deletions in this transcript.
- codonChange(Exon) - Method in class org.snpeff.interval.codonChange.CodonChangeIns
-
Analyze insertions in this transcript.
- codonChange(Exon) - Method in class org.snpeff.interval.codonChange.CodonChangeInterval
-
Interval is not a variant, nothing to do
- codonChange(Exon) - Method in class org.snpeff.interval.codonChange.CodonChangeSnp
-
Analyze SNPs in this transcript.
- CodonChange - Class in org.snpeff.interval.codonChange
-
Analyze codon changes based on a variant and a Transcript
- CodonChange(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChange
- CodonChangeDel - Class in org.snpeff.interval.codonChange
-
Calculate codon changes produced by a deletion
- CodonChangeDel(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeDel
- CodonChangeDup - Class in org.snpeff.interval.codonChange
-
Calculate codon changes produced by a duplication
- CodonChangeDup(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeDup
- CodonChangeIns - Class in org.snpeff.interval.codonChange
-
Calculate codon changes produced by an insertion
- CodonChangeIns(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeIns
- CodonChangeInterval - Class in org.snpeff.interval.codonChange
-
Calculate codon changes produced by a Interval Note: An interval does not produce any effect.
- CodonChangeInterval(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeInterval
- CodonChangeInv - Class in org.snpeff.interval.codonChange
-
Calculate codon changes produced by an inversion
- CodonChangeInv(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeInv
- CodonChangeMixed - Class in org.snpeff.interval.codonChange
-
Calculate codon changes produced by a 'mixed' variant Essentially every 'mixed' variant can be represented as a concatenation of a SNP/MNP + an INS/DEL
- CodonChangeMixed(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeMixed
- CodonChangeMnp - Class in org.snpeff.interval.codonChange
-
Calculate codon changes produced by a MNP
- CodonChangeMnp(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeMnp
- CodonChangeSnp - Class in org.snpeff.interval.codonChange
-
Calculate codon changes produced by a SNP
- CodonChangeSnp(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeSnp
- CodonChangeStructural - Class in org.snpeff.interval.codonChange
-
Calculate codon changes produced by a duplication
- CodonChangeStructural(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeStructural
- codonChangeSuper() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
- codonDegeneracy - Variable in class org.snpeff.snpEffect.VariantEffect
- codonIndex - Variable in class org.snpeff.snpEffect.VariantEffect
- codonNum - Variable in class org.snpeff.snpEffect.VariantEffect
- codonNumber2Pos(int) - Method in class org.snpeff.interval.Transcript
-
Return an array of 3 genomic positions where amino acid number 'aaNum' maps
- codonOldNew() - Method in class org.snpeff.interval.codonChange.CodonChangeMnp
-
Calculate codons old / codons new
- CODONS_AROUND - Static variable in class org.snpeff.snpEffect.PurityChange
- CODONS_SIZE - Static variable in class org.snpeff.snpEffect.PurityChange
- codonsAlt - Variable in class org.snpeff.snpEffect.VariantEffect
- codonsAlt() - Method in class org.snpeff.interval.codonChange.CodonChange
-
Calculate new codons
- codonsAlt() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
-
Get alternative codons
- codonsAlt() - Method in class org.snpeff.interval.codonChange.CodonChangeIns
-
Get new (modified) codons
- codonsAlt() - Method in class org.snpeff.interval.codonChange.CodonChangeMnp
- codonsAlt() - Method in class org.snpeff.interval.codonChange.CodonChangeSnp
-
Get new (modified) codons
- codonsAroundNew - Variable in class org.snpeff.snpEffect.VariantEffect
- codonsAroundOld - Variable in class org.snpeff.snpEffect.VariantEffect
- codonsRef - Variable in class org.snpeff.snpEffect.VariantEffect
- codonsRef() - Method in class org.snpeff.interval.codonChange.CodonChange
-
Calculate 'reference' codons
- codonsRef() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
-
Get original codons in CDS
- codonsRef() - Method in class org.snpeff.interval.codonChange.CodonChangeMnp
-
Calculate old codons
- codonsRef() - Method in class org.snpeff.interval.codonChange.CodonChangeSnp
-
Get original codons in CDS
- codonsRef(int) - Method in class org.snpeff.interval.codonChange.CodonChange
-
Calculate 'reference' codons
- codonsRefAlt() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
-
Calculate codons by applying the variant and calculating the differences in CDS sequences This is a slow method, makes sense only for complex variants
- codonTable() - Method in class org.snpeff.interval.Marker
-
Get a suitable codon table
- CodonTable - Class in org.snpeff.codons
-
A codon translation table
- CodonTable(String, String) - Constructor for class org.snpeff.codons.CodonTable
- CodonTables - Class in org.snpeff.codons
-
All codon tables are stored here.
- collapseZeroGap() - Method in class org.snpeff.interval.Transcript
-
Collapses exons having gaps of zero (i.e.
- collapseZeroGap(Markers) - Static method in class org.snpeff.interval.MarkerUtil
-
Collapse adjacent intervals (i.e.
- collapseZeroLenIntrons() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Collapse exons having zero size introns between them
- CombinatorialIterator - Class in org.snpeff.util
-
Generate all possible 'count' combinations
- CombinatorialIterator(int) - Constructor for class org.snpeff.util.CombinatorialIterator
- command - Variable in class org.snpeff.SnpEff
- COMMAND_LINE_WIDTH - Static variable in class org.snpeff.SnpEff
- CommandLine - Interface in org.snpeff.snpEffect.commandLine
-
Command line and arguments The way to run a command from 'main' is usually: public static void main(String[] args) { Command cmd = new Command(); cmd.parseArgs(args); cmd.run(); }
- commandLineStr(boolean) - Method in class org.snpeff.SnpEff
-
Command line argument list (try to fit it into COMMAND_LINE_WIDTH)
- Common - Enum constant in enum class org.snpeff.vcf.VcfEntry.AlleleFrequencyType
- compare(Long, Long) - Method in class org.snpeff.binseq.indexer.SequenceIndexer
-
Compare two references
- compare(Object, Object) - Method in class org.snpeff.geneOntology.CompareByValue
- compare(Object, Object) - Method in class org.snpeff.geneSets.CompareByValue
- compare(String, String) - Static method in class org.snpeff.interval.Chromosome
-
Compare chromosome names
- compare(DnaAndQualitySequence, int, DnaAndQualitySequence, int) - Method in class org.snpeff.binseq.comparator.DnaQualSubsequenceComparator
- compare(DnaSequence, int, DnaSequence, int) - Method in class org.snpeff.binseq.comparator.DnaSubsequenceComparator
- compare(Marker, Marker) - Method in class org.snpeff.interval.IntervalComparatorByEnd
- compare(Marker, Marker) - Method in class org.snpeff.interval.IntervalComparatorByStart
- compare(T, int, T, int) - Method in class org.snpeff.binseq.comparator.SubsequenceComparator
- compareByPos(DistanceResult) - Method in class org.snpeff.pdb.DistanceResult
-
Compare by genomic position
- CompareByValue - Class in org.snpeff.geneOntology
-
Compare two elements in a Map (e.g.
- CompareByValue - Class in org.snpeff.geneSets
-
Compare two elements in a Map (e.g.
- CompareByValue(Map) - Constructor for class org.snpeff.geneOntology.CompareByValue
- CompareByValue(Map, boolean) - Constructor for class org.snpeff.geneSets.CompareByValue
- compareCancerGenotypes(VcfEntry) - Method in class org.snpeff.vcf.Pedigree
-
Analyze which comparisons to make in cancer genomes
- compareChromoName(Interval) - Method in class org.snpeff.interval.Chromosome
-
Compare only chromosome's name
- compareNull(Comparable, Comparable) - Static method in class org.snpeff.util.Gpr
- compareTo(BinarySequence) - Method in class org.snpeff.binseq.DnaAndQualitySequence
- compareTo(BinarySequence) - Method in class org.snpeff.binseq.DnaSequence
- compareTo(BinarySequence) - Method in class org.snpeff.binseq.DnaSequencePe
- compareTo(BlastResultEntry) - Method in class org.snpeff.fileIterator.BlastResultEntry
- compareTo(GoTerm) - Method in class org.snpeff.geneOntology.GoTerm
- compareTo(GeneSet) - Method in class org.snpeff.geneSets.GeneSet
-
Comparable interface (to order terms)
- compareTo(Result) - Method in class org.snpeff.geneSets.Result
- compareTo(Interval) - Method in class org.snpeff.interval.Interval
-
Compare by start and end
- compareTo(Interval) - Method in class org.snpeff.interval.Marker
-
Compare by start and end
- compareTo(Interval) - Method in class org.snpeff.interval.Variant
-
Compare by start and end
- compareTo(IdMapperEntry) - Method in class org.snpeff.pdb.IdMapperEntry
- compareTo(PedPedigree) - Method in class org.snpeff.ped.PedPedigree
- compareTo(TfamEntry) - Method in class org.snpeff.ped.TfamEntry
- compareTo(Entity) - Method in class org.snpeff.reactome.Entity
- compareTo(VariantEffect) - Method in class org.snpeff.snpEffect.VariantEffect
- compareTo(KeyValue<A, B>) - Method in class org.snpeff.util.KeyValue
- compareTo(LineChrPos) - Method in class org.snpeff.vcf.LineChrPos
- compareToNumbers(double, double, String, String, boolean) - Method in class org.snpeff.geneSets.GeneSet
-
Compare 2 numbers and 2 'names' (if both numbers are equal) - NaN sorted in a way that they remain at the end of a sorted list - When two numbers are equal, the sort is done alphabetically by name
- compareToPos(Interval) - Method in class org.snpeff.interval.Marker
-
Compare genomic coordinates
- compartment - Variable in class org.snpeff.reactome.Entity
- Compartment - Class in org.snpeff.reactome
-
A Reactome compartment (a part of a cell)
- Compartment(int, String) - Constructor for class org.snpeff.reactome.Compartment
- COMPATIBLE_WITH_5_1 - Static variable in class org.snpeff.snpEffect.Config
- COMPATIBLE_WITH_5_2 - Static variable in class org.snpeff.snpEffect.Config
- compileDate(Class<?>) - Static method in class org.snpeff.util.Gpr
- compileTimeStamp() - Static method in class org.snpeff.util.Gpr
- compileTimeStamp(Class<?>) - Static method in class org.snpeff.util.Gpr
-
Return a time-stamp showing When was the JAR file created OR when was a class compiled
- compileTimeStamp(Class<?>, SimpleDateFormat) - Static method in class org.snpeff.util.Gpr
-
Return a time-stamp showing When was the JAR file created OR when was a class compiled
- complement - Variable in class org.snpeff.genBank.FeatureCoordinates
- COMPLEMENT - Static variable in class org.snpeff.genBank.Features
- COMPLEMENT_STRING - Static variable in class org.snpeff.genBank.Feature
- completed() - Method in enum class org.snpeff.logStatsServer.LogStats.RequestResult
-
A request is "Completed" if the communication worked
- Complex - Class in org.snpeff.reactome.events
-
A Reactome complex (a bunch of molecules or complexes
- Complex(int, String) - Constructor for class org.snpeff.reactome.events.Complex
- complexity(String) - Method in class org.snpeff.complexity.SequenceComplexity
-
Measure string's complexity
- compressGenotypes() - Method in class org.snpeff.vcf.VcfEntry
-
Compress genotypes into "HO/HE/NA" INFO fields
- config - Variable in class org.snpeff.SnpEff
- config() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
-
Read config file, load invalid input: '&' build database
- Config - Class in org.snpeff.snpEffect
- Config(String) - Constructor for class org.snpeff.snpEffect.Config
-
Create a config (uses DEFAULT_CONFIG_FILE)
- Config(String, String) - Constructor for class org.snpeff.snpEffect.Config
-
Create a configuration from 'configFileName'
- Config(String, String, String, Map<String, String>) - Constructor for class org.snpeff.snpEffect.Config
-
Create a configuration from 'configFileName'
- Config(String, String, String, Map<String, String>, boolean) - Constructor for class org.snpeff.snpEffect.Config
- Config(Genome) - Constructor for class org.snpeff.snpEffect.Config
-
This constructor is used in test cases
- configFile - Variable in class org.snpeff.SnpEff
- configOverride - Variable in class org.snpeff.SnpEff
- connect() - Method in class org.snpeff.logStatsServer.LogStats
-
Connect to server
- consensus(Regulation) - Method in class org.snpeff.RegulationFileConsensus
-
Add to consensus
- conservation() - Method in class org.snpeff.nextProt.NextProtMarkerFactory
-
Sequence conservations analysis.
- CONSERVATION_THRESHOLD - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
- considerOverlap(DnaSequenceId, DnaSequenceId) - Method in class org.snpeff.binseq.indexer.OverlapFilterCompareAllAll
-
Consider overlap between two sequences?
- considerOverlap(DnaSequenceId, DnaSequenceId) - Method in class org.snpeff.binseq.indexer.OverlapFilterDnaId
-
Consider overlap between two sequences?
- considerOverlap(T, T) - Method in interface org.snpeff.binseq.indexer.OverlapFilter
-
Consider overlap between two sequences?
- contains(long, long) - Method in class org.snpeff.collections.HashLongLongArray
-
Return true if value is in the hash
- contains(Object) - Method in class org.snpeff.interval.Markers
- contains(Object) - Method in class org.snpeff.reactome.events.Complex
- contains(Object) - Method in class org.snpeff.reactome.events.Pathway
- contains(String) - Method in class org.snpeff.stats.CountByType
- containsAll(Collection<?>) - Method in class org.snpeff.interval.Markers
- containsId(String) - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Is 'id' in the subintervals?
- convertFrame(int) - Method in enum class org.snpeff.interval.FrameType
- copy(GeneSets) - Method in class org.snpeff.geneSets.GeneSets
-
Copy all data from geneSets
- copyBases(long[], int, long[], int, int) - Method in class org.snpeff.binseq.coder.DnaCoder
-
Copy 'length' bases from 'src' (starting from 'srcStart') to 'dst' (starting from 'dstStart')
- copyBases(long[], long[], int, int) - Method in class org.snpeff.binseq.coder.DnaCoder
-
Copy 'length' bases from 'src' to 'dst' (starting from 'start')
- CORE_SPLICE_SITE_SIZE - Static variable in class org.snpeff.interval.SpliceSite
- correct() - Method in class org.snpeff.interval.CircularCorrection
-
Return a circular corrected transcript or null if no correction is needed
- count - Variable in class org.snpeff.stats.Counter
- count - Variable in class org.snpeff.stats.CounterDouble
- count() - Method in class org.snpeff.align.StringDiff
-
Count number of differences between strings
- count() - Method in class org.snpeff.coverage.CountReads
-
Count markers from a file
- count() - Method in class org.snpeff.coverage.CountReadsOnMarkers
-
Count markers from all files
- count(Nmer) - Method in class org.snpeff.nmer.NmerCount
-
Count an instance of this Nmer
- count(Nmer) - Method in class org.snpeff.nmer.NmerCountWc
- COUNT_DIFFS - Variable in class org.snpeff.binseq.coder.DnaCoder
- countAffectedExons() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
-
How many full / partial exons does the variant affect?
- countBases() - Method in class org.snpeff.stats.ReadsOnMarkersModel
-
Count bases covered for each marker type
- CountByKey<T> - Class in org.snpeff.stats
-
Counters indexed by key.
- CountByKey() - Constructor for class org.snpeff.stats.CountByKey
- CountByType - Class in org.snpeff.stats
-
Counters indexed by 'type' (type is a generic string that can mean anything)
- CountByType() - Constructor for class org.snpeff.stats.CountByType
- countColumns(String) - Static method in class org.snpeff.util.Gpr
-
Count number of column in a file
- Counter - Class in org.snpeff.stats
-
A simple class that counts...
- Counter() - Constructor for class org.snpeff.stats.Counter
- CounterDouble - Class in org.snpeff.stats
-
A simple class that counts...
- CounterDouble() - Constructor for class org.snpeff.stats.CounterDouble
- CountFragments - Class in org.snpeff.coverage
-
Base by base coverage (one chromsome)
- CountFragments() - Constructor for class org.snpeff.coverage.CountFragments
- countGenes(List<Marker>) - Method in class org.snpeff.snpEffect.VariantEffectStructural
- countGenotypes() - Method in class org.snpeff.ped.PedEntry
-
Number of phenotypes available
- countIUB(String) - Static method in class org.snpeff.util.IubString
-
How many IUB bases are in this string?
- countLessThan(int) - Method in class org.snpeff.nmer.NmerCount
-
Count how many nmers are below a given threshold
- countLines(String) - Static method in class org.snpeff.util.Gpr
-
Count lines in a file (same as 'wc -l file' in unix)
- countMissingCategory(String) - Method in class org.snpeff.nextProt.NextProtHandler
- countNewLineChars - Variable in class org.snpeff.fileIterator.FileIterator
- countNewLineChars() - Method in class org.snpeff.fileIterator.FileIterator
-
Guess number of newline characters used (e.g.
- countOverlap(GeneSet) - Method in class org.snpeff.geneSets.GeneSet
-
COunt how many genes are in both GeneSets
- CountReads - Class in org.snpeff.coverage
-
Count how many reads map (from many SAM/BAM files) onto markers
- CountReads(String, SnpEffectPredictor) - Constructor for class org.snpeff.coverage.CountReads
- CountReadsOnMarkers - Class in org.snpeff.coverage
-
Count how many reads map (from many SAM/BAM files) onto markers
- CountReadsOnMarkers(SnpEffectPredictor) - Constructor for class org.snpeff.coverage.CountReadsOnMarkers
- countTranscripts() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Count number of transcripts
- coverage(int, int) - Method in class org.snpeff.coverage.CoverageChr
-
Calculate Coverage per base
- coverage(Marker) - Method in class org.snpeff.coverage.Coverage
-
Calculate total coverage per base
- Coverage - Class in org.snpeff.coverage
-
Base by base coverage (one chromsome)
- Coverage() - Constructor for class org.snpeff.coverage.Coverage
- coverageByType - Variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
- CoverageByType - Class in org.snpeff.stats
- CoverageByType() - Constructor for class org.snpeff.stats.CoverageByType
- CoverageChr - Class in org.snpeff.coverage
-
Base by base coverage (one chromsome)
- CoverageChr(int) - Constructor for class org.snpeff.coverage.CoverageChr
- cpgExonBias() - Method in class org.snpeff.interval.Gene
-
Calculate CpG bias: number of CpG / expected[CpG]
- cpgExonBias() - Method in class org.snpeff.interval.Transcript
-
Calculate CpG bias: number of CpG / expected[CpG]
- cpgExons() - Method in class org.snpeff.interval.Transcript
-
Count total CpG in this transcript's exons
- create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
- create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenesFile
- create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
- create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene
- create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
- create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRefSeq
- createCacheFile() - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Create a cache file
- createChr(String, int) - Method in class org.snpeff.coverage.CountFragments
-
Create new chromosome coverage
- createChr(String, int) - Method in class org.snpeff.coverage.Coverage
-
Create new chromosome coverage
- createChromos - Variable in class org.snpeff.fileIterator.MarkerFileIterator
- createCircularGenes() - Method in class org.snpeff.interval.Genes
-
In a circular genome, a gene can have negative coordinates or crosses over chromosome end.
- createFromFaidx(String, String) - Static method in class org.snpeff.interval.Genome
-
Create a genome from a faidx file.
- createGenomicRegions() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Create (and add) up-down stream, splice sites, intergenic, etc
- createIntergenic() - Method in class org.snpeff.interval.Genes
-
Creates a list of Intergenic regions
- createIntergenic(Gene, Gene) - Static method in class org.snpeff.interval.Intergenic
-
Creates an intergenic marker based on the "space" between two genes
- createObject(String) - Method in class org.snpeff.fileIterator.LineClassFileIterator
-
Create an object using
- createRandSequences() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Create random sequences for exons Note: This is only used for test cases!
- createSpliceFasta(String) - Method in class org.snpeff.spliceSites.SpliceTypes
-
Create one fasta file for each donor-acceptor pair
- createSpliceSiteAcceptor(int) - Method in class org.snpeff.interval.Intron
-
Create a splice site acceptor of 'size' length Acceptor site: 3' end of the intron
- createSpliceSiteDonor(int) - Method in class org.snpeff.interval.Intron
-
Create a splice site donor of 'maxSize' length Donor site: 5' end of the intron
- createSpliceSiteRegionEnd(int) - Method in class org.snpeff.interval.Exon
-
Create splice site regions
- createSpliceSiteRegionEnd(int, int) - Method in class org.snpeff.interval.Intron
-
Create splice site region
- createSpliceSiteRegionStart(int) - Method in class org.snpeff.interval.Exon
-
Create splice site regions
- createSpliceSiteRegionStart(int, int) - Method in class org.snpeff.interval.Intron
-
Create splice site region
- createSpliceSites(int, int, int, int) - Method in class org.snpeff.interval.Genes
-
Create splice sites.
- createSpliceSites(int, int, int, int) - Method in class org.snpeff.interval.Transcript
-
Find all splice sites.
- createUpDownStream(int) - Method in class org.snpeff.interval.Genes
-
Creates a list of UP/DOWN stream regions (for each transcript) Upstream (downstream) stream is defined as upDownLength before (after) transcript Note: If upDownLength invalid input: '<'=0 no interval is created
- createUpDownStream(int) - Method in class org.snpeff.interval.Transcript
-
Creates a list of UP/DOWN stream regions (for each transcript) Upstream (downstream) stream is defined as upDownLength before (after) transcript
- Custom - Class in org.snpeff.interval
-
This is a custom interval (i.e.
- Custom() - Constructor for class org.snpeff.interval.Custom
- Custom(Marker, int, int, boolean, String, String) - Constructor for class org.snpeff.interval.Custom
- CUSTOM - Enum constant in enum class org.snpeff.snpEffect.EffectType
- customIntervalFiles - Variable in class org.snpeff.SnpEff
- CvTerm - Class in org.snpeff.nextProt
-
A controlled vocabulary term
- CvTerm(Attributes) - Constructor for class org.snpeff.nextProt.CvTerm
- CytoBands - Class in org.snpeff.interval
-
Cytband definitions E.g.: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz
- CytoBands(Genome) - Constructor for class org.snpeff.interval.CytoBands
D
- DARK_ROW - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
- DATABASE_COMPATIBLE_VERSIONS - Static variable in class org.snpeff.snpEffect.Config
- dataDir - Variable in class org.snpeff.SnpEff
- debug - Static variable in class org.snpeff.binseq.coder.DnaCoder
- debug - Static variable in class org.snpeff.coverage.CountReadsOnMarkers
- debug - Static variable in class org.snpeff.fastq.FastqTrimmer
- debug - Static variable in class org.snpeff.fileIterator.FastqFileIterator
- debug - Variable in class org.snpeff.fileIterator.FileIterator
- debug - Static variable in class org.snpeff.fileIterator.GuessTableTypes
- debug - Static variable in class org.snpeff.fileIterator.LineClassFileIterator
- debug - Static variable in class org.snpeff.fileIterator.LineFileIterator
- debug - Static variable in class org.snpeff.fileIterator.LineSeqFileIterator
- debug - Static variable in class org.snpeff.fileIterator.SamFileIterator
- debug - Static variable in class org.snpeff.genBank.Features
- debug - Static variable in class org.snpeff.geneOntology.GoTerm
- debug - Static variable in class org.snpeff.geneOntology.GoTerms
- debug - Static variable in class org.snpeff.geneSets.GeneSet
- debug - Static variable in class org.snpeff.geneSets.GeneSets
- debug - Static variable in class org.snpeff.interval.codonChange.CodonChangeMixed
- debug - Static variable in class org.snpeff.interval.codonChange.CodonChangeStructural
- debug - Variable in class org.snpeff.interval.Genes
- debug - Static variable in class org.snpeff.interval.Motif
- debug - Static variable in class org.snpeff.interval.ProteinInteractionLocus
- debug - Variable in class org.snpeff.interval.tree.IntervalTreeArray
- debug - Static variable in class org.snpeff.logStatsServer.LogStats
- debug - Static variable in class org.snpeff.logStatsServer.VersionCheck
- debug - Static variable in class org.snpeff.nmer.NmerCount
- debug - Static variable in class org.snpeff.osCmd.ExecuteOsCommand
- debug - Static variable in class org.snpeff.osCmd.OsCmdQueue
- debug - Static variable in class org.snpeff.outputFormatter.VcfOutputFormatter
- debug - Static variable in class org.snpeff.overlap.OverlapDnaSeq
- debug - Static variable in class org.snpeff.pdb.DistanceResult
- debug - Static variable in class org.snpeff.ped.PlinkMap
- debug - Static variable in class org.snpeff.reactome.Entity
- debug - Variable in class org.snpeff.SnpEff
- debug - Static variable in class org.snpeff.snpEffect.HgvsDna
- debug - Static variable in class org.snpeff.snpEffect.HgvsProtein
- debug - Static variable in class org.snpeff.snpEffect.PurityChange
- debug - Static variable in class org.snpeff.snpEffect.VariantEffects
- debug - Static variable in class org.snpeff.stats.ChrPosStats
- debug - Static variable in class org.snpeff.stats.GeneCountByTypeTable
- debug - Static variable in class org.snpeff.svg.Svg
- debug - Static variable in class org.snpeff.vcf.VcfEffect
- debug(Object) - Static method in class org.snpeff.util.Log
-
Prints a debug message (prints class name, method and line number)
- debug(Object, int) - Static method in class org.snpeff.util.Log
-
Prints a debug message (prints class name, method and line number)
- debug(Object, int, boolean) - Static method in class org.snpeff.util.Log
-
Prints a debug message (prints class name, method and line number)
- dec() - Method in class org.snpeff.stats.Counter
- dec() - Method in class org.snpeff.stats.CounterDouble
- decodeWord(long, int) - Method in class org.snpeff.binseq.coder.Coder
-
Decode bits from a given position in a word
- decodeWord(long, int) - Method in class org.snpeff.binseq.coder.DnaCoder
-
Decode bits from a given position
- decompose() - Method in class org.snpeff.interval.Variant
-
Decompose a variant into basic constituents At the moment this only makes sense for MIXED variants which are decomposed into two variants: MNP + InDel
- DEFAULT_BASE_Y - Static variable in class org.snpeff.svg.Svg
- DEFAULT_BINS - Static variable in class org.snpeff.stats.PosStats
- DEFAULT_BUFFER_SIZE - Static variable in class org.snpeff.fileIterator.SeekableBufferedReader
- DEFAULT_CACHE_FILE - Static variable in class org.snpeff.probablility.RankSumNoReplacementPdf
- DEFAULT_COMMAND - Static variable in class org.snpeff.SnpEff
- DEFAULT_CONFIG_FILE - Static variable in class org.snpeff.snpEffect.Config
- DEFAULT_COORDINATES - Static variable in class org.snpeff.snpEffect.Config
- DEFAULT_CYTOBAND_BED_FILE - Static variable in class org.snpeff.interval.CytoBands
- DEFAULT_DATA_DIR - Static variable in class org.snpeff.snpEffect.Config
- DEFAULT_DELETE_PROTEIN_CODING_BASES - Static variable in class org.snpeff.snpEffect.LossOfFunction
-
Larger deletions removing either the first exon or more than 50% of the protein-coding sequence of the affected transcript
- DEFAULT_DISTANCE_THRESHOLD - Static variable in class org.snpeff.pdb.ProteinInteractions
- DEFAULT_FORMAT_VERSION - Static variable in enum class org.snpeff.vcf.EffFormatVersion
- DEFAULT_IGNORE_PROTEIN_CODING_AFTER - Static variable in class org.snpeff.snpEffect.LossOfFunction
-
It is assumed that even with a protein coding change at the last 5% of the protein, the protein could still be functional.
- DEFAULT_IGNORE_PROTEIN_CODING_BEFORE - Static variable in class org.snpeff.snpEffect.LossOfFunction
-
It is assumed that even with a protein coding change at the first 5% of the protein: "..suggesting some disrupted transcripts are rescued by transcriptional reinitiation at an alternative start codon."
- DEFAULT_MAX_MISMATCH_RATE - Static variable in class org.snpeff.pdb.ProteinInteractions
- DEFAULT_MAX_PVALUE - Static variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- DEFAULT_PDB_DIR - Static variable in class org.snpeff.pdb.ProteinInteractions
- DEFAULT_PDB_MIN_AA_SEPARATION - Static variable in class org.snpeff.pdb.ProteinInteractions
- DEFAULT_PDB_ORGANISM_COMMON - Static variable in class org.snpeff.pdb.ProteinInteractions
- DEFAULT_PDB_ORGANISM_SCIENTIFIC - Static variable in class org.snpeff.pdb.ProteinInteractions
- DEFAULT_PDB_RESOLUTION - Static variable in class org.snpeff.pdb.ProteinInteractions
- DEFAULT_PROXY_PORT - Static variable in class org.snpeff.util.Download
- DEFAULT_REPORT_HTML_FILE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
- DEFAULT_SIZE_X - Static variable in class org.snpeff.svg.Svg
- DEFAULT_SIZE_Y - Static variable in class org.snpeff.svg.Svg
- DEFAULT_START_CODON - Static variable in class org.snpeff.codons.CodonTable
-
All start codons are translated as "M".
- DEFAULT_SUMMARY_CSV_FILE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- DEFAULT_SUMMARY_GENES_FILE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- DEFAULT_SUMMARY_HTML_FILE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- DEFAULT_TYPES - Static variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
- DEFAULT_UP_DOWN_LENGTH - Static variable in class org.snpeff.snpEffect.SnpEffectPredictor
- defaultConfigFile() - Static method in class org.snpeff.snpEffect.Config
-
If Debian-preferred config file is available, give it.
- degenerate(String, int) - Method in class org.snpeff.codons.CodonTable
-
Degree of "degenerate site" What is a "degenerate site"? Here is an explanation form Stephen Wright (Univ.
- del() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Deletions remove one or more amino acid residues from the protein and are described using "del" after an indication of the first and last amino acid(s) deleted separated by a "_" (underscore).
- DEL - Enum constant in enum class org.snpeff.interval.Variant.VariantType
- deleteOutputDb() - Method in class org.snpeff.pdb.ProteinInteractions
- deleteProteinCodingBases - Variable in class org.snpeff.snpEffect.LossOfFunction
- deleteRedundant() - Method in class org.snpeff.interval.Transcript
-
Deletes redundant exons (i.e.
- deleteRedundant() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Consolidate transcripts: If two exons are one right next to the other, join them E.g.
- delFilter(String) - Method in class org.snpeff.vcf.VcfEntry
-
Remove a string from FILTER field
- delins() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Mixed variants Deletion/insertions (indels) replace one or more amino acid residues with one or more other amino acid residues.
- Depolymerisation - Class in org.snpeff.reactome.events
-
A depolymerization event
- Depolymerisation(int, String) - Constructor for class org.snpeff.reactome.events.Depolymerisation
- depth() - Method in class org.snpeff.vcf.VcfGenotype
-
Depth of coverage
- derived() - Method in class org.snpeff.vcf.Pedigree
-
A list of all derived pedigree entries
- description - Variable in class org.snpeff.nextProt.CvTerm
- description - Variable in class org.snpeff.vcf.VcfHeaderInfo
- description() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- detectCircular() - Method in class org.snpeff.interval.Chromosome
-
Is this a circular chromosome? See if any exon has evidence of 'circular coordinates'
- Diff - Class in org.snpeff.util
- Diff(String, String) - Constructor for class org.snpeff.util.Diff
- diffString() - Method in class org.snpeff.align.StringDiff
-
Create a string that shows the difference between two strings
- dirName(String) - Static method in class org.snpeff.util.Gpr
-
Return file's dir
- disjointSet(List<GoTerm>, int) - Method in class org.snpeff.geneOntology.GoTerms
-
Produce a GOTerm based on a list of GOTerms and a 'mask'
- disjointSet(List<GeneSet>, int) - Method in class org.snpeff.geneSets.GeneSets
-
Produce a GeneSet based on a list of GeneSets and a 'mask'
- distance - Variable in class org.snpeff.pdb.DistanceResult
- distance - Variable in class org.snpeff.snpEffect.VariantEffect
- distance(Marker) - Method in class org.snpeff.interval.Marker
-
How far apart are these intervals?
- distanceBases(List<? extends Marker>, boolean) - Method in class org.snpeff.interval.Marker
-
Distance from the beginning/end of a list of intervals, until this SNP It count the number of bases in 'markers'
- distanceMin(AminoAcid, AminoAcid) - Static method in class org.snpeff.pdb.PdbUtil
-
Minimum distance between all atoms in two amino acids
- DistanceResult - Class in org.snpeff.pdb
- DistanceResult() - Constructor for class org.snpeff.pdb.DistanceResult
- DistanceResult(String) - Constructor for class org.snpeff.pdb.DistanceResult
- DistanceResult(String, AminoAcid, AminoAcid, Transcript, Transcript, double) - Constructor for class org.snpeff.pdb.DistanceResult
- distanceToTr(Variant) - Method in class org.snpeff.interval.Downstream
-
Distance to transcript
- distanceToTr(Variant) - Method in class org.snpeff.interval.Upstream
-
Distance to transcript
- DNA_TO_CODE - Static variable in class org.snpeff.util.GprSeq
- dna2Code(char) - Static method in class org.snpeff.util.GprSeq
-
Convert from DNA letter to code
- DnaAndQualitySequence - Class in org.snpeff.binseq
-
Binary packed DNA sequence and base calling quality Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 8 bits: - Six bits for the base quality [0 , ..
- DnaAndQualitySequence(String) - Constructor for class org.snpeff.binseq.DnaAndQualitySequence
- DnaAndQualitySequence(String, String, FastqVariant) - Constructor for class org.snpeff.binseq.DnaAndQualitySequence
- DnaAndQualitySequence(Fastq) - Constructor for class org.snpeff.binseq.DnaAndQualitySequence
- DnaAndQualitySequenceWithId - Class in org.snpeff.binseq
-
DnaAndQualitySequence with an ID
- DnaAndQualitySequenceWithId(String) - Constructor for class org.snpeff.binseq.DnaAndQualitySequenceWithId
- DnaAndQualitySequenceWithId(String, String, FastqVariant) - Constructor for class org.snpeff.binseq.DnaAndQualitySequenceWithId
- dnaBaseChange() - Method in class org.snpeff.snpEffect.HgvsDna
-
DNA level base changes
- DnaCoder - Class in org.snpeff.binseq.coder
-
Class used to encode invalid input: '&' decode sequences into binary and vice-versa Note:This is a singleton class.
- DnaNSequence - Class in org.snpeff.binseq
-
Binary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}
- DnaNSequence(int, long[]) - Constructor for class org.snpeff.binseq.DnaNSequence
- DnaNSequence(String) - Constructor for class org.snpeff.binseq.DnaNSequence
- DnaQualityCoder - Class in org.snpeff.binseq.coder
-
Class used to encode invalid input: '&' decode sequences into binary and vice-versa - Every base is encoded in 8 bits: - Six bits for the base quality [0 , ..
- DnaQualSubsequenceComparator - Class in org.snpeff.binseq.comparator
-
Compares two subsequences of DNA (DnaAndQualitySequence)
- DnaQualSubsequenceComparator(boolean) - Constructor for class org.snpeff.binseq.comparator.DnaQualSubsequenceComparator
- DnaQualSubsequenceComparator(boolean, int) - Constructor for class org.snpeff.binseq.comparator.DnaQualSubsequenceComparator
- DnaSeqFileIterator - Class in org.snpeff.fileIterator
- DnaSeqFileIterator(String) - Constructor for class org.snpeff.fileIterator.DnaSeqFileIterator
- DnaSeqIdFileIterator - Class in org.snpeff.fileIterator
- DnaSeqIdFileIterator(String) - Constructor for class org.snpeff.fileIterator.DnaSeqIdFileIterator
- DnaSeqPeFileIterator - Class in org.snpeff.fileIterator
- DnaSeqPeFileIterator(String) - Constructor for class org.snpeff.fileIterator.DnaSeqPeFileIterator
- DnaSequence - Class in org.snpeff.binseq
-
Binary packed DNA sequence Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 2 bits {a, c, g, t} invalid input: '<'=> {0, 1, 2, 3} - All bits are stored in an array of 'words' (integers) - Most significant bits are the first bases in the sequence (makes comparison easier)
- DnaSequence(int, long[]) - Constructor for class org.snpeff.binseq.DnaSequence
- DnaSequence(String) - Constructor for class org.snpeff.binseq.DnaSequence
- DnaSequence(String, boolean) - Constructor for class org.snpeff.binseq.DnaSequence
- DnaSequenceByte - Class in org.snpeff.binseq
-
Binary packed DNA sequence.
- DnaSequenceByte(int, byte[]) - Constructor for class org.snpeff.binseq.DnaSequenceByte
- DnaSequenceByte(String) - Constructor for class org.snpeff.binseq.DnaSequenceByte
- DnaSequenceId - Class in org.snpeff.binseq
-
Binary packed DNA sequence with an ID (long)
- DnaSequenceId(long, int, long[]) - Constructor for class org.snpeff.binseq.DnaSequenceId
- DnaSequenceId(long, String) - Constructor for class org.snpeff.binseq.DnaSequenceId
- DnaSequenceId(String) - Constructor for class org.snpeff.binseq.DnaSequenceId
- DnaSequencePe - Class in org.snpeff.binseq
-
Pair end DNA sequence (binary packed) It consists of 2 DNA sequences separated by a gap.
- DnaSequencePe(String) - Constructor for class org.snpeff.binseq.DnaSequencePe
- DnaSequencePe(String, String, int) - Constructor for class org.snpeff.binseq.DnaSequencePe
- DnaSubsequenceComparator<T> - Class in org.snpeff.binseq.comparator
-
Compares two subsequences of DNA (DnaSequence)
- DnaSubsequenceComparator(boolean) - Constructor for class org.snpeff.binseq.comparator.DnaSubsequenceComparator
- DnaSubsequenceComparator(boolean, int) - Constructor for class org.snpeff.binseq.comparator.DnaSubsequenceComparator
- doNotSave(Marker) - Method in class org.snpeff.serializer.MarkerSerializer
- download - Variable in class org.snpeff.SnpEff
- download(String, String) - Method in class org.snpeff.util.Download
- download(URL, String) - Method in class org.snpeff.util.Download
-
Download a file
- Download - Class in org.snpeff.util
-
Command line program: Build database
- Download() - Constructor for class org.snpeff.util.Download
- downloadUrl(String) - Method in class org.snpeff.snpEffect.Config
-
Get a list of URLs that can be used to download a database Use compatible versions from 'getDatabaseCompatibilityVersions()'
- downloadUrl(String, String) - Method in class org.snpeff.snpEffect.Config
-
Build the URL for downloading a database file
- Downstream - Class in org.snpeff.interval
-
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
- Downstream() - Constructor for class org.snpeff.interval.Downstream
- Downstream(Transcript, int, int, boolean, String) - Constructor for class org.snpeff.interval.Downstream
- DOWNSTREAM - Enum constant in enum class org.snpeff.snpEffect.EffectType
- dump(String, int, int, boolean) - Method in class org.snpeff.vcf.FileIndexChrPos
-
Dump all lines in the interval chr:posStart-posEnd
- DUMP - Enum constant in enum class org.snpeff.snpEffect.commandLine.SnpEffCmdDump.DumpFormat
- dup() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Duplications
- DUP - Enum constant in enum class org.snpeff.interval.Variant.VariantType
- duplication - Variable in class org.snpeff.snpEffect.Hgvs
E
- EFF_FIELD_NAMES - Static variable in class org.snpeff.vcf.VcfEffect
- effect() - Method in class org.snpeff.snpEffect.VariantEffectStructural
- effect(boolean, boolean, boolean, boolean, boolean) - Method in class org.snpeff.snpEffect.VariantEffect
-
Show a string with overall effect
- effect(Marker, EffectType, boolean) - Method in class org.snpeff.interval.codonChange.CodonChange
-
Calculate variant effect
- EFFECT_TYPE_SEPARATOR - Static variable in enum class org.snpeff.vcf.EffFormatVersion
- EFFECT_TYPE_SEPARATOR_OLD - Static variable in enum class org.snpeff.vcf.EffFormatVersion
- effectImpact - Variable in class org.snpeff.snpEffect.VariantEffect
- effectImpact() - Method in enum class org.snpeff.snpEffect.EffectType
-
Return effect impact
- effectImpacts - Variable in class org.snpeff.snpEffect.VariantEffect
- effectNoCodon(Marker, EffectType) - Method in class org.snpeff.interval.codonChange.CodonChange
- effectNoCodon(Marker, EffectType, VariantEffect.EffectImpact) - Method in class org.snpeff.interval.codonChange.CodonChange
- effectTranscript() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
- effectTranscript() - Method in class org.snpeff.interval.codonChange.CodonChangeDup
- effectTranscript() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
- effectType - Variable in class org.snpeff.snpEffect.VariantEffect
- EffectType - Enum Class in org.snpeff.snpEffect
-
Effect type: Note that effects are sorted (declared) by impact (highest to lowest putative impact).
- effectTypes - Variable in class org.snpeff.snpEffect.VariantEffect
- EffFormatVersion - Enum Class in org.snpeff.vcf
-
VcfFields in SnpEff version 2.X have a different format than 3.X As of version 4.1 we switch to a standard annotation format
- elapsed() - Method in class org.snpeff.util.Timer
-
Elapsed time in milliseconds
- EMAIL - Static variable in class org.snpeff.Pcingola
- Embl - Class in org.snpeff.genBank
-
A class representing the same data as an EMBL file References: http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
- Embl(String) - Constructor for class org.snpeff.genBank.Embl
-
Create a Genbank record from a 'GB' file
- Embl(LineFileIterator) - Constructor for class org.snpeff.genBank.Embl
-
Create a Genbank record from a 'GB' file
- EMBL - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
- EmblFile - Class in org.snpeff.genBank
-
A file containing one or more set of features (e.g.
- EmblFile(String) - Constructor for class org.snpeff.genBank.EmblFile
- empty() - Static method in class org.snpeff.binseq.DnaAndQualitySequence
- empty() - Static method in class org.snpeff.binseq.DnaAndQualitySequenceWithId
- empty() - Static method in class org.snpeff.binseq.DnaNSequence
-
Empty sequence singleton
- empty() - Static method in class org.snpeff.binseq.DnaSequence
-
Empty sequence singleton
- empty() - Static method in class org.snpeff.binseq.DnaSequenceId
-
Empty sequence singleton
- EMPTY_MARKER_ARRAY - Static variable in class org.snpeff.interval.tree.IntervalTreeArray
- EMPTY_STRING_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
- EMPTY_VALUE - Static variable in class org.snpeff.collections.HashLongLongArray
- encodeWord(char, int) - Method in class org.snpeff.binseq.coder.DnaCoder
-
Encode a base to a given position in a word
- end - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- end - Variable in class org.snpeff.genBank.FeatureCoordinates
- end - Variable in class org.snpeff.interval.Interval
- end - Variable in class org.snpeff.nextProt.Location
- end() - Method in class org.snpeff.util.Timer
- endElement(String, String, String) - Method in class org.snpeff.nextProt.NextProtHandler
-
Parse XML's element end
- endSection(Marker) - Method in class org.snpeff.outputFormatter.BedOutputFormatter
-
Finish up section
- endSection(Marker) - Method in class org.snpeff.outputFormatter.OutputFormatter
-
Finish up section
- endSection(Marker) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
-
Finish up section
- EnrichmentAlgorithm - Class in org.snpeff.geneSets.algorithm
-
A generic enrichment algorithm for selecting gene-sets from a collection of gene-sets
- EnrichmentAlgorithm(GeneSets, int) - Constructor for class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- EnrichmentAlgorithm.EnrichmentAlgorithmType - Enum Class in org.snpeff.geneSets.algorithm
- EnrichmentAlgorithmGreedy - Class in org.snpeff.geneSets.algorithm
-
A generic greedy enrichment algorithm for selecting gene-sets
- EnrichmentAlgorithmGreedy(GeneSets, int) - Constructor for class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- EnrichmentAlgorithmGreedyVariableSize - Class in org.snpeff.geneSets.algorithm
-
A greedy enrichment algorithm for selecting gene-sets using a variable geneSet-size strategy: i) Select only from geneSets in low-sizes e.g.
- EnrichmentAlgorithmGreedyVariableSize(GeneSets, int) - Constructor for class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
- ensureCapacity(long) - Method in class org.snpeff.collections.OpenBitSet
-
Ensure that the long[] is big enough to hold numBits, expanding it if necessary.
- ensureCapacityWords(int) - Method in class org.snpeff.collections.OpenBitSet
-
Expand the long[] with the size given as a number of words (64 bit longs).
- Entity - Class in org.snpeff.reactome
-
A reactome basic entity (e.g.
- Entity(int, String) - Constructor for class org.snpeff.reactome.Entity
- Entity.TransferFunction - Enum Class in org.snpeff.reactome
- entropy() - Method in class org.snpeff.spliceSites.AcgtTree
-
Calculate the entropy
- entropyAll(int) - Method in class org.snpeff.spliceSites.AcgtTree
- EPSILON - Static variable in class org.snpeff.probablility.Binomial
-
A small number
- EPSILON - Static variable in class org.snpeff.probablility.CochranArmitageTest
-
A small number
- EPSILON - Static variable in class org.snpeff.probablility.Hypergeometric
-
A small number
- EPSILON - Static variable in class org.snpeff.reactome.Reactome
- equalPos(DistanceResult) - Method in class org.snpeff.pdb.DistanceResult
-
Same genomic positions
- equals() - Method in class org.snpeff.util.Diff
- equals(Object) - Method in class org.snpeff.collections.OpenBitSet
-
returns true if both sets have the same bits set
- equals(Object) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- equals(Object) - Method in class org.snpeff.util.KeyValue
- equals(Object) - Method in class org.snpeff.util.Tuple
- equals(Interval) - Method in class org.snpeff.interval.Interval
- equals(Markers) - Method in class org.snpeff.interval.Markers
-
Are all intervals equal?
- error - Variable in class org.snpeff.snpEffect.VariantEffect
- error() - Method in class org.snpeff.align.StringDiff
-
Error ratio (number of mismatches divided by string length
- error(String) - Static method in class org.snpeff.util.Log
-
Show a warning message (up to MAX_ERRORS times)
- error(Throwable, String) - Static method in class org.snpeff.util.Log
- ERROR - Enum constant in enum class org.snpeff.logStatsServer.LogStats.RequestResult
- ERROR_CHROMOSOME_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- ERROR_FILE_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- ERROR_MISSING_CDS_SEQUENCE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- ERROR_OUT_OF_CHROMOSOME_RANGE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- ERROR_OUT_OF_EXON - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- ErrorWarningType - Enum Class in org.snpeff.snpEffect
-
Errors and warnings
- ETC_CONFIG_FILE - Static variable in class org.snpeff.snpEffect.Config
- evaluate() - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
-
Random sample and evaluate
- evalue - Variable in class org.snpeff.fileIterator.BlastResultEntry
- Event - Class in org.snpeff.reactome.events
-
A reactome event (any generic event, from pathways to polymerizations)
- Event(int, String) - Constructor for class org.snpeff.reactome.events.Event
- EXCEPTION - Enum constant in enum class org.snpeff.util.Log.FatalErrorBehabiour
- EXCEPTION_QUIET - Enum constant in enum class org.snpeff.util.Log.FatalErrorBehabiour
- exec() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- ExecuteOsCommand - Class in org.snpeff.osCmd
-
Launches an 'OS command' (e.g.
- ExecuteOsCommand(String) - Constructor for class org.snpeff.osCmd.ExecuteOsCommand
- ExecuteOsCommand(String[]) - Constructor for class org.snpeff.osCmd.ExecuteOsCommand
- exists(String) - Static method in class org.snpeff.util.Gpr
-
Does 'file' exist?
- EXIT - Enum constant in enum class org.snpeff.util.Log.FatalErrorBehabiour
- Exon - Class in org.snpeff.interval
-
Interval for an exon
- Exon() - Constructor for class org.snpeff.interval.Exon
- Exon(Transcript, int, int, boolean, String, int) - Constructor for class org.snpeff.interval.Exon
- EXON - Enum constant in enum class org.snpeff.interval.GffType
- EXON - Enum constant in enum class org.snpeff.snpEffect.EffectType
- EXON_DELETED - Enum constant in enum class org.snpeff.snpEffect.EffectType
- EXON_DELETED_PARTIAL - Enum constant in enum class org.snpeff.snpEffect.EffectType
- EXON_DUPLICATION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- EXON_DUPLICATION_PARTIAL - Enum constant in enum class org.snpeff.snpEffect.EffectType
- EXON_INVERSION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- EXON_INVERSION_PARTIAL - Enum constant in enum class org.snpeff.snpEffect.EffectType
- Exon.ExonSpliceType - Enum Class in org.snpeff.interval
-
Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)
- exonFull - Variable in class org.snpeff.interval.codonChange.CodonChangeStructural
- exonPartial - Variable in class org.snpeff.interval.codonChange.CodonChangeStructural
- exons() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
-
Deletion analysis using full transcript information.
- exons() - Method in class org.snpeff.interval.codonChange.CodonChangeDup
- exons() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
-
Variant affect one or more exons
- exonsCoding() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
- exonsCoding() - Method in class org.snpeff.interval.codonChange.CodonChangeDup
-
One or more exons fully included (no partial overlap)
- exonsCoding() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
-
Variant affect one or more coding exons
- exonsFromCds() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Create exons from CDS info
- exonsFromCds(Transcript) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Create exons from CDS info WARNING: We might end up with redundant exons if some exons existed before this process
- exonsNoncoding() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
- exonsNoncoding() - Method in class org.snpeff.interval.codonChange.CodonChangeDup
-
Effects for non-coding transcripts
- exonsNoncoding() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
-
Variant affect one or more non-coding exons
- ExonSpliceCharacterizer - Class in org.snpeff.interval
-
Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)
- ExonSpliceCharacterizer(String) - Constructor for class org.snpeff.interval.ExonSpliceCharacterizer
- ExonSpliceCharacterizer(Genome) - Constructor for class org.snpeff.interval.ExonSpliceCharacterizer
- expandingWordNum(long) - Method in class org.snpeff.collections.OpenBitSet
- expandIub - Variable in class org.snpeff.SnpEff
- expected(String) - Method in class org.snpeff.stats.ObservedOverExpected
- expected(String) - Method in class org.snpeff.stats.ObservedOverExpectedCHG
- expected(String) - Method in class org.snpeff.stats.ObservedOverExpectedCHH
- expected(String) - Method in class org.snpeff.stats.ObservedOverExpectedCpG
- expected(Exon) - Method in class org.snpeff.stats.ObservedOverExpected
-
Expected number of sequences (average between plus and minus strand)
- expected(Gene) - Method in class org.snpeff.stats.ObservedOverExpected
-
Expected number of sequences (average between plus and minus strand)
- expected(Transcript) - Method in class org.snpeff.stats.ObservedOverExpected
-
Expected number of sequences (average between plus and minus strand)
- EXTENSION_EMBL - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryEmbl
- EXTENSION_GENBANK - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenBank
- externalName - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- extName(String) - Static method in class org.snpeff.util.Gpr
-
Get a file's extension (all letters after the last '.'
F
- factory() - Method in class org.snpeff.binseq.DnaNSequence
-
Create sequences
- factory() - Method in class org.snpeff.binseq.DnaSequence
-
Create a new sequence
- factory() - Method in class org.snpeff.binseq.DnaSequenceId
-
Create sequences
- factory(String) - Static method in class org.snpeff.vcf.VcfHeaderEntry
- factory(GoTerms) - Static method in class org.snpeff.geneSets.GeneSets
-
Create gene sets form GoTerms
- factory(Chromosome, int, String, String, String, boolean) - Static method in class org.snpeff.interval.Variant
-
Create variants from ALT (which can be multiple values)
- factory(Marker, Svg) - Static method in class org.snpeff.svg.Svg
- factory(Transcript, int, Transcript, String) - Static method in class org.snpeff.interval.ProteinInteractionLocus
-
Create interaction.
- factory(Variant, Transcript, VariantEffects) - Static method in class org.snpeff.interval.codonChange.CodonChange
-
Create a specific codon change for a variant
- factory(VcfEntry) - Static method in class org.snpeff.vcf.VariantVcfEntry
-
Create a collection of all invalid input: '<'Variant, VcfEntry>
- FAKE_COUNTS - Static variable in class org.snpeff.spliceSites.AcgtTree
- families() - Method in class org.snpeff.ped.PedPedigree
-
Split data into families
- FASTA_DELIMITER - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
- FastaFileIterator - Class in org.snpeff.fileIterator
-
Opens a fasta file and iterates over all fasta sequences in the file
- FastaFileIterator(String) - Constructor for class org.snpeff.fileIterator.FastaFileIterator
- fastaHeader2Ids() - Method in class org.snpeff.fileIterator.FastaFileIterator
-
Try to parse IDs from a fasta header
- fastaSimpleRead(String) - Static method in class org.snpeff.util.GprSeq
-
Read a fasta file containing one (and only one) sequence
- fastClear(int) - Method in class org.snpeff.collections.OpenBitSet
-
clears a bit.
- fastClear(long) - Method in class org.snpeff.collections.OpenBitSet
-
clears a bit.
- fastFlip(int) - Method in class org.snpeff.collections.OpenBitSet
-
flips a bit.
- fastFlip(long) - Method in class org.snpeff.collections.OpenBitSet
-
flips a bit.
- fastGet(int) - Method in class org.snpeff.collections.OpenBitSet
-
Returns true or false for the specified bit index.
- fastGet(long) - Method in class org.snpeff.collections.OpenBitSet
-
Returns true or false for the specified bit index.
- FASTQ_SANGER_ZERO - Static variable in class org.snpeff.util.GprSeq
- Fastq2Fastq - Class in org.snpeff
-
Convert FASTQ (phred64) file to FASTQ (phred33)
- Fastq2Fastq() - Constructor for class org.snpeff.Fastq2Fastq
- FastqFileIterator - Class in org.snpeff.fileIterator
-
Opens a fastq file and iterates over all fastq sequences in the file Unlike BioJava's version, this one does NOT load all sequences in memory.
- FastqFileIterator(InputStream, FastqVariant) - Constructor for class org.snpeff.fileIterator.FastqFileIterator
- FastqFileIterator(String) - Constructor for class org.snpeff.fileIterator.FastqFileIterator
- FastqFileIterator(String, FastqVariant) - Constructor for class org.snpeff.fileIterator.FastqFileIterator
- fastqId(Fastq) - Static method in class org.snpeff.util.GprSeq
-
Get an ID from a fastq
- FastqSplit - Class in org.snpeff.fastq
-
Split a fastq into N files
- FastqSplit() - Constructor for class org.snpeff.fastq.FastqSplit
- FastqTools - Class in org.snpeff.fastq
-
Simple maipulation of fastq sequences
- FastqTools() - Constructor for class org.snpeff.fastq.FastqTools
- FastqTrimmer - Class in org.snpeff.fastq
-
Trim fastq sequence when quality drops below a threshold The resulting sequence has to ba at least 'minBases'
- FastqTrimmer(int, int) - Constructor for class org.snpeff.fastq.FastqTrimmer
- FastqTrimmerAdrian - Class in org.snpeff.fastq
-
Trim fastq sequence when: - Median quality drops below a threshold (mean is calculated every 2 bases instead of every base) - Sequence length is at least 'minBases' From Adrian Platts ...Also the sliding window was not every base.
- FastqTrimmerAdrian(int, int, int) - Constructor for class org.snpeff.fastq.FastqTrimmerAdrian
- FastqTrimmerMedian - Class in org.snpeff.fastq
-
Trim fastq sequence when median quality drops below a threshold
- FastqTrimmerMedian(int, int, int) - Constructor for class org.snpeff.fastq.FastqTrimmerMedian
- fastSet(int) - Method in class org.snpeff.collections.OpenBitSet
-
Sets the bit at the specified index.
- fastSet(long) - Method in class org.snpeff.collections.OpenBitSet
-
Sets the bit at the specified index.
- fatalError(String) - Static method in class org.snpeff.util.Log
-
Show an error message and exit
- fatalError(Throwable, String) - Static method in class org.snpeff.util.Log
- father - Variable in class org.snpeff.vcf.PedigreeEntry
- fatherNum - Variable in class org.snpeff.vcf.PedigreeEntry
- FDR - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
- feature - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- Feature - Class in org.snpeff.genBank
-
A feature in a GenBank or EMBL file
- Feature(Feature.Type, String) - Constructor for class org.snpeff.genBank.Feature
- Feature(Feature.Type, String, int, int, boolean, int) - Constructor for class org.snpeff.genBank.Feature
- FEATURE_FUSION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- FEATURE_KEY_LEN - Static variable in class org.snpeff.genBank.Embl
- FEATURE_NAME_FIELD_LEN - Static variable in class org.snpeff.genBank.GenBank
- FEATURE_NAME_LEN - Static variable in class org.snpeff.genBank.Embl
- Feature.Type - Enum Class in org.snpeff.genBank
- FeatureCoordinates - Class in org.snpeff.genBank
-
A feature in a GenBank or EMBL file
- FeatureCoordinates(int, int, boolean) - Constructor for class org.snpeff.genBank.FeatureCoordinates
- Features - Class in org.snpeff.genBank
-
A class representing a set of features References: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
- Features(String) - Constructor for class org.snpeff.genBank.Features
-
Create features from a file
- Features(LineFileIterator) - Constructor for class org.snpeff.genBank.Features
-
Create features from a file
- FeaturesFile - Class in org.snpeff.genBank
-
A file containing one or more set of features (e.g.
- FeaturesFile(String) - Constructor for class org.snpeff.genBank.FeaturesFile
- Female - Enum constant in enum class org.snpeff.ped.Sex
- FIELD_BIOTYPE - Static variable in class org.snpeff.interval.GffMarker
- FIELD_DB_XREF - Static variable in class org.snpeff.interval.GffMarker
- FIELD_EXON_ID - Static variable in class org.snpeff.interval.GffMarker
- FIELD_GENE - Static variable in class org.snpeff.interval.GffMarker
- FIELD_GENE_BIOTYPE - Static variable in class org.snpeff.interval.GffMarker
- FIELD_GENE_ID - Static variable in class org.snpeff.interval.GffMarker
- FIELD_GENE_NAME - Static variable in class org.snpeff.interval.GffMarker
- FIELD_GENE_TYPE - Static variable in class org.snpeff.interval.GffMarker
- FIELD_ID - Static variable in class org.snpeff.interval.GffMarker
- FIELD_NAME - Static variable in class org.snpeff.interval.GffMarker
- FIELD_NAME_SEPARATOR - Static variable in class org.snpeff.fileIterator.LineClassFileIterator
- FIELD_NAME_SEPARATOR - Static variable in class org.snpeff.fileIterator.TableFile
- FIELD_NAMEU - Static variable in class org.snpeff.interval.GffMarker
- FIELD_PARENT - Static variable in class org.snpeff.interval.GffMarker
- FIELD_PROTEIN_ID - Static variable in class org.snpeff.interval.GffMarker
- FIELD_TAG - Static variable in class org.snpeff.interval.GffMarker
- FIELD_TRANSCRIPT_ID - Static variable in class org.snpeff.interval.GffMarker
- FIELD_TRANSCRIPT_TSL - Static variable in class org.snpeff.interval.GffMarker
- FIELD_TRANSCRIPT_VERSION - Static variable in class org.snpeff.interval.GffMarker
- fieldByName - Variable in class org.snpeff.fileIterator.LineClassFileIterator
- fieldByName - Variable in class org.snpeff.fileIterator.TableFile
- fieldMap() - Method in class org.snpeff.fileIterator.LineClassFileIterator
-
Map field names to Field objects
- fieldNames - Variable in class org.snpeff.fileIterator.LineClassFileIterator
- fieldNames - Variable in class org.snpeff.fileIterator.TableFile
- fieldNum(String) - Static method in class org.snpeff.vcf.VcfLof
-
Convert from field name to field number
- fieldNum(String) - Static method in class org.snpeff.vcf.VcfNmd
-
Convert from field name to field number
- fieldStr - Variable in class org.snpeff.fileIterator.LineClassFileIterator
- fieldStr - Variable in class org.snpeff.fileIterator.TableFile
- fileExists(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
-
Does either 'path' or 'path'+'.gz' exist?
- FileIndexChrPos - Class in org.snpeff.vcf
-
Index a file that has "chr \t pos" as the beginning of a line (e.g.
- FileIndexChrPos(String) - Constructor for class org.snpeff.vcf.FileIndexChrPos
- FileIndexChrPos.FileRegion - Class in org.snpeff.vcf
-
A part of a file
- FileIndexChrPos.LineAndPos - Class in org.snpeff.vcf
-
A line and the position on the file where it begins
- FileIterator<T> - Class in org.snpeff.fileIterator
-
Opens a file and iterates over all objects
in the file Note: The file is not loaded in memory, thus allows to iterate over very large files - FileIterator(BufferedReader) - Constructor for class org.snpeff.fileIterator.FileIterator
- FileIterator(String) - Constructor for class org.snpeff.fileIterator.FileIterator
- fileName - Variable in class org.snpeff.fileIterator.FileIterator
- fileName - Variable in class org.snpeff.fileIterator.TableFile
- fileName2ProteinId() - Method in class org.snpeff.pdb.PdbFile
-
Parse ProteinId from PDB file name
- FileRegion() - Constructor for class org.snpeff.vcf.FileIndexChrPos.FileRegion
- fileSize - Variable in class org.snpeff.fileIterator.FileIterator
- filter - Variable in class org.snpeff.vcf.VcfEntry
- filter() - Method in class org.snpeff.spliceSites.TranscriptSet
-
Filter out "bad transcripts"
- filter(String) - Method in interface org.snpeff.osCmd.LineFilter
-
Filter and prossible change a line
- filter(VariantEffect) - Method in class org.snpeff.filter.VariantEffectFilter
-
Filter a sequence change
- filter(T) - Method in interface org.snpeff.filter.Filter
-
Does 'objectToTest' satisfy the filter?
- Filter<T> - Interface in org.snpeff.filter
-
A Generic filter interface
- FILTER_PASS - Static variable in class org.snpeff.vcf.VcfEntry
- filterIntervalFiles - Variable in class org.snpeff.SnpEff
- filterTags() - Method in class org.snpeff.SnpEff
-
Filter by tags
- filterTags(Set<String>, Set<String>) - Method in class org.snpeff.interval.Gene
-
Filter transcripts by tags
- filterTags(Set<String>, Set<String>) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Filter transcripts by tags
- filterTranscript(String) - Method in class org.snpeff.pdb.ProteinInteractions
-
Return true if the transcript passes the criteria (i.e.
- filterTranscriptSupportLevel(TranscriptSupportLevel) - Method in class org.snpeff.interval.Gene
-
Filter transcripts by TSL
- filterTranscriptSupportLevel(TranscriptSupportLevel) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Filter transcripts by TSL
- find(String, int, boolean) - Method in class org.snpeff.vcf.FileIndexChrPos
-
Find the position in the file for the first character of the first line equal or less than a specific chr:pos
- findBestOverlap(T) - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
-
Find best overlap for 'sequence'
- findCds(Exon) - Method in class org.snpeff.interval.Transcript
-
Find a CDS that matches exactly the exon
- findExon(int) - Method in class org.snpeff.interval.Transcript
-
Return the an exon that intersects 'pos'
- findExon(Marker) - Method in class org.snpeff.interval.Transcript
-
Return an exon intersecting 'marker' (first exon found)
- findGene(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- findGene(String, String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- findIntron(int) - Method in class org.snpeff.interval.Transcript
-
Return an intron overlapping position 'pos'
- findMarker(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- findNodeNames(double, double, int) - Method in class org.snpeff.spliceSites.AcgtTree
-
Find node names that are within the thresholds
- findOrCreateExon(String, GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Find an exon for a given parentId
- findOrCreateGene(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Find or create a gene based on GffMarker
- findOrCreateTranscript(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Create and add a transcript based on GffMarker
- findParent(Class) - Method in class org.snpeff.interval.Interval
-
Go up (parent) until we find an instance of 'clazz'
- findRareAa(String) - Method in class org.snpeff.codons.FindRareAaIntervals
-
Find all sites having rare amino acids
- FindRareAaIntervals - Class in org.snpeff.codons
-
Find intervals where rare amino acids occur
- FindRareAaIntervals(Genome) - Constructor for class org.snpeff.codons.FindRareAaIntervals
- findTag(String) - Method in class org.snpeff.sam.SamEntry
-
Does this entry have a tag?
- findTranscript(String) - Method in class org.snpeff.interval.Genes
-
Find a transcript by ID
- findTranscript(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- findTranscript(String, String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- findTranscriptIds(String) - Method in class org.snpeff.pdb.ProteinInteractions
- findUtr(int) - Method in class org.snpeff.interval.Transcript
-
Return the UTR that hits position 'pos'
- findUtrs(Marker) - Method in class org.snpeff.interval.Transcript
-
Return the UTR that intersects 'marker' (null if not found)
- finish() - Method in class org.snpeff.osCmd.OsCmdRunner
-
Stop execution of this thread
- first - Variable in class org.snpeff.util.Tuple
- FISHER - Enum constant in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
- FISHER_CHI_SQUARE - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
- FISHER_GREEDY - Enum constant in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
- FisherExactTest - Class in org.snpeff.probablility
-
Calculate Fisher's exact test (based on hypergeometric distribution)
- fisherExactTestDown(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
-
Fisher's exact test for 'k' or less (lower tail)
- fisherExactTestDown(int, int, int, int, double) - Method in class org.snpeff.probablility.FisherExactTest
-
Fisher's exact test for less than 'k' (lower tail) It also compares to a 'threshold' value to speedup the process.
- fisherExactTestUp(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
-
Fisher's exact test for 'k' or more (upper tail)
- fisherExactTestUp(int, int, int, int, double) - Method in class org.snpeff.probablility.FisherExactTest
-
Fisher's exact test for 'k' or more It also compares to a 'threshold' value to speedup the process.
- FisherPValueAlgorithm - Class in org.snpeff.geneSets.algorithm
- FisherPValueAlgorithm(GeneSets, int) - Constructor for class org.snpeff.geneSets.algorithm.FisherPValueAlgorithm
- FisherPValueGreedyAlgorithm - Class in org.snpeff.geneSets.algorithm
- FisherPValueGreedyAlgorithm(GeneSets, int) - Constructor for class org.snpeff.geneSets.algorithm.FisherPValueGreedyAlgorithm
- fixedOutput - Variable in class org.snpeff.reactome.Entity
- fixStartEnd() - Method in class org.snpeff.fileIterator.BlastResultEntry
-
Swap start- end positions if they are not in order
- Flag - Enum constant in enum class org.snpeff.vcf.VcfInfoType
- flip(long) - Method in class org.snpeff.collections.OpenBitSet
-
flips a bit, expanding the set size if necessary
- flip(long, long) - Method in class org.snpeff.collections.OpenBitSet
-
Flips a range of bits, expanding the set size if necessary
- flipAndGet(int) - Method in class org.snpeff.collections.OpenBitSet
-
flips a bit and returns the resulting bit value.
- flipAndGet(long) - Method in class org.snpeff.collections.OpenBitSet
-
flips a bit and returns the resulting bit value.
- Float - Enum constant in enum class org.snpeff.vcf.VcfInfoType
- FloatStats - Class in org.snpeff.stats
-
A simple class that does some basic statistics on double numbers
- FloatStats() - Constructor for class org.snpeff.stats.FloatStats
- format - Variable in class org.snpeff.vcf.VcfEntry
- FORMAT_ANN - Enum constant in enum class org.snpeff.vcf.EffFormatVersion
- FORMAT_ANN_1 - Enum constant in enum class org.snpeff.vcf.EffFormatVersion
- FORMAT_EFF - Enum constant in enum class org.snpeff.vcf.EffFormatVersion
- FORMAT_EFF_2 - Enum constant in enum class org.snpeff.vcf.EffFormatVersion
- FORMAT_EFF_3 - Enum constant in enum class org.snpeff.vcf.EffFormatVersion
- FORMAT_EFF_4 - Enum constant in enum class org.snpeff.vcf.EffFormatVersion
- FORMAT_PREFIX - Static variable in class org.snpeff.vcf.VcfHeader
- formatFields - Variable in class org.snpeff.vcf.VcfEntry
- formatVersion() - Method in class org.snpeff.vcf.VcfEffect
-
Guess effect format version
- formatVersion(String) - Method in class org.snpeff.vcf.VcfEffect
-
Guess format 'main' version (either 'ANN' of 'EFF') without trying to guess sub-version
- foundAllTypes() - Method in class org.snpeff.fileIterator.GuessTableTypes
- FRAME - Enum constant in enum class org.snpeff.interval.FrameType
- FRAME_SHIFT - Enum constant in enum class org.snpeff.snpEffect.EffectType
- FRAME_SHIFT_AFTER_CDS_END - Enum constant in enum class org.snpeff.snpEffect.EffectType
- FRAME_SHIFT_BEFORE_CDS_START - Enum constant in enum class org.snpeff.snpEffect.EffectType
- frameCorrection() - Method in class org.snpeff.interval.Transcript
-
Correct exons based on frame information.
- frameCorrection(int) - Method in class org.snpeff.interval.Cds
-
Correct coordinates according to frame differences
- frameCorrection(int) - Method in class org.snpeff.interval.Exon
-
Correct exons according to frame information Shift the start position one base
- frameFromLength(int) - Method in enum class org.snpeff.interval.FrameType
-
Calculate frame from cds length
- FrameType - Enum Class in org.snpeff.interval
-
Type of frame calculations Internally, we use GFF style frame calculation for Exon / Transcript Technically, these are 'frame' and 'phase' which are calculated in different ways UCSC type: Indicated the coding base number modulo 3.
- fs() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Frame shifts are a special type of amino acid deletion/insertion affecting an amino acid between the first (initiation, ATG) and last codon (termination, stop), replacing the normal C-terminal sequence with one encoded by another reading frame (specified 2013-10-11).
- FTP_PROTOCOL - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
- fusions() - Method in class org.snpeff.snpEffect.VariantEffectStructural
-
Is there another 'fusion' effect?
G
- G - Static variable in class org.snpeff.fastq.FastqSplit
- GAP_CODE - Static variable in class org.snpeff.util.GprSeq
- gapopen - Variable in class org.snpeff.fileIterator.BlastResultEntry
- GATK - Enum constant in enum class org.snpeff.SnpEff.OutputFormat
- GB - Static variable in class org.snpeff.util.Gpr
- GenBank - Class in org.snpeff.genBank
-
A class representing the same data as a GenBank file (a 'GB' file) References: http://www.insdc.org/documents/feature-table http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord
- GenBank(String) - Constructor for class org.snpeff.genBank.GenBank
-
Create a Genbank record from a 'GB' file
- GenBank(LineFileIterator) - Constructor for class org.snpeff.genBank.GenBank
- GENBANK - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
- GenBankFile - Class in org.snpeff.genBank
-
A file containing one or more set of features (e.g.
- GenBankFile(String) - Constructor for class org.snpeff.genBank.GenBankFile
- Gene - Class in org.snpeff.interval
-
Interval for a gene, as well as transcripts
- Gene() - Constructor for class org.snpeff.interval.Gene
- Gene(Marker, int, int, boolean, String, String, BioType) - Constructor for class org.snpeff.interval.Gene
- GENE - Enum constant in enum class org.snpeff.genBank.Feature.Type
- GENE - Enum constant in enum class org.snpeff.interval.GffType
- GENE - Enum constant in enum class org.snpeff.snpEffect.EffectType
- GENE_CPG_NUM_BINS - Static variable in class org.snpeff.stats.GeneCountByTypeTable
- GENE_DELETED - Enum constant in enum class org.snpeff.snpEffect.EffectType
- GENE_DUPLICATION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- GENE_FUSION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- GENE_FUSION_HALF - Enum constant in enum class org.snpeff.snpEffect.EffectType
- GENE_FUSION_REVERESE - Enum constant in enum class org.snpeff.snpEffect.EffectType
- GENE_INVERSION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- GENE_REARRANGEMENT - Enum constant in enum class org.snpeff.snpEffect.EffectType
- Gene.GeneType - Enum Class in org.snpeff.interval
- GeneCountByTypeTable - Class in org.snpeff.stats
-
Count for each 'type' and 'gene'.
- GeneCountByTypeTable() - Constructor for class org.snpeff.stats.GeneCountByTypeTable
- geneId(Feature, int, int) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
-
Try to get geneIDs
- geneIds - Variable in class org.snpeff.reactome.Entity
- GeneIds - Class in org.snpeff.reactome
-
Maps different Gene IDs: - ENSEMBL Gene ID to transcript ID - ENSEMBL Gene ID to Gene Name - ENSEMBL Gene ID to Refseq Gene ID - ENSEMBL Gene ID to Refseq Protein ID
- GeneIds(String) - Constructor for class org.snpeff.reactome.GeneIds
- geneName(Feature, int, int) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
-
Get gene name from feature
- GenericMarker - Class in org.snpeff.interval
-
An interval intended as a mark
- GenericMarker() - Constructor for class org.snpeff.interval.GenericMarker
- GenericMarker(Marker, int, int, String) - Constructor for class org.snpeff.interval.GenericMarker
- GenericMarkerFileIterator - Class in org.snpeff.fileIterator
-
Opens a file and creates generic markers (one per line)
- GenericMarkerFileIterator(String, int, int, int, int) - Constructor for class org.snpeff.fileIterator.GenericMarkerFileIterator
- Genes - Class in org.snpeff.interval
-
A collection of genes (marker intervals) Note: It is assumed that all genes belong to the same genome
- Genes(Genome) - Constructor for class org.snpeff.interval.Genes
- GeneSet - Class in org.snpeff.geneSets
-
An set of genes (that belongs to a collection of gene-sets)
- GeneSet(String, String, GeneSets) - Constructor for class org.snpeff.geneSets.GeneSet
-
Create an empty gene set (that belongs to a collection of gene sets 'geneSets')
- GeneSet(List<GeneSet>, GeneSets) - Constructor for class org.snpeff.geneSets.GeneSet
-
Create a new GeneSet by joining all GeneSets in the list
- GeneSets - Class in org.snpeff.geneSets
-
A collection of GeneSets Genes have associated "experimental values"
- GeneSets() - Constructor for class org.snpeff.geneSets.GeneSets
-
Default constructor
- GeneSets(String) - Constructor for class org.snpeff.geneSets.GeneSets
- GeneSets(GeneSets) - Constructor for class org.snpeff.geneSets.GeneSets
- GeneSetsRanked - Class in org.snpeff.geneSets
-
A collection of GeneSets Genes are ranked (usually by 'value')
- GeneSetsRanked() - Constructor for class org.snpeff.geneSets.GeneSetsRanked
-
Default constructor
- GeneSetsRanked(String) - Constructor for class org.snpeff.geneSets.GeneSetsRanked
- GeneSetsRanked(GeneSets) - Constructor for class org.snpeff.geneSets.GeneSetsRanked
- geneSetsSorted() - Method in class org.snpeff.geneSets.GeneSets
-
Iterate through each GeneSet in this GeneSets
- geneSetsSortedSize(boolean) - Method in class org.snpeff.geneSets.GeneSets
-
Gene sets sorted by size (if same size, sort by name).
- genesSorted() - Method in class org.snpeff.geneSets.GeneSet
-
Return a sorted list of genes
- GeneStats - Class in org.snpeff.geneSets
-
Some statistics about a gene
- GeneStats() - Constructor for class org.snpeff.geneSets.GeneStats
- geneType() - Method in class org.snpeff.interval.Gene
- genome - Variable in class org.snpeff.fileIterator.MarkerFileIterator
- genome - Variable in class org.snpeff.fileIterator.VcfHapMapFileIterator
- genome - Variable in class org.snpeff.SnpEff
- genome - Variable in class org.snpeff.snpEffect.Hgvs
- Genome - Class in org.snpeff.interval
-
This is just used for the Interval class.
- Genome() - Constructor for class org.snpeff.interval.Genome
- Genome(String) - Constructor for class org.snpeff.interval.Genome
- Genome(String, Config) - Constructor for class org.snpeff.interval.Genome
- GENOME - Enum constant in enum class org.snpeff.snpEffect.EffectType
- GENOMES_DIR - Static variable in class org.snpeff.snpEffect.Config
- genomeVer - Variable in class org.snpeff.SnpEff
- GenomicSequences - Class in org.snpeff.binseq
-
This class stores all "relevant" sequences in a genome This class is able to: i) Add all regions of interest ii) Store genomic sequences for those regions of interest iii) Retrieve genomic sequences by interval
- GenomicSequences(Genome) - Constructor for class org.snpeff.binseq.GenomicSequences
- genotype - Variable in class org.snpeff.interval.Variant
- GENOTYPE - Enum constant in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
- genotypeFields - Variable in class org.snpeff.vcf.VcfEntry
- genotypeFieldsStr - Variable in class org.snpeff.vcf.VcfEntry
- Genotypes - Class in org.snpeff.genotypes
-
Simple test program
- Genotypes() - Constructor for class org.snpeff.genotypes.Genotypes
- genotypeScores - Variable in class org.snpeff.vcf.VcfEntry
- GenotypeStats - Class in org.snpeff.stats
-
Calculate statistics on genotype
- GenotypeStats() - Constructor for class org.snpeff.stats.GenotypeStats
- GenotypeVector - Class in org.snpeff.genotypes
-
A vector of genotypes in a 'compact' structure Note: Genotypes 0/0, 0/1, 1/0, 1/1 are stored in 2 bits.
- GenotypeVector(int) - Constructor for class org.snpeff.genotypes.GenotypeVector
- get() - Static method in class org.snpeff.binseq.coder.DnaCoder
- get() - Static method in class org.snpeff.binseq.coder.DnaQualityCoder
- get() - Static method in class org.snpeff.probablility.Binomial
- get() - Static method in class org.snpeff.probablility.CochranArmitageTest
- get() - Static method in class org.snpeff.probablility.FisherExactTest
- get() - Static method in class org.snpeff.probablility.Hypergeometric
- get() - Static method in class org.snpeff.probablility.RankSumNoReplacementPdf
- get() - Static method in class org.snpeff.snpEffect.Config
- get() - Method in class org.snpeff.snpEffect.VariantEffects
-
Get (or create) the latest ChangeEffect
- get() - Method in class org.snpeff.stats.Counter
- get() - Method in class org.snpeff.stats.CounterDouble
- get(char) - Method in class org.snpeff.spliceSites.AcgtTree
-
Get a node
- get(int) - Method in class org.snpeff.binseq.indexer.SequenceIndexer
-
Get sequence in entry number 'idx'
- get(int) - Method in class org.snpeff.collections.OpenBitSet
-
Returns true or false for the specified bit index.
- get(int) - Method in class org.snpeff.genotypes.GenotypeVector
- get(int) - Method in class org.snpeff.interval.Markers
- get(int) - Method in class org.snpeff.ped.PedGenotype
- get(int) - Method in class org.snpeff.snpEffect.VariantEffects
- get(long) - Method in class org.snpeff.collections.OpenBitSet
-
Returns true or false for the specified bit index
- get(long) - Method in class org.snpeff.nmer.NmerCount
- get(long) - Method in class org.snpeff.vcf.FileIndexChrPos
-
Get a byte from a file
- get(long, int) - Method in class org.snpeff.vcf.FileIndexChrPos
-
Read 'len' bytes after 'bytePosition' or until a '\n' is reached.
- get(String) - Method in class org.snpeff.coverage.CountFragments
- get(String) - Method in class org.snpeff.coverage.Coverage
- get(String) - Method in class org.snpeff.genBank.Feature
-
Get a qualifier by name
- get(String) - Static method in class org.snpeff.interval.ChromosomeSimpleName
-
Get a simple name for the chromosome
- get(String) - Method in class org.snpeff.interval.Genes
-
Obtain a gene interval
- get(String) - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Obtain a subinterval
- get(String) - Method in class org.snpeff.ped.PedPedigree
- get(String) - Method in class org.snpeff.spliceSites.AcgtTree
-
Get node indexed by this string
- get(String) - Method in class org.snpeff.stats.CountByType
-
How many counts of this type?
- get(String) - Method in class org.snpeff.vcf.VcfConsequence
- get(String) - Method in class org.snpeff.vcf.VcfGenotype
-
Get a genotype field
- get(Nmer) - Method in class org.snpeff.nmer.NmerCount
-
Get kmer count
- get(T) - Method in class org.snpeff.stats.CountByKey
-
How many counts of this type?
- get3primeUtrs() - Method in class org.snpeff.interval.Transcript
-
Create a list of 3 prime UTRs
- get3primeUtrsSorted() - Method in class org.snpeff.interval.Transcript
- get5primeUtrs() - Method in class org.snpeff.interval.Transcript
-
Create a list of 5 prime UTRs
- get5primeUtrsSorted() - Method in class org.snpeff.interval.Transcript
- getAa() - Method in class org.snpeff.vcf.VcfEffect
- getAaAlt() - Method in class org.snpeff.snpEffect.VariantEffect
- getAaChange() - Method in class org.snpeff.snpEffect.VariantEffect
-
Amino acid change string (HGVS style)
- getAaChangeColor(String, String) - Method in class org.snpeff.stats.VariantEffectStats
-
Background color used for AA change table
- getAaChangeCount(String, String) - Method in class org.snpeff.stats.VariantEffectStats
-
How many changes from oldAa to newAa do we have?
- getAaChangeOld() - Method in class org.snpeff.snpEffect.VariantEffect
-
Amino acid change string (old style)
- getAaIdxEnd() - Method in class org.snpeff.interval.Exon
- getAaIdxStart() - Method in class org.snpeff.interval.Exon
- getAaLen() - Method in class org.snpeff.vcf.VcfEffect
- getAaLength() - Method in class org.snpeff.snpEffect.VariantEffect
-
Amino acid length (negative if there is none)
- getAaList() - Method in class org.snpeff.stats.VariantEffectStats
-
Get list of all amino acisd involved
- getAaMinSeparation() - Method in class org.snpeff.pdb.ProteinInteractions
- getAaNetChange() - Method in class org.snpeff.snpEffect.VariantEffect
-
Net AA change (InDels)
- getAaNumLeftEnd() - Method in class org.snpeff.snpEffect.VariantEffectFusion
- getAaNumLeftStart() - Method in class org.snpeff.snpEffect.VariantEffectFusion
- getAaNumRightEnd() - Method in class org.snpeff.snpEffect.VariantEffectFusion
- getAaNumRightStart() - Method in class org.snpeff.snpEffect.VariantEffectFusion
- getAaPos() - Method in class org.snpeff.vcf.VcfEffect
- getAaRef() - Method in class org.snpeff.snpEffect.VariantEffect
- getAasequence() - Method in class org.snpeff.genBank.Feature
-
Get translated amino acid sequence
- getAcc() - Method in class org.snpeff.geneOntology.GoTerm
- getAcceptor(int) - Method in class org.snpeff.spliceSites.SpliceTypes
- getAcceptorsByIntron(String) - Method in class org.snpeff.spliceSites.SpliceTypes
- getAccession() - Method in class org.snpeff.genBank.Features
- getAccession() - Method in class org.snpeff.nextProt.NextProtXmlNode
- getAintersectB() - Method in class org.snpeff.stats.MineTwoMarkerIntervals
- getAlert() - Method in class org.snpeff.osCmd.StreamGobbler
- getAlertNotify() - Method in class org.snpeff.osCmd.StreamGobbler
- getAligmentScore() - Method in class org.snpeff.align.NeedlemanWunschOverlap
- getAlignment() - Method in class org.snpeff.align.NeedlemanWunsch
- getAlignment() - Method in class org.snpeff.align.NeedlemanWunschOverlap
- getAlignmentByTrId() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- getAlignmentScore() - Method in class org.snpeff.align.NeedlemanWunsch
- getAllele() - Method in class org.snpeff.vcf.VcfEffect
- getAlleleCount() - Method in class org.snpeff.stats.GenotypeStats
- getAlleleCountHistoUrl() - Method in class org.snpeff.stats.GenotypeStats
- getAlleleFrequency() - Method in class org.snpeff.stats.GenotypeStats
- getAlleleFrequencyHistoUrl() - Method in class org.snpeff.stats.GenotypeStats
- getAllLines() - Method in class org.snpeff.osCmd.StreamGobbler
- getAlt() - Method in class org.snpeff.interval.Variant
- getAltIndex(String) - Method in class org.snpeff.vcf.VcfEntry
-
Get index of matching ALT entry
- getAltRealign() - Method in class org.snpeff.align.VariantRealign
- getAlts() - Method in class org.snpeff.vcf.VcfEntry
- getAltsStr() - Method in class org.snpeff.vcf.VcfEntry
-
Create a comma separated ALTS string
- getAndSet(int) - Method in class org.snpeff.collections.OpenBitSet
-
Sets a bit and returns the previous value.
- getAndSet(long) - Method in class org.snpeff.collections.OpenBitSet
-
Sets a bit and returns the previous value.
- getAnnotations() - Method in class org.snpeff.nextProt.NextProtXmlEntry
- getArgs() - Method in class org.snpeff.fastq.FastqSplit
- getArgs() - Method in class org.snpeff.SnpEff
- getArgs() - Method in interface org.snpeff.snpEffect.commandLine.CommandLine
- getArgs() - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
- getAssembly() - Method in class org.snpeff.sam.SamHeaderRecordSq
- getAttr(String) - Method in class org.snpeff.interval.GffMarker
- getAvg() - Method in class org.snpeff.stats.Average
- getAvg() - Method in class org.snpeff.stats.AverageInt
- getBarSpace() - Method in class org.snpeff.stats.plot.GooglePlotInt
- getBarWidth() - Method in class org.snpeff.stats.plot.GooglePlotInt
- getBase(int) - Method in class org.snpeff.binseq.BinarySequence
-
Return the base at position 'index'
- getBase(int) - Method in class org.snpeff.binseq.DnaAndQualitySequence
- getBase(int) - Method in class org.snpeff.binseq.DnaNSequence
- getBase(int) - Method in class org.snpeff.binseq.DnaSequence
- getBase(int) - Method in class org.snpeff.binseq.DnaSequenceByte
- getBaseFileNameGenes() - Method in class org.snpeff.snpEffect.Config
-
Genes file path (no extension)
- getBaseFileNameMotif() - Method in class org.snpeff.snpEffect.Config
- getBaseFileNameRegulation() - Method in class org.snpeff.snpEffect.Config
-
Regulation file (GFF format)
- getBaseFileNameSequence() - Method in class org.snpeff.snpEffect.Config
- getBases() - Method in class org.snpeff.stats.VariantStats
- getBases(int, int) - Method in class org.snpeff.binseq.DnaNSequence
-
Get a few bases from this sequence
- getBases(int, int) - Method in class org.snpeff.binseq.DnaSequence
-
Get a few bases from this sequence
- getBasesChangesColor(String, String) - Method in class org.snpeff.stats.VariantStats
-
Background color used for base change table
- getBasesChangesCount(String, String) - Method in class org.snpeff.stats.VariantStats
- getBestOffset() - Method in class org.snpeff.overlap.Overlap
- getBestScore() - Method in class org.snpeff.overlap.Overlap
- getBestSequence() - Method in class org.snpeff.motif.Pwm
-
Get best matching sequence (highest score)
- getBestSequenceStr() - Method in class org.snpeff.motif.Pwm
- getBiotype() - Method in class org.snpeff.interval.GffMarker
- getBiotype() - Method in class org.snpeff.snpEffect.VariantEffect
-
Get biotype
- getBioType() - Method in class org.snpeff.interval.Gene
- getBioType() - Method in class org.snpeff.interval.GffMarker
- getBioType() - Method in class org.snpeff.interval.Transcript
- getBioType() - Method in class org.snpeff.vcf.VcfEffect
- getBioType(String) - Method in class org.snpeff.stats.GeneCountByTypeTable
- getBiotypeGeneric() - Method in class org.snpeff.interval.GffMarker
- getBit(int) - Method in class org.snpeff.collections.OpenBitSet
-
returns 1 if the bit is set, 0 if not.
- getBits() - Method in class org.snpeff.collections.OpenBitSet
-
Expert: returns the long[] storing the bits
- getBranchByIntron(String) - Method in class org.snpeff.spliceSites.SpliceTypes
- getBranchU12(String) - Method in class org.snpeff.spliceSites.SpliceTypes
-
Add a SpliceSiteBranchU12 for this donor-Acceptor pair
- getBucket(long) - Method in class org.snpeff.collections.HashLongLongArray
-
Return all values for a given key WARNING: Not all elements in a bucket are used.
- getBucketLength(long) - Method in class org.snpeff.collections.HashLongLongArray
-
Return used length of a bucket
- getBundleName(String) - Method in class org.snpeff.snpEffect.Config
-
Is this genome packed in a bundle?
- getByChromo(String) - Method in class org.snpeff.spliceSites.TranscriptSet
- getById(int) - Method in class org.snpeff.serializer.MarkerSerializer
- getByPdbId(String) - Method in class org.snpeff.pdb.IdMapper
- getByPdbId(String, String) - Method in class org.snpeff.pdb.IdMapper
- getByProteinId(String) - Method in class org.snpeff.pdb.ProteinInteractions
- getByTrId(String) - Method in class org.snpeff.pdb.IdMapper
- getCacheFile() - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
- getCatalyst() - Method in class org.snpeff.reactome.events.Reaction
- getCategory() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- getcDnaLen() - Method in class org.snpeff.vcf.VcfEffect
- getcDnaPos() - Method in class org.snpeff.snpEffect.VariantEffect
- getcDnaPos() - Method in class org.snpeff.vcf.VcfEffect
- getCds() - Method in class org.snpeff.interval.Transcript
-
Get all CDSs
- getCdsEnd() - Method in class org.snpeff.interval.Transcript
- getCdsLen() - Method in class org.snpeff.vcf.VcfEffect
- getCdsLength() - Method in class org.snpeff.snpEffect.VariantEffect
-
CDS length (negative if there is none)
- getCdsPos() - Method in class org.snpeff.vcf.VcfEffect
- getCdsStart() - Method in class org.snpeff.interval.Transcript
- getCenter() - Method in class org.snpeff.interval.tree.IntervalNode
- getCenter() - Method in class org.snpeff.interval.tree.IntervalNodeOri
- getChangeEffectResutStats() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- getChangeType() - Method in class org.snpeff.stats.VariantStats
- getChangeTypeLength() - Method in class org.snpeff.stats.VariantStats
- getChilds() - Method in class org.snpeff.geneOntology.GoTerm
- getChr1() - Method in class org.snpeff.stats.TranslocationReport
- getChr2() - Method in class org.snpeff.stats.TranslocationReport
- getChrName(int) - Method in class org.snpeff.ped.PlinkMap
- getChromo() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
- getChromoFastaFiles() - Method in class org.snpeff.interval.Genome
- getChromos() - Method in class org.snpeff.vcf.FileIndexChrPos
-
Available chromosomes
- getChromoSequence() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
- getChromosome() - Method in class org.snpeff.interval.Interval
- getChromosome(int) - Method in class org.snpeff.gsa.ChrPosScoreList
- getChromosome(String) - Method in class org.snpeff.fileIterator.MarkerFileIterator
-
Find chromosome 'chromoName'.
- getChromosome(String) - Method in class org.snpeff.interval.Genome
-
Find chromosome 'chromoName'
- getChromosomeCount() - Method in class org.snpeff.interval.Genome
- getChromosomeLength(String) - Method in class org.snpeff.stats.VariantStats
-
Choromosome length
- getChromosomeName() - Method in class org.snpeff.interval.Interval
-
Find chromosome name
- getChromosomeName(int) - Method in class org.snpeff.gsa.ChrPosScoreList
- getChromosomeNameOri() - Method in class org.snpeff.interval.Interval
- getChromosomeNameOri() - Method in class org.snpeff.vcf.VcfEntry
-
Original chromosome name (as it appeared in the VCF file)
- getChromosomeNamesEffective() - Method in class org.snpeff.stats.VariantStats
-
A list of chromosomes that had at least one change Note: Chromosome names are sorted.
- getChromosomeNum() - Method in class org.snpeff.interval.Interval
-
Find chromosome and return it's number
- getChromosomes() - Method in class org.snpeff.interval.Genome
- getChromosomesSortedSize() - Method in class org.snpeff.interval.Genome
-
Return chromosomes sorted by size (largest chromosomes first)
- getChrPosStats(String) - Method in class org.snpeff.stats.VariantStats
- getChrPosStatsChartUrl(String) - Method in class org.snpeff.stats.VariantStats
- getCigar() - Method in class org.snpeff.sam.SamEntry
- getCode(int) - Method in class org.snpeff.binseq.BinarySequence
-
Return the code at position 'index'
- getCode(int) - Method in class org.snpeff.binseq.DnaAndQualitySequence
- getCode(int) - Method in class org.snpeff.binseq.DnaSequence
-
Return the base at position 'index'
- getCode(int) - Method in class org.snpeff.binseq.DnaSequencePe
- getCoder() - Method in class org.snpeff.binseq.BinarySequence
-
Get sequence encoder invalid input: '&' decoder
- getCoder() - Method in class org.snpeff.binseq.DnaAndQualitySequence
- getCoder() - Method in class org.snpeff.binseq.DnaSequence
- getCoder() - Method in class org.snpeff.binseq.DnaSequencePe
- getCodes() - Method in class org.snpeff.binseq.DnaAndQualitySequence
- getCodes() - Method in class org.snpeff.binseq.DnaSequence
- getCodes() - Method in class org.snpeff.binseq.DnaSequenceByte
- getCoding() - Method in class org.snpeff.vcf.VcfEffect
- getCodon() - Method in class org.snpeff.vcf.VcfEffect
- getCodonChange() - Method in class org.snpeff.snpEffect.VariantEffect
-
Codon change string
- getCodonChangeColor(String, String) - Method in class org.snpeff.stats.VariantEffectStats
- getCodonChangeCount(String, String) - Method in class org.snpeff.stats.VariantEffectStats
-
How many changes from oldCodo to newCodon do we have?
- getCodonChangeMax() - Method in class org.snpeff.snpEffect.VariantEffect
-
Codon change string (if it's not too long)
- getCodonIndex() - Method in class org.snpeff.snpEffect.VariantEffect
- getCodonList() - Method in class org.snpeff.stats.VariantEffectStats
-
Get a list of all codons involved
- getCodonNum() - Method in class org.snpeff.snpEffect.VariantEffect
- getCodonsAlt() - Method in class org.snpeff.snpEffect.VariantEffect
- getCodonsRef() - Method in class org.snpeff.snpEffect.VariantEffect
- getCodonTable() - Method in class org.snpeff.interval.Chromosome
- getColorHtml(String) - Method in class org.snpeff.stats.CountByType
-
Background color used for table (heatmap)
- getCommandArgs() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- getCompartment() - Method in class org.snpeff.reactome.Entity
- getConfig() - Method in class org.snpeff.SnpEff
- getConfigFile() - Method in class org.snpeff.SnpEff
- getConfigFileCanonicaPath() - Method in class org.snpeff.snpEffect.Config
- getConfigFileName() - Method in class org.snpeff.snpEffect.Config
- getConsequence() - Method in class org.snpeff.vcf.VcfConsequence
- getCoordinates() - Method in class org.snpeff.snpEffect.Config
- getCount() - Method in class org.snpeff.coverage.CoverageChr
- getCount() - Method in class org.snpeff.stats.Average
- getCount() - Method in class org.snpeff.stats.AverageInt
- getCount() - Method in class org.snpeff.stats.Counter
- getCount() - Method in class org.snpeff.stats.CounterDouble
- getCount() - Method in class org.snpeff.stats.FloatStats
- getCount() - Method in class org.snpeff.stats.IntStats
- getCount() - Method in class org.snpeff.stats.VariantStats
-
Total number of variants
- getCount(char, int) - Method in class org.snpeff.motif.Pwm
-
Get counts for a given position
- getCount(int) - Method in class org.snpeff.stats.ChrPosStats
- getCount(int) - Method in class org.snpeff.stats.IntStats
- getCount(String) - Method in class org.snpeff.stats.CountByType
-
Count for this type
- getCountBases() - Method in class org.snpeff.coverage.CountReads
- getCountBases() - Method in class org.snpeff.stats.ReadsOnMarkersModel
- getCountByChangeType() - Method in class org.snpeff.stats.VariantStats
-
Number of variants by type
- getCountByChromosome(String) - Method in class org.snpeff.stats.VariantStats
-
Number of changes by chromosome
- getCountByEffect() - Method in class org.snpeff.stats.VariantEffectStats
- getCountByFunctionalClass() - Method in class org.snpeff.stats.VariantEffectStats
- getCountByGeneRegion() - Method in class org.snpeff.stats.VariantEffectStats
- getCountByImpact() - Method in class org.snpeff.stats.VariantEffectStats
- getCounter(String) - Method in class org.snpeff.stats.GeneCountByTypeTable
-
Get counter for this type
- getCountErrors() - Method in class org.snpeff.stats.VariantEffectStats
- getCounterSize(String) - Method in class org.snpeff.stats.GeneCountByTypeTable
-
Get size counter for this type
- getCountExceptions() - Method in class org.snpeff.coverage.CountReads
- getCountMarkers() - Method in class org.snpeff.stats.ReadsOnMarkersModel
- getCountMultiallelic() - Method in class org.snpeff.stats.VcfStats
- getCountNonEmptyId() - Method in class org.snpeff.stats.VariantStats
- getCountNonVariants() - Method in class org.snpeff.stats.VariantStats
- getCountReads() - Method in class org.snpeff.coverage.CountReads
- getCountTotalReads() - Method in class org.snpeff.coverage.CountReads
- getCountTypes() - Method in class org.snpeff.coverage.CountReads
- getCountWarnings() - Method in class org.snpeff.stats.VariantEffectStats
- getCoverageByExons() - Method in class org.snpeff.coverage.CountReads
- getCoverageByType() - Method in class org.snpeff.coverage.CountReads
- getCvTerm() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- getCytoBands() - Method in class org.snpeff.interval.Genome
- getData() - Method in class org.snpeff.logStatsServer.VersionCheck
-
Get page as string
- getDatabaseCompatibilityVersions() - Method in class org.snpeff.snpEffect.Config
-
Return a list of databases that are compatible with this SnpEff version number
- getDatabaseLocal(String) - Method in class org.snpeff.snpEffect.Config
-
Database local file for a specific database, such as 'dbSnp', 'ClinVar', etc.
- getDatabaseLocalKey(String) - Method in class org.snpeff.snpEffect.Config
- getDatabaseRepository() - Method in class org.snpeff.snpEffect.Config
- getDatabaseRepository(String) - Method in class org.snpeff.snpEffect.Config
-
Database repository for a specific database, such as 'dbSnp', 'ClinVar', etc.
- getDatabaseRepositoryUrl(String) - Method in class org.snpeff.snpEffect.Config
- getDate() - Method in class org.snpeff.genBank.Features
- getDbNsfpFields() - Method in class org.snpeff.snpEffect.Config
- getDefaultValue() - Method in class org.snpeff.gsa.PvaluesList
- getDefaultValue() - Method in class org.snpeff.gsa.ScoreList
- getDefaultWaitTime() - Method in class org.snpeff.osCmd.OsCmdRunner
- getDefinition() - Method in class org.snpeff.genBank.Features
- getDerived() - Method in class org.snpeff.vcf.PedigreeEntry
- getDerivedNum() - Method in class org.snpeff.vcf.PedigreeEntry
- getDescription() - Method in class org.snpeff.geneOntology.GoTerm
- getDescription() - Method in class org.snpeff.geneSets.GeneSet
- getDescription() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- getDescription() - Method in class org.snpeff.vcf.VcfHeaderInfo
- getDirData() - Method in class org.snpeff.snpEffect.Config
-
Main data directory
- getDirDataGenomeVersion() - Method in class org.snpeff.snpEffect.Config
-
Data dir for a specific genome version (i.e.
- getDirMain() - Method in class org.snpeff.snpEffect.Config
-
Main dir
- getDirRegulationBed() - Method in class org.snpeff.snpEffect.Config
-
Directory where regulation 'BED' files are
- getDistance() - Method in class org.snpeff.snpEffect.VariantEffect
- getDistance() - Method in class org.snpeff.vcf.VcfEffect
- getDistanceResults() - Method in class org.snpeff.pdb.ProteinInteractions
- getDistanceResults() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
-
Get distance results.
- getDistanceStats() - Method in class org.snpeff.stats.MineMarkerIntervals
- getDistanceThreshold() - Method in class org.snpeff.pdb.ProteinInteractions
- getDistanceThresholdNon() - Method in class org.snpeff.pdb.ProteinInteractions
- getDivision() - Method in class org.snpeff.genBank.Features
- getDnaSequence() - Method in class org.snpeff.interval.Chromosome
- getDoesAintersectB() - Method in class org.snpeff.stats.MineTwoMarkerIntervals
- getDoesBintersectA() - Method in class org.snpeff.stats.MineTwoMarkerIntervals
- getDonor(int) - Method in class org.snpeff.spliceSites.SpliceTypes
- getDonorAccPairSize() - Method in class org.snpeff.spliceSites.SpliceTypes
- getDonorByIntron(String) - Method in class org.snpeff.spliceSites.SpliceTypes
- getDouble(String, double) - Method in class org.snpeff.snpEffect.Config
-
Get a property as a double
- getDownstream() - Method in class org.snpeff.interval.Transcript
- getEffectDetails() - Method in class org.snpeff.vcf.VcfEffect
- getEffectImpact() - Method in class org.snpeff.snpEffect.VariantEffect
-
Return impact of this effect
- getEffectsStr() - Method in class org.snpeff.vcf.VcfEffect
- getEffectsStrSo() - Method in class org.snpeff.vcf.VcfEffect
- getEffectType() - Method in class org.snpeff.snpEffect.VariantEffect
-
Highest effect type
- getEffectType() - Method in class org.snpeff.vcf.VcfEffect
- getEffectTypes() - Method in class org.snpeff.snpEffect.VariantEffect
-
Highest effect type
- getEffectTypes() - Method in class org.snpeff.vcf.VcfEffect
- getEffectTypesStr() - Method in class org.snpeff.vcf.VcfEffect
- getEffectTypeString(boolean) - Method in class org.snpeff.snpEffect.VariantEffect
- getEffectTypeString(boolean, boolean) - Method in class org.snpeff.snpEffect.VariantEffect
- getEffectTypeString(boolean, boolean, EffFormatVersion) - Method in class org.snpeff.snpEffect.VariantEffect
-
Get Effect Type as a string
- getEffString() - Method in class org.snpeff.vcf.VcfEffect
- getEnd() - Method in class org.snpeff.genBank.Feature
- getEnd() - Method in class org.snpeff.interval.Interval
- getEnd(int) - Method in class org.snpeff.gsa.ChrPosScoreList
- getEnd(String) - Method in class org.snpeff.vcf.FileIndexChrPos
-
Get position where 'chr' ends
- getEndPoint() - Method in class org.snpeff.interval.VariantBnd
- getEntries() - Method in class org.snpeff.pdb.IdMapper
- getError() - Method in class org.snpeff.osCmd.OsCmdRunner
- getError() - Method in class org.snpeff.snpEffect.VariantEffect
- getErrorsWarning() - Method in class org.snpeff.vcf.VcfEffect
- getExitValue() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- getExitValue() - Method in class org.snpeff.osCmd.OsCmdRunner
- getExon() - Method in class org.snpeff.snpEffect.VariantEffect
-
Get exon (if any)
- getExonAfter() - Method in class org.snpeff.interval.Intron
- getExonBefore() - Method in class org.snpeff.interval.Intron
- getExonId() - Method in class org.snpeff.vcf.VcfEffect
- getExons() - Method in class org.snpeff.interval.Transcript
-
A more intuitive name for 'subintervals'
- getFamilyId() - Method in class org.snpeff.ped.PedPedigree
- getFamilyId() - Method in class org.snpeff.ped.TfamEntry
- getFatherId() - Method in class org.snpeff.ped.TfamEntry
- getFeature() - Method in class org.snpeff.vcf.VcfConsequence
- getFeatureId() - Method in class org.snpeff.vcf.VcfEffect
- getFeatures() - Method in class org.snpeff.genBank.Features
- getFeatureType() - Method in class org.snpeff.vcf.VcfEffect
- getFieldByName(String) - Method in class org.snpeff.vcf.VcfEffect
-
Get a subfield by name
- getFieldNames() - Method in class org.snpeff.fileIterator.GuessTableTypes
- getFieldNames() - Method in class org.snpeff.vcf.VcfConsequenceHeader
- getFieldNum(String) - Method in class org.snpeff.vcf.VcfConsequenceHeader
- getFileListGenomeFasta() - Method in class org.snpeff.snpEffect.Config
-
Filenames for reference sequence (fasta files)
- getFileName() - Method in class org.snpeff.fileIterator.GuessTableTypes
- getFileNameCds() - Method in class org.snpeff.snpEffect.Config
- getFileNameGenomeFasta() - Method in class org.snpeff.snpEffect.Config
-
Filename for reference sequence (fasta file) Scans the list of files 'getFileListGenomeFasta()' and finds the first file that exists
- getFileNameProteins() - Method in class org.snpeff.snpEffect.Config
- getFileNameSequence() - Method in class org.snpeff.snpEffect.Config
- getFileNameSequence(String) - Method in class org.snpeff.snpEffect.Config
- getFilePointer() - Method in class org.snpeff.fileIterator.FileIterator
-
Get position within file
- getFilePointer() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- getFileSnpEffectPredictor() - Method in class org.snpeff.snpEffect.Config
- getFilter() - Method in class org.snpeff.vcf.VcfEntry
- getFirst() - Method in class org.snpeff.util.Tuple
- getFirstChild() - Method in class org.snpeff.geneOntology.GoTerm
-
Return first child in the list
- getFirstCodingExon() - Method in class org.snpeff.interval.Transcript
-
Get first coding exon
- getFirstParent() - Method in class org.snpeff.geneOntology.GoTerm
-
Return first parent in the list
- getFlag() - Method in class org.snpeff.sam.SamEntry
- getFormat() - Method in class org.snpeff.vcf.VcfEntry
- getFormatFields() - Method in class org.snpeff.vcf.VcfEntry
- getFormatVersion() - Method in class org.snpeff.vcf.VcfEffect
- getFrame() - Method in class org.snpeff.interval.Cds
- getFrame() - Method in class org.snpeff.interval.Exon
- getFrame() - Method in class org.snpeff.interval.GffMarker
- getFrame() - Method in interface org.snpeff.interval.MarkerWithFrame
- getFunClass() - Method in class org.snpeff.vcf.VcfEffect
- getFunctionalClass() - Method in class org.snpeff.snpEffect.VariantEffect
-
Return functional class of this effect (i.e.
- getGap() - Method in class org.snpeff.binseq.DnaSequencePe
- getGene() - Method in class org.snpeff.interval.Transcript
- getGene() - Method in class org.snpeff.snpEffect.VariantEffect
- getGene() - Method in class org.snpeff.snpEffect.VariantEffectFusion
- getGene() - Method in class org.snpeff.snpEffect.VariantEffectStructural
- getGene(String) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Obtain a gene by geneId
- getGeneBiotype() - Method in class org.snpeff.interval.GffMarker
- getGeneByName(String) - Method in class org.snpeff.interval.Genes
-
Obtain a gene by GeneName WARNING: The first match is returned.
- getGeneCount() - Method in class org.snpeff.geneSets.GeneSet
-
Number of symbols in this node (total = interesting + not-interesting)
- getGeneCount() - Method in class org.snpeff.geneSets.GeneSets
-
How many genes do we have?
- getGeneCountByEffectTable() - Method in class org.snpeff.stats.VariantEffectStats
- getGeneCountByImpactTable() - Method in class org.snpeff.stats.VariantEffectStats
- getGeneCountByRegionTable() - Method in class org.snpeff.stats.VariantEffectStats
- getGeneId() - Method in class org.snpeff.genBank.Feature
- getGeneId() - Method in class org.snpeff.gsa.ScoreList
- getGeneId() - Method in class org.snpeff.interval.GffMarker
- getGeneId() - Method in class org.snpeff.vcf.VcfEffect
- getGeneId() - Method in class org.snpeff.vcf.VcfLof
- getGeneIds() - Method in class org.snpeff.gtex.Gtex
- getGeneIds() - Method in class org.snpeff.reactome.Entity
- getGeneLeft() - Method in class org.snpeff.snpEffect.VariantEffectFusion
- getGeneName() - Method in class org.snpeff.genBank.Feature
-
Get gene name from feature
- getGeneName() - Method in class org.snpeff.interval.Gene
- getGeneName() - Method in class org.snpeff.interval.GffMarker
- getGeneName() - Method in class org.snpeff.vcf.VcfEffect
- getGeneName() - Method in class org.snpeff.vcf.VcfLof
- getGeneName1() - Method in class org.snpeff.stats.TranslocationReport
- getGeneName2() - Method in class org.snpeff.stats.TranslocationReport
- getGeneRegion() - Method in enum class org.snpeff.snpEffect.EffectType
- getGeneRegion() - Method in class org.snpeff.snpEffect.VariantEffect
- getGeneRight() - Method in class org.snpeff.snpEffect.VariantEffectFusion
- getGenes() - Method in class org.snpeff.geneSets.GeneSet
- getGenes() - Method in class org.snpeff.geneSets.GeneSets
-
Get all genes in this set
- getGenes() - Method in class org.snpeff.interval.Genome
- getGenes() - Method in class org.snpeff.snpEffect.VariantEffect
- getGenes() - Method in class org.snpeff.snpEffect.VariantEffectStructural
- getGeneSet(String) - Method in class org.snpeff.geneSets.GeneSets
-
Get a gene set named 'geneSetName'
- getGeneSetCount() - Method in class org.snpeff.geneSets.GeneSets
-
Get number of gene sets
- getGeneSetCount() - Method in class org.snpeff.geneSets.Result
- getGeneSetCountLast() - Method in class org.snpeff.geneSets.Result
- getGeneSets() - Method in class org.snpeff.geneSets.GeneSet
- getGeneSets() - Method in class org.snpeff.geneSets.Result
- getGeneSetsByGene(String) - Method in class org.snpeff.geneSets.GeneSets
-
All gene sets that this gene belongs to
- getGeneSetsByName() - Method in class org.snpeff.geneSets.GeneSets
- getGenesSorted() - Method in class org.snpeff.interval.Genome
-
Create a sorted list of genes (sorted by gene Id)
- getGenesSortedPos() - Method in class org.snpeff.interval.Genome
-
Create a sorted list of genes (sorted by genomic position)
- getGenome() - Method in class org.snpeff.fileIterator.MarkerFileIterator
- getGenome() - Method in class org.snpeff.interval.Interval
-
Find genome
- getGenome() - Method in class org.snpeff.snpEffect.Config
- getGenome() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- getGenome(String) - Method in class org.snpeff.snpEffect.Config
- getGenomeId() - Method in class org.snpeff.interval.Genome
- getGenomeLen() - Method in class org.snpeff.stats.VariantStats
-
Genome length
- getGenomeLenEffective() - Method in class org.snpeff.stats.VariantStats
-
Genome effective length: The sum of length of every chromosome that had a change (e.g.
- getGenomeName() - Method in class org.snpeff.interval.Interval
-
Find genome name
- getGenomeVersion() - Method in class org.snpeff.snpEffect.Config
- getGenomicSequences() - Method in class org.snpeff.interval.Genome
- getGenotype() - Method in class org.snpeff.interval.Variant
- getGenotype() - Method in class org.snpeff.interval.VariantNonRef
- getGenotype() - Method in class org.snpeff.snpEffect.VariantEffect
-
Get genotype string
- getGenotype() - Method in class org.snpeff.vcf.VcfEffect
- getGenotype() - Method in class org.snpeff.vcf.VcfGenotype
-
Get genotype numbers as an array E.g.
- getGenotype(int) - Method in class org.snpeff.ped.PedEntry
-
Get genotype WARNING: Empty string means that no genotpye is available
- getGenotype(int) - Method in class org.snpeff.vcf.VcfGenotype
-
Get genotype string by index WARNING: If the genotype is missing, it returns an empty string.
- getGenotype(String) - Method in class org.snpeff.ped.PedEntry
-
Get phenotype by String ID
- getGenotypeCode() - Method in class org.snpeff.vcf.VcfGenotype
-
Return as a genotype SNP code: -1: if missing data of more than one ALT 0: if aa (0/0) 1: if Aa (0/1 or 1/0) 2: if AA (1/1) WARNING: In multi-allelic case, any non-ref is treated as ALT
- getGenotypeCodeIgnoreMissing() - Method in class org.snpeff.vcf.VcfGenotype
-
Return as a genotype SNP code: 0: if aa (0/0) or any missing value 1: if Aa (0/1 or 1/0) 2: if AA (1/1)
- getGenotypeNames() - Method in class org.snpeff.ped.PedEntry
-
Get all genotype names WARNING: the returned string collection is unsorted!
- getGenotypeNames() - Method in class org.snpeff.ped.PlinkMap
- getGenotypeNames(String) - Method in class org.snpeff.ped.PlinkMap
- getGenotypes() - Method in class org.snpeff.ped.PedEntry
- getGenotypes() - Method in class org.snpeff.ped.PedGenotype
- getGenotypesScores() - Method in class org.snpeff.vcf.VcfEntry
-
Return genotypes parsed as an array of codes
- getGenotypeStats() - Method in class org.snpeff.stats.VcfStats
- getGenotypeStr() - Method in class org.snpeff.vcf.VcfGenotype
-
Return genotypes as string (e.g.
- getGffParentId(boolean) - Method in class org.snpeff.interval.GffMarker
- getGffParentIds() - Method in class org.snpeff.interval.GffMarker
-
Parent can have multiple, comma separated entries
- getGffType() - Method in class org.snpeff.interval.GffMarker
- getGoTerm(String) - Method in class org.snpeff.geneOntology.GoTerms
- getGoTerms() - Method in class org.snpeff.geneOntology.GoTerm
- getGoTermsByGoTermAcc() - Method in class org.snpeff.geneOntology.GoTerms
- getGoTermsBySymbolId() - Method in class org.snpeff.geneOntology.GoTerms
- getGoTermsBySymbolId(String) - Method in class org.snpeff.geneOntology.GoTerms
- getGtex() - Method in class org.snpeff.gtex.GtexExperiment
- getHandler() - Method in class org.snpeff.nextProt.NextProtXmlEntry
- getHead() - Method in class org.snpeff.osCmd.ExecuteOsCommand
-
First lines of stdout
- getHead() - Method in class org.snpeff.osCmd.OsCmdRunner
- getHead() - Method in class org.snpeff.osCmd.StreamGobbler
-
Head: First HEAD_SIZE lines of this output
- getHeader() - Method in class org.snpeff.fileIterator.FastaFileIterator
-
Current sequence header
- getHeaders() - Method in class org.snpeff.fileIterator.SamFileIterator
- getHeadStderr() - Method in class org.snpeff.osCmd.ExecuteOsCommand
-
First lines of stderr
- getHeadStderr() - Method in class org.snpeff.osCmd.OsCmdRunner
- getHetBySampleUrl() - Method in class org.snpeff.stats.GenotypeStats
- getHgvs() - Method in class org.snpeff.snpEffect.VariantEffect
-
Change in HGVS notation
- getHgvsC() - Method in class org.snpeff.stats.TranslocationReport
- getHgvsC() - Method in class org.snpeff.vcf.VcfEffect
- getHgvsDna() - Method in class org.snpeff.snpEffect.VariantEffect
-
Change in HGVS (Dna) notation
- getHgvsDna() - Method in class org.snpeff.vcf.VcfConsequence
- getHgvsDna() - Method in class org.snpeff.vcf.VcfEffect
- getHgvsP() - Method in class org.snpeff.stats.TranslocationReport
- getHgvsP() - Method in class org.snpeff.vcf.VcfEffect
- getHgvsProt() - Method in class org.snpeff.snpEffect.VariantEffect
-
Change in HGVS (Protein) notation
- getHgvsProt() - Method in class org.snpeff.vcf.VcfConsequence
- getHgvsProt() - Method in class org.snpeff.vcf.VcfEffect
- getHomBySampleUrl() - Method in class org.snpeff.stats.GenotypeStats
- getHomHetTable() - Method in class org.snpeff.stats.GenotypeStats
- getId() - Method in class org.snpeff.binseq.DnaAndQualitySequenceWithId
- getId() - Method in class org.snpeff.binseq.DnaSequenceId
- getId() - Method in class org.snpeff.gtex.GtexExperiment
- getId() - Method in class org.snpeff.interval.Interval
- getId() - Method in class org.snpeff.motif.Pwm
- getId() - Method in class org.snpeff.pdb.DistanceResult
- getId() - Method in class org.snpeff.ped.TfamEntry
- getId() - Method in class org.snpeff.reactome.Entity
- getId() - Method in class org.snpeff.sam.SamEntry
- getId() - Method in class org.snpeff.vcf.VcfHeaderEntry
- getId(int) - Method in class org.snpeff.ped.PlinkMap
- getId2geneName() - Method in class org.snpeff.reactome.GeneIds
- getId2refseqId() - Method in class org.snpeff.reactome.GeneIds
- getId2refseqProtId() - Method in class org.snpeff.reactome.GeneIds
- getId2tr() - Method in class org.snpeff.reactome.GeneIds
- getIdByMarker(Marker) - Method in class org.snpeff.serializer.MarkerSerializer
- getIdentifiers() - Method in class org.snpeff.nextProt.NextProtXmlEntry
- getIdFromFastaHeader() - Method in class org.snpeff.fileIterator.FastaFileIterator
-
Get transcript name from FASTA header (ENSEMBL protein files) Format example: '>ENSP00000356130 pep:known chromosome:GRCh37:1:205111633:205180694:-1 gene:ENSG00000133059 transcript:ENST00000367162'
- getIdMapFile() - Method in class org.snpeff.pdb.ProteinInteractions
- getIds(String) - Method in class org.snpeff.gtex.IdMap
-
Get all IDs corresponding to this name
- getImpact() - Method in class org.snpeff.stats.TranslocationReport
- getImpact() - Method in class org.snpeff.vcf.VcfEffect
- getIndelLen() - Method in class org.snpeff.stats.VariantStats
- getIndelLenHistoUrl() - Method in class org.snpeff.stats.VariantStats
- getIndex() - Method in class org.snpeff.stats.TranslocationReport
- getIndex(String) - Method in class org.snpeff.gtex.Gtex
- getInfo(String) - Method in class org.snpeff.vcf.VcfEntry
-
Get info string
- getInfo(String, String) - Method in class org.snpeff.vcf.VcfEntry
-
Get info string for a specific allele
- getInfo(String, Variant) - Method in class org.snpeff.vcf.VcfEntry
-
Get an INFO field matching a variant
- getInfoFlag(String) - Method in class org.snpeff.vcf.VcfEntry
-
Does the entry exists?
- getInfoFloat(String) - Method in class org.snpeff.vcf.VcfEntry
-
Get info field as a 'double' number The norm specifies data type as 'FLOAT', that is why the name of this method might be not intuitive
- getInfoInt(String) - Method in class org.snpeff.vcf.VcfEntry
-
Get info field as an long number The norm specifies data type as 'INT', that is why the name of this method might be not intuitive
- getInfoKeys() - Method in class org.snpeff.vcf.VcfEntry
-
Get all keys available in the info field
- getInfoStr() - Method in class org.snpeff.vcf.VcfEntry
-
Get the full (unparsed) INFO field
- getInputs() - Method in class org.snpeff.reactome.events.Reaction
- getInstance() - Static method in class org.snpeff.codons.CodonTables
- getInterestingGenes() - Method in class org.snpeff.geneSets.GeneSet
-
Get 'interesting' genes
- getInterestingGenes() - Method in class org.snpeff.geneSets.GeneSets
- getInterestingGenesCount() - Method in class org.snpeff.geneSets.GeneSet
-
Number of 'interesting' symbols
- getInterestingGenesCount() - Method in class org.snpeff.geneSets.GeneSets
- getInterestingSymbolIdSet() - Method in class org.snpeff.geneOntology.GoTerm
- getInterestingSymbolIdsSet() - Method in class org.snpeff.geneOntology.GoTerms
- getInterestingSymbolIdsSize() - Method in class org.snpeff.geneOntology.GoTerm
-
Number of 'interesting' symbols
- getInterestingSymbolIdsSize() - Method in class org.snpeff.geneOntology.GoTerms
- getIntervalForest() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- getIntervals() - Method in class org.snpeff.interval.tree.IntervalTree
- getIntervals() - Method in class org.snpeff.interval.tree.IntervalTreeArray
- getIntervals() - Method in class org.snpeff.interval.tree.IntervalTreeOri
- getIntervals() - Method in interface org.snpeff.interval.tree.Itree
- getIntron() - Method in class org.snpeff.snpEffect.VariantEffect
-
Get intron (if any)
- getIntronKeySet() - Method in class org.snpeff.spliceSites.SpliceTypes
- getIsoform(String) - Method in class org.snpeff.nextProt.NextProtXmlEntry
-
Get or create an isoform
- getIsoformsByAccession() - Method in class org.snpeff.nextProt.NextProtXmlEntry
- getJobId() - Method in class org.snpeff.osCmd.OsCmdRunner
- getKey() - Method in class org.snpeff.util.KeyValue
- getKeyList() - Method in class org.snpeff.stats.GeneCountByTypeTable
-
Get a sorted list of keys
- getKeywords() - Method in class org.snpeff.genBank.Features
- getKnownRatio() - Method in class org.snpeff.stats.VariantStats
-
Ratio of known variants (the one with a non-empty ID) and total variants
- getLabel() - Method in class org.snpeff.geneOntology.GoTerms
- getLabel() - Method in class org.snpeff.geneSets.GeneSets
- getLabel() - Method in class org.snpeff.interval.Custom
- getLatestBucketLength() - Method in class org.snpeff.collections.HashLongLongArray
-
Get bucket length for latest bucket search WARNING: Obviously this is not a thread safe operation
- getLatestGeneSet() - Method in class org.snpeff.geneSets.Result
- getLatestReleaseDate() - Method in class org.snpeff.logStatsServer.VersionCheck
- getLatestUrl() - Method in class org.snpeff.logStatsServer.VersionCheck
- getLatestVersion() - Method in class org.snpeff.logStatsServer.VersionCheck
- getLeft() - Method in class org.snpeff.interval.tree.IntervalNode
- getLeft() - Method in class org.snpeff.interval.tree.IntervalNodeOri
- getLength() - Method in class org.snpeff.binseq.DnaSequenceByte
- getLength() - Method in class org.snpeff.sam.SamHeaderRecordSq
- getLengthStats() - Method in class org.snpeff.stats.MineMarkerIntervals
- getLevel() - Method in class org.snpeff.geneOntology.GoTerm
-
Calculate node's level
- getLine() - Method in class org.snpeff.fileIterator.FileIterator
- getLine() - Method in class org.snpeff.interval.GenericMarker
- getLine() - Method in class org.snpeff.sam.SamEntry
- getLine() - Method in class org.snpeff.vcf.LineChrPos
- getLine() - Method in class org.snpeff.vcf.VcfEntry
-
Original VCF line (from file)
- getLine(long) - Method in class org.snpeff.vcf.FileIndexChrPos
-
Get the line where 'pos' hits
- getLineNum() - Method in class org.snpeff.fileIterator.FastqFileIterator
- getLineNum() - Method in class org.snpeff.fileIterator.FileIterator
- getLineNum() - Method in class org.snpeff.vcf.VcfEntry
- getLines() - Method in class org.snpeff.vcf.VcfHeader
- getLineSlow(long) - Method in class org.snpeff.vcf.FileIndexChrPos
-
A slow method for getLine
- getLocations() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- getLocusName() - Method in class org.snpeff.genBank.Features
- getLofDeleteProteinCodingBases() - Method in class org.snpeff.snpEffect.Config
- getLofIgnoreProteinCodingAfter() - Method in class org.snpeff.snpEffect.Config
- getLofIgnoreProteinCodingBefore() - Method in class org.snpeff.snpEffect.Config
- getLogOdds(char, int) - Method in class org.snpeff.motif.Pwm
- getLong(String, long) - Method in class org.snpeff.snpEffect.Config
-
Get a property as a long
- getMapq() - Method in class org.snpeff.sam.SamEntry
- getMarker() - Method in class org.snpeff.snpEffect.VariantEffect
- getMarker() - Method in class org.snpeff.snpEffect.VariantEffectFusion
- getMarker() - Method in class org.snpeff.snpEffect.VariantEffectStructural
- getMarker(Genome) - Method in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
-
Create a MicroRnaBindingSite marker
- getMarkerById(int) - Method in class org.snpeff.serializer.MarkerSerializer
- getMarkers() - Method in class org.snpeff.interval.Markers
- getMarkers() - Method in class org.snpeff.nextProt.NextProtMarkerFactory
- getMarkers() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- getMarkerTypes() - Method in class org.snpeff.coverage.CountReads
- getMarkerTypes() - Method in class org.snpeff.coverage.CountReadsOnMarkers
- getMaturePeptideId() - Method in class org.snpeff.genBank.Feature
-
Create an ID based on a feature
- getMax() - Method in class org.snpeff.stats.FloatStats
- getMax() - Method in class org.snpeff.stats.IntStats
- getMaxBins() - Method in class org.snpeff.stats.IntStats
- getMaxBins() - Method in class org.snpeff.stats.plot.GoogleHistogram
- getMaxCount() - Method in class org.snpeff.stats.IntStats
- getMaxMismatchRate() - Method in class org.snpeff.pdb.ProteinInteractions
- getMaxPvalueAdjusted() - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- getMaxRank() - Method in class org.snpeff.geneOntology.GoTerm
- getMaxRank() - Method in class org.snpeff.geneOntology.GoTerms
- getMaxRank() - Method in class org.snpeff.geneSets.GeneSet
- getMaxRank() - Method in class org.snpeff.geneSets.GeneSetsRanked
-
Get maximum rank
- getMd5() - Method in class org.snpeff.sam.SamHeaderRecordSq
- getMean() - Method in class org.snpeff.stats.IntStats
- getMedian() - Method in class org.snpeff.interval.Markers
-
Calculate the median point in this set of markers
- getMedian() - Method in class org.snpeff.stats.IntStats
-
Calculate the median
- getMin() - Method in class org.snpeff.stats.FloatStats
- getMin() - Method in class org.snpeff.stats.IntStats
- getMinCount() - Method in class org.snpeff.stats.IntStats
- getMinOverlap() - Method in class org.snpeff.overlap.OverlapDnaSeq
- getMissingBySampleUrl() - Method in class org.snpeff.stats.GenotypeStats
- getMissingCategories() - Method in class org.snpeff.nextProt.NextProtHandler
- getMoleculeType() - Method in class org.snpeff.genBank.Features
- getMonitor() - Method in class org.snpeff.reactome.Reactome
- getMonitorTrace() - Method in class org.snpeff.reactome.Reactome
- getMotherId() - Method in class org.snpeff.ped.TfamEntry
- getMultipleValues() - Method in class org.snpeff.fileIterator.GuessTableTypes
- getN() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
- getName() - Method in class org.snpeff.codons.CodonTable
- getName() - Method in class org.snpeff.fileIterator.FastaFileIterator
-
Sequence name (first 'word') It extracts the characters after the leading '>' and before the first space, then removes leading 'chr', 'chr:', etc.
- getName() - Method in class org.snpeff.geneSets.GeneSet
- getName() - Method in class org.snpeff.interval.Intergenic
- getName() - Method in class org.snpeff.interval.Markers
- getName() - Method in class org.snpeff.interval.NextProt
- getName() - Method in class org.snpeff.interval.Regulation
- getName() - Method in class org.snpeff.interval.tree.IntervalForest
- getName() - Method in class org.snpeff.motif.Pwm
- getName() - Method in class org.snpeff.reactome.Entity
- getName(String) - Method in class org.snpeff.snpEffect.Config
- getNames(String) - Method in class org.snpeff.gtex.IdMap
-
Get all names corresponding to this Id
- getNames2index() - Method in class org.snpeff.fileIterator.GuessTableTypes
- getNameSpace() - Method in class org.snpeff.geneOntology.GoTerm
- getNameSpace() - Method in class org.snpeff.geneOntology.GoTerms
- getNewHeaderLines() - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
-
New lines to be added to header
- getNextField() - Method in class org.snpeff.serializer.MarkerSerializer
- getNextFieldBoolean() - Method in class org.snpeff.serializer.MarkerSerializer
- getNextFieldInt() - Method in class org.snpeff.serializer.MarkerSerializer
- getNextFieldMarker() - Method in class org.snpeff.serializer.MarkerSerializer
- getNextFieldMarkers() - Method in class org.snpeff.serializer.MarkerSerializer
- getNextId() - Method in class org.snpeff.serializer.MarkerSerializer
- getNextSize(int) - Static method in class org.snpeff.collections.ArrayUtil
- getNmer() - Method in class org.snpeff.nmer.Nmer
-
Set nmer (binary coded)
- getNumber() - Method in class org.snpeff.vcf.VcfHeaderInfo
- getNumberLabelsXaxis() - Method in class org.snpeff.stats.plot.GooglePlotInt
- getNumberOfSamples() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
- getNumberOfSamples() - Method in class org.snpeff.vcf.VcfEntry
-
number of samples in this VCF file
- getNumberOfSamples() - Method in class org.snpeff.vcf.VcfHeader
-
Number of samples
- getNumTranscripts() - Method in class org.snpeff.vcf.VcfLof
- getNumWords() - Method in class org.snpeff.collections.OpenBitSet
-
Expert: gets the number of longs in the array that are in use
- getOffset() - Method in class org.snpeff.align.NeedlemanWunsch
- getOrCreate(char) - Method in class org.snpeff.spliceSites.AcgtTree
-
Get a node (create it if it doesn't exist)
- getOrCreate(K) - Method in class org.snpeff.collections.AutoHashMap
- getOrCreate(K) - Method in class org.snpeff.collections.MultivalueHashMap
-
Get a list of values (or create it if not available)
- getOrCreateChromosome(String) - Method in class org.snpeff.interval.Genome
-
Get or create a chromosome
- getOrCreateChromosome(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Get a chromosome.
- getOrCreateIsoform(String) - Method in class org.snpeff.nextProt.NextProtXmlEntry
- getOrCreateTree(String) - Method in class org.snpeff.interval.tree.IntervalForest
-
Get (or create) an interval tree for ID
- getOrCreateTreeChromo(String) - Method in class org.snpeff.interval.tree.IntervalForest
-
Get (or create) an interval tree based for "chromo" (chromosome name)
- getOrganism() - Method in class org.snpeff.genBank.Features
- getOriginal() - Method in class org.snpeff.vcf.PedigreeEntry
- getOriginalNum() - Method in class org.snpeff.vcf.PedigreeEntry
- getOsCmd() - Method in class org.snpeff.osCmd.OsCmdRunner
- getOutput() - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- getOutput() - Method in class org.snpeff.reactome.Entity
- getOutput() - Method in class org.snpeff.SnpEff
- getOutputs() - Method in class org.snpeff.reactome.events.Reaction
- getOverlapFilter() - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
- getParent() - Method in class org.snpeff.interval.Interval
- getParent() - Method in class org.snpeff.interval.Marker
- getParentId() - Method in class org.snpeff.interval.MarkerParentId
- getParents() - Method in class org.snpeff.geneOntology.GoTerm
- getPdbOrganismCommon() - Method in class org.snpeff.pdb.ProteinInteractions
- getPdbOrganismScientific() - Method in class org.snpeff.pdb.ProteinInteractions
- getPdbResolution() - Method in class org.snpeff.pdb.ProteinInteractions
- getPedigree() - Method in class org.snpeff.vcf.VcfHeader
-
Get pedigree (if any)
- getPercentAffected() - Method in class org.snpeff.vcf.VcfLof
- getPercentAffectedStr() - Method in class org.snpeff.vcf.VcfLof
- getPhenotype() - Method in class org.snpeff.ped.TfamEntry
- getPlinkMap() - Method in class org.snpeff.ped.PedFileIterator
- getPlinkMap() - Method in class org.snpeff.ped.PedPedigree
- getPlotGene() - Method in class org.snpeff.stats.VariantEffectStats
-
Barplot of different gene regions
- getPlotMaxData() - Method in class org.snpeff.stats.plot.GooglePlotInt
- getPlotSizeX() - Method in class org.snpeff.stats.plot.GooglePlotInt
- getPlotSizeY() - Method in class org.snpeff.stats.plot.GooglePlotInt
- getPnext() - Method in class org.snpeff.sam.SamEntry
- getPos() - Method in class org.snpeff.sam.SamEntry
- getPos1OneBased() - Method in class org.snpeff.stats.TranslocationReport
-
Get position (as one-based coordinates)
- getPos2OneBased() - Method in class org.snpeff.stats.TranslocationReport
-
Get position (as one-based coordinates)
- getPosition() - Method in class org.snpeff.ped.PedGenotype
- getPosition(int) - Method in class org.snpeff.ped.PlinkMap
- getProb() - Method in class org.snpeff.stats.ReadsOnMarkersModel
- getProgress() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- getProgress() - Method in class org.snpeff.osCmd.OsCmdRunner
- getProgress() - Method in interface org.snpeff.osCmd.Progress
- getProperty(String) - Method in class org.snpeff.snpEffect.Config
- getProteinByTrId() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- getProteinByTrId() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
- getProteinId() - Method in class org.snpeff.interval.GffMarker
- getProteinId() - Method in class org.snpeff.interval.Transcript
- getProteinId() - Method in class org.snpeff.pdb.PdbFile
- getProteinIds() - Method in class org.snpeff.nextProt.NextProtXmlIsoform
- getPvalue() - Method in class org.snpeff.geneSets.Result
- getPvalueAdjusted() - Method in class org.snpeff.geneSets.Result
-
P-Value adjusted using
- getPvalueDouble() - Method in class org.snpeff.geneSets.Result
- getPwd() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- getPwm() - Method in class org.snpeff.interval.Motif
- getPwm(String) - Method in class org.snpeff.motif.Jaspar
- getPwmId() - Method in class org.snpeff.interval.Motif
- getPwmName() - Method in class org.snpeff.interval.Motif
- getQname() - Method in class org.snpeff.sam.SamEntry
- getQual() - Method in class org.snpeff.sam.SamEntry
- getQuality() - Method in class org.snpeff.binseq.DnaAndQualitySequence
-
Get quality string (encoded FastQ-Sanger style)
- getQuality() - Method in class org.snpeff.vcf.VcfEntry
- getQuality(int) - Method in class org.snpeff.binseq.DnaAndQualitySequence
- getQualityStats() - Method in class org.snpeff.stats.VcfStats
- getQualityStatsHistoUrl() - Method in class org.snpeff.stats.VcfStats
- getQuantile(double) - Method in class org.snpeff.stats.IntStats
-
Get value at a given quantile
- getRank() - Method in class org.snpeff.interval.Exon
- getRank() - Method in class org.snpeff.interval.Intron
- getRank() - Method in class org.snpeff.vcf.VcfEffect
- getRank(String) - Method in class org.snpeff.geneOntology.GoTerms
-
Get symbol's rank
- getRank(String) - Method in class org.snpeff.geneSets.GeneSetsRanked
-
Get gene's rank
- getRankByGene() - Method in class org.snpeff.geneSets.GeneSetsRanked
-
Get geneId invalid input: '<'-> Rank mapping
- getRankedGenesCount() - Method in class org.snpeff.geneSets.GeneSet
- getRankedSetsCount() - Method in class org.snpeff.geneSets.GeneSetsRanked
-
How many gene sets have ranked genes (i.e.
- getRankedSymbols() - Method in class org.snpeff.geneOntology.GoTerm
- getRankMax() - Method in class org.snpeff.vcf.VcfEffect
- getRankSum() - Method in class org.snpeff.geneSets.GeneSet
- getRankSum() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
- getRankSymbolId() - Method in class org.snpeff.geneOntology.GoTerms
- getRareThreshold() - Method in class org.snpeff.codons.FindRareAaIntervals
- getRateOfChange() - Method in class org.snpeff.stats.VariantStats
-
Rate of change
- getRateOfChangeByChromosome(String) - Method in class org.snpeff.stats.VariantStats
-
Rate of change by chromosome
- getRawCountBases() - Method in class org.snpeff.stats.ReadsOnMarkersModel
- getRawCountMarkers() - Method in class org.snpeff.stats.ReadsOnMarkersModel
- getReadLengthAvg() - Method in class org.snpeff.coverage.CountReads
-
Average read length
- getReadLengthAvg() - Method in class org.snpeff.coverage.CountReadsOnMarkers
-
Average read length
- getReadLengthCount() - Method in class org.snpeff.coverage.CountReads
- getReadLengthSum() - Method in class org.snpeff.coverage.CountReads
- getRecords(String) - Method in class org.snpeff.sam.SamHeader
-
Get a list of records for this 'recordType'
- getRecordTypeCode() - Method in class org.snpeff.sam.SamHeaderRecord
- getRedirectStderr() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- getRedirectStdout() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- getRedirectTo() - Method in class org.snpeff.osCmd.StreamGobbler
- getRef() - Method in class org.snpeff.vcf.VcfEntry
- getReference() - Method in class org.snpeff.interval.Variant
- getReference(int, int) - Static method in class org.snpeff.binseq.comparator.SequenceReference
- getReference(String) - Method in class org.snpeff.snpEffect.Config
- getReferences() - Method in class org.snpeff.genBank.Features
- getRefRealign() - Method in class org.snpeff.align.VariantRealign
- getRegFileNames() - Method in class org.snpeff.RegulationFileSplitBytType
- getRegTypes() - Method in class org.snpeff.RegulationFileConsensus
- getRegTypes() - Method in class org.snpeff.RegulationFileSplitBytType
- getRegulationList(String) - Method in class org.snpeff.RegulationFileConsensus
-
Get regulation list by type (or create a new list)
- getRegulationType() - Method in class org.snpeff.interval.Regulation
- getRegulator() - Method in class org.snpeff.reactome.events.Reaction
- getRes() - Method in class org.snpeff.logStatsServer.LogStats
- getRight() - Method in class org.snpeff.interval.tree.IntervalNode
- getRight() - Method in class org.snpeff.interval.tree.IntervalNodeOri
- getRname() - Method in class org.snpeff.sam.SamEntry
- getRnext() - Method in class org.snpeff.sam.SamEntry
- getSampleIds() - Method in class org.snpeff.ped.PedPedigree
-
Get a list of sample IDs
- getSampleNames() - Method in class org.snpeff.fileIterator.VcfFileIterator
-
Get sample names
- getSampleNames() - Method in class org.snpeff.vcf.VcfHeader
-
Get sample names
- getSampleNum(String) - Method in class org.snpeff.vcf.VcfHeader
-
Sample number (position in "#CHROM" line)
- getSamples() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
- getScore() - Method in class org.snpeff.interval.Custom
- getScore() - Method in class org.snpeff.interval.VariantWithScore
- getScore(int) - Method in class org.snpeff.gsa.ChrPosScoreList
- getScore(int) - Method in class org.snpeff.gsa.ScoreList
- getScore(String) - Method in class org.snpeff.stats.CountByType
-
Score for this type
- getSecond() - Method in class org.snpeff.util.Tuple
- getSeq() - Method in class org.snpeff.sam.SamEntry
- getSeq1() - Method in class org.snpeff.binseq.DnaSequencePe
- getSeq2() - Method in class org.snpeff.binseq.DnaSequencePe
- getSeqIdx(long) - Static method in class org.snpeff.binseq.comparator.SequenceReference
- getSequence() - Method in class org.snpeff.binseq.BinarySequence
-
Get the sequence as a String
- getSequence() - Method in class org.snpeff.binseq.DnaAndQualitySequence
- getSequence() - Method in class org.snpeff.binseq.DnaSequence
- getSequence() - Method in class org.snpeff.binseq.DnaSequencePe
- getSequence() - Method in class org.snpeff.genBank.Features
- getSequence() - Method in class org.snpeff.interval.Chromosome
- getSequence() - Method in class org.snpeff.interval.MarkerSeq
-
Get sequence WARNING: Sequence is always according to coding strand.
- getSequence() - Method in class org.snpeff.interval.Utr5prime
- getSequence() - Method in class org.snpeff.nextProt.NextProtXmlIsoform
- getSequence(Marker) - Method in class org.snpeff.interval.MarkerSeq
-
Get sequence intersecting 'marker' WARNING: Sequence is always according to coding strand.
- getSequenceLength() - Method in class org.snpeff.genBank.Features
- getSequenceName() - Method in class org.snpeff.sam.SamHeaderRecordSq
- getSex() - Method in class org.snpeff.ped.TfamEntry
- getShape() - Method in class org.snpeff.genBank.Features
- getShrinkSize(int, int) - Static method in class org.snpeff.collections.ArrayUtil
- getSilentRatio() - Method in class org.snpeff.stats.VariantEffectStats
- getSizeByType(String, String) - Method in class org.snpeff.stats.GeneCountByTypeTable
- getSnpEffCmdCds() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
- getSnpEffCmdProtein() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
- getSnpEffectPredictor() - Method in class org.snpeff.snpEffect.Config
- getSource() - Method in class org.snpeff.genBank.Features
- getSpecies() - Method in class org.snpeff.interval.Genome
- getSpecies() - Method in class org.snpeff.sam.SamHeaderRecordSq
- getSpliceRegionExonSize() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- getSpliceRegionIntronMax() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- getSpliceRegionIntronMin() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- getSpliceSites() - Method in class org.snpeff.interval.Exon
- getSpliceSites() - Method in class org.snpeff.interval.Intron
- getSpliceType() - Method in class org.snpeff.interval.Exon
- getSpliceType() - Method in class org.snpeff.interval.Intron
- getSplitFileNames() - Method in class org.snpeff.fastq.FastqSplit
- getStart() - Method in class org.snpeff.genBank.Feature
- getStart() - Method in class org.snpeff.interval.Interval
- getStart(int) - Method in class org.snpeff.gsa.ChrPosScoreList
- getStart(long) - Static method in class org.snpeff.binseq.comparator.SequenceReference
- getStart(String) - Method in class org.snpeff.vcf.FileIndexChrPos
-
Get position where 'chr' starts
- getStd() - Method in class org.snpeff.stats.IntStats
-
Calculate the standard deviation
- getStderr() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- getStderr() - Method in class org.snpeff.osCmd.OsCmdRunner
- getStdin() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- getStdout() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- getStdout() - Method in class org.snpeff.osCmd.OsCmdRunner
- getStdOutFilter() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- getStr() - Method in class org.snpeff.vcf.VcfEntry
- getStrand() - Method in class org.snpeff.interval.Interval
- getString(String) - Method in class org.snpeff.snpEffect.Config
-
Get a property as a string
- getString(String, String) - Method in class org.snpeff.snpEffect.Config
-
Get a property as a string
- getSubType(Marker) - Method in class org.snpeff.coverage.MarkerTypes
-
Some markers have sub-types
- getSum() - Method in class org.snpeff.stats.Average
- getSum() - Method in class org.snpeff.stats.AverageInt
- getSum() - Method in class org.snpeff.stats.FloatStats
- getSum() - Method in class org.snpeff.stats.IntStats
- getSvgPlot() - Method in class org.snpeff.stats.TranslocationReport
- getSymbolIdSet() - Method in class org.snpeff.geneOntology.GoTerm
-
Number of symbols in this node (total = interesting + not-interesting)
- getTable(String) - Method in class org.snpeff.codons.CodonTables
-
Get a codon table by name
- getTable(Genome) - Method in class org.snpeff.codons.CodonTables
-
Get default genome-wide codon table
- getTable(Genome, String) - Method in class org.snpeff.codons.CodonTables
-
Get a codon table WARNING: It will return the standard codon table if nothing if found
- getTags() - Method in class org.snpeff.interval.GffMarker
- getTags() - Method in class org.snpeff.interval.Transcript
- getTissueType() - Method in class org.snpeff.gtex.GtexExperiment
- getTissueTypeDetail() - Method in class org.snpeff.gtex.GtexExperiment
- getTitle() - Method in class org.snpeff.stats.plot.GooglePlotInt
- getTlen() - Method in class org.snpeff.sam.SamEntry
- getTotal() - Method in class org.snpeff.stats.ChrPosStats
- getTotalCount() - Method in class org.snpeff.geneOntology.GoTerm
-
Number of symbols in this node (total = interesting + not-interesting)
- getTotalCount() - Method in class org.snpeff.motif.Pwm
- getTotalCount() - Method in class org.snpeff.spliceSites.AcgtTree
- getTotalCount() - Method in class org.snpeff.stats.CountByType
- getTotalErrors() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- getTotalErrs() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- getTotalNotFound() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- getTotalOk() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- getTotalWarnings() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- getTranscript() - Method in class org.snpeff.snpEffect.VariantEffect
- getTranscript(String) - Method in class org.snpeff.pdb.ProteinInteractions
- getTranscript(String) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- getTranscriptBiotype() - Method in class org.snpeff.interval.GffMarker
- getTranscriptId() - Method in class org.snpeff.genBank.Feature
-
Create a transcript ID based on a feature
- getTranscriptId() - Method in class org.snpeff.interval.GffMarker
- getTranscriptId() - Method in class org.snpeff.interval.NextProt
- getTranscriptId() - Method in class org.snpeff.vcf.VcfEffect
- getTranscriptIds() - Method in class org.snpeff.nextProt.NextProtXmlIsoform
- getTranscriptSupportLevel() - Method in class org.snpeff.interval.Transcript
- getTranscriptTsl() - Method in class org.snpeff.interval.GffMarker
- getTranscriptVersion() - Method in class org.snpeff.interval.GffMarker
- getTransitions() - Method in class org.snpeff.stats.TsTvStats
- getTransversions() - Method in class org.snpeff.stats.TsTvStats
- getTree(String) - Method in class org.snpeff.interval.tree.IntervalForest
-
Get an interval tree using an ID
- getTreeChromo(String) - Method in class org.snpeff.interval.tree.IntervalForest
-
Get an interval tree using a chromosome name
- getTrId1() - Method in class org.snpeff.stats.TranslocationReport
- getTrId2() - Method in class org.snpeff.stats.TranslocationReport
- getTrLeft() - Method in class org.snpeff.snpEffect.VariantEffectFusion
- getTrRight() - Method in class org.snpeff.snpEffect.VariantEffectFusion
- getTss() - Method in class org.snpeff.interval.Transcript
-
Create a TSS marker
- getTsTvRatio() - Method in class org.snpeff.stats.TsTvStats
-
Transitions / transverions ratio WARNING: I removed the '2.0' factor because it mostly confused people.
- getTsTvStats() - Method in class org.snpeff.stats.VcfStats
- getTsTvStatsKnown() - Method in class org.snpeff.stats.VcfStats
- getType() - Method in class org.snpeff.genBank.Feature
- getType() - Method in class org.snpeff.interval.Marker
- getType(String) - Method in class org.snpeff.fileIterator.GuessTableTypes
-
Get field type
- getType(Marker) - Method in class org.snpeff.coverage.MarkerTypes
-
Get marker type
- getTypeList() - Method in class org.snpeff.stats.CountByType
-
List all types (alphabetically sorted) We need it as a getter for summary page (freemarker)
- getTypeList() - Method in class org.snpeff.stats.GeneCountByTypeTable
-
Get a sorted list of keys
- getTypeRank(Marker) - Method in class org.snpeff.coverage.MarkerTypes
-
Get marker + rank (in case of exon or intron)
- getTypes() - Method in class org.snpeff.fileIterator.GuessTableTypes
-
Get an array of types (ordered by column)
- getUpDownStreamLength() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- getUpstream() - Method in class org.snpeff.interval.Transcript
- getUri() - Method in class org.snpeff.sam.SamHeaderRecordSq
- getUtrs() - Method in class org.snpeff.interval.Transcript
-
Get all UTRs
- getValue() - Method in class org.snpeff.util.KeyValue
- getValue(int) - Method in class org.snpeff.gtex.GtexExperiment
- getValue(String) - Method in class org.snpeff.geneSets.GeneSets
-
Get experimental value
- getValue(String) - Method in class org.snpeff.gtex.GtexExperiment
-
Get value by geneID
- getValueByGene() - Method in class org.snpeff.geneSets.GeneSets
- getValues() - Method in class org.snpeff.fileIterator.MatrixEntry
-
Get an array of values
- getVariant() - Method in class org.snpeff.snpEffect.VariantEffect
- getVariantEffect() - Method in class org.snpeff.stats.TranslocationReport
- getVariantRealigned() - Method in class org.snpeff.align.VariantRealign
- getVariantRef() - Method in class org.snpeff.interval.VariantNonRef
- getvariantStats() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- getVariantType() - Method in class org.snpeff.align.VcfRefAltAlign
- getVariantType() - Method in class org.snpeff.interval.Variant
- getVcfEffect() - Method in class org.snpeff.stats.TranslocationReport
- getVcfEffects() - Method in class org.snpeff.vcf.VcfEntry
- getVcfEffects(EffFormatVersion) - Method in class org.snpeff.vcf.VcfEntry
-
Parse 'EFF' info field and get a list of effects
- getVcfEntry() - Method in class org.snpeff.vcf.VariantVcfEntry
- getVcfEntry() - Method in class org.snpeff.vcf.VcfGenotype
- getVcfEntry() - Method in class org.snpeff.vcf.VcfLof
- getVcfFieldString() - Method in class org.snpeff.vcf.VcfEffect
-
String from VCF file (original, unparsed, string)
- getVcfFieldString(int) - Method in class org.snpeff.vcf.VcfEffect
-
Get a subfield as an index
- getVcfFileIterator() - Method in class org.snpeff.vcf.VcfEntry
- getVcfGenotype(int) - Method in class org.snpeff.vcf.VcfEntry
- getVcfGenotypes() - Method in class org.snpeff.vcf.VcfEntry
- getVcfHeader() - Method in class org.snpeff.fileIterator.VcfFileIterator
-
Get VcfHeader
- getVcfHeaderFormat() - Method in class org.snpeff.vcf.VcfHeader
- getVcfHeaderFormat(String) - Method in class org.snpeff.vcf.VcfHeader
- getVcfHeaderInfo() - Method in class org.snpeff.vcf.VcfHeader
-
Get all VcfInfo entries
- getVcfHeaderInfo(String) - Method in class org.snpeff.vcf.VcfHeader
-
Get Info type for a given ID
- getVcfInfo(String) - Method in class org.snpeff.vcf.VcfEntry
-
Get VcfInfo type for a given ID
- getVcfInfoNumber() - Method in class org.snpeff.vcf.VcfHeaderInfo
- getVcfInfoNumber(String) - Method in class org.snpeff.vcf.VcfEntry
-
Get Info number for a given ID
- getVcfInfoType() - Method in class org.snpeff.vcf.VcfHeaderInfo
- getVersion() - Method in class org.snpeff.genBank.Features
- getVersion() - Method in class org.snpeff.interval.Genome
- getVersion() - Method in class org.snpeff.interval.Transcript
- getVersionsUrl() - Method in class org.snpeff.snpEffect.Config
- getWarnCount() - Static method in class org.snpeff.util.Log
- getWarning() - Method in class org.snpeff.snpEffect.VariantEffect
- getWeight() - Method in class org.snpeff.reactome.Entity
- getxAxisLabel() - Method in class org.snpeff.stats.plot.GooglePlotInt
- GFF - Enum constant in enum class org.snpeff.interval.FrameType
- GFF_OFFSET - Static variable in class org.snpeff.fileIterator.MotifFileIterator
- GFF_OFFSET - Static variable in class org.snpeff.fileIterator.RegulationGffFileIterator
- GFF2 - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
- GFF3 - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
- Gff3FileIterator - Class in org.snpeff.fileIterator
-
Opens a sequence change file and iterates over all intervals in GFF3 format.
- Gff3FileIterator(String) - Constructor for class org.snpeff.fileIterator.Gff3FileIterator
- Gff3FileIterator(String, Genome) - Constructor for class org.snpeff.fileIterator.Gff3FileIterator
- Gff3FileIterator(String, Genome, int) - Constructor for class org.snpeff.fileIterator.Gff3FileIterator
- GffMarker - Class in org.snpeff.interval
-
An interval intended as a mark
- GffMarker() - Constructor for class org.snpeff.interval.GffMarker
- GffMarker(Genome, String) - Constructor for class org.snpeff.interval.GffMarker
- GffMarker(Marker, int, int, boolean, String) - Constructor for class org.snpeff.interval.GffMarker
- GffType - Enum Class in org.snpeff.interval
- GoogleBarChart - Class in org.snpeff.stats.plot
- GoogleBarChart(String) - Constructor for class org.snpeff.stats.plot.GoogleBarChart
- GoogleBarChart(String, int, int) - Constructor for class org.snpeff.stats.plot.GoogleBarChart
- GoogleChartVenn - Class in org.snpeff.stats.plot
-
A simple wrapper to goolge charts API (from charts4j) Plots integer data
- GoogleChartVenn(String, String, String, int, int, int, int, int, int, int) - Constructor for class org.snpeff.stats.plot.GoogleChartVenn
- GoogleGenePercentBar - Class in org.snpeff.stats.plot
-
A simple wrapper to goolge charts API (from charts4j)
- GoogleGenePercentBar(String, String, String, double, double, double, double, double, double, double, double, double) - Constructor for class org.snpeff.stats.plot.GoogleGenePercentBar
- GoogleGeneRegionChart - Class in org.snpeff.stats.plot
- GoogleGeneRegionChart(CoverageByType, String) - Constructor for class org.snpeff.stats.plot.GoogleGeneRegionChart
- GoogleGeneRegionNumExonsChart - Class in org.snpeff.stats.plot
- GoogleGeneRegionNumExonsChart(CoverageByType, String, int) - Constructor for class org.snpeff.stats.plot.GoogleGeneRegionNumExonsChart
- GoogleHistogram - Class in org.snpeff.stats.plot
-
A simple wrapper to goolge charts API (from charts4j)
- GoogleHistogram(int[], int[], String, String, String) - Constructor for class org.snpeff.stats.plot.GoogleHistogram
- GoogleLineChart - Class in org.snpeff.stats.plot
- GoogleLineChart(String) - Constructor for class org.snpeff.stats.plot.GoogleLineChart
- GoogleLineChart(String, int, int) - Constructor for class org.snpeff.stats.plot.GoogleLineChart
- GooglePlot - Class in org.snpeff.stats.plot
-
A simple wrapper to goolge charts API (from charts4j)
- GooglePlot(double[], double[], String, String, String) - Constructor for class org.snpeff.stats.plot.GooglePlot
- GooglePlotInt - Class in org.snpeff.stats.plot
-
A simple wrapper to goolge charts API (from charts4j) Plots integer data
- GooglePlotInt(int[], int[], String, String, String) - Constructor for class org.snpeff.stats.plot.GooglePlotInt
- GoTerm - Class in org.snpeff.geneOntology
-
An instance of a GO term (a node in the DAG)
- GoTerm(String, GoTerms, String, String) - Constructor for class org.snpeff.geneOntology.GoTerm
- GoTerm(List<GoTerm>, GoTerms) - Constructor for class org.snpeff.geneOntology.GoTerm
-
Create a new GOTerm by joining all GOTerms in the list
- GoTerms - Class in org.snpeff.geneOntology
-
A collection of GO terms
- GoTerms() - Constructor for class org.snpeff.geneOntology.GoTerms
-
Default constructor
- GoTerms(String, String, String, String, boolean, boolean) - Constructor for class org.snpeff.geneOntology.GoTerms
-
Constructor
- Gpr - Class in org.snpeff.util
-
General pupose rutines
- Gpr() - Constructor for class org.snpeff.util.Gpr
- GprHtml - Class in org.snpeff.util
-
General stuff realted to HTML
- GprHtml() - Constructor for class org.snpeff.util.GprHtml
- GprSeq - Class in org.snpeff.util
- GprSeq() - Constructor for class org.snpeff.util.GprSeq
- greedyPvalue(Result) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
-
Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum)
- greedyPvalue(Result) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
-
Find best p-value using a greedy algorithm (smaller gene sets first)
- greedyPvalue(Result, int, int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
-
Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum) Only look for genesets within [minGeneSetSize, maxGeneSetSize] size range
- group - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- grow(byte[]) - Static method in class org.snpeff.collections.ArrayUtil
- grow(byte[], int) - Static method in class org.snpeff.collections.ArrayUtil
- grow(int[]) - Static method in class org.snpeff.collections.ArrayUtil
- grow(int[], int) - Static method in class org.snpeff.collections.ArrayUtil
- grow(long[]) - Static method in class org.snpeff.collections.ArrayUtil
- grow(long[], int) - Static method in class org.snpeff.collections.ArrayUtil
- GT_FIELD_ALLELIC_DEPTH_OF_COVERAGE - Static variable in class org.snpeff.vcf.VcfGenotype
- GT_FIELD_DEPTH_OF_COVERAGE - Static variable in class org.snpeff.vcf.VcfGenotype
- Gtex - Class in org.snpeff.gtex
-
Load data from GTEx files.
- Gtex() - Constructor for class org.snpeff.gtex.Gtex
- GtexExperiment - Class in org.snpeff.gtex
-
A 'column' in a GTEx file (values from one experiment
- GtexExperiment(Gtex, String) - Constructor for class org.snpeff.gtex.GtexExperiment
- GtexExperiment(Gtex, String, String, String) - Constructor for class org.snpeff.gtex.GtexExperiment
- GTF22 - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
- Gtf2Marker - Class in org.snpeff.interval
-
An interval intended as a mark
- Gtf2Marker() - Constructor for class org.snpeff.interval.Gtf2Marker
- Gtf2Marker(Genome, String) - Constructor for class org.snpeff.interval.Gtf2Marker
- Gtf2Marker(Marker, int, int, boolean, String) - Constructor for class org.snpeff.interval.Gtf2Marker
- guessGenesFormat() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
-
Try to guess database format by checking which file type is present
- guessNewLineChars() - Method in class org.snpeff.fileIterator.FileIterator
-
Guess number of newline characters used (e.g.
- GuessTableTypes - Class in org.snpeff.fileIterator
-
Given a table in a TXT file, try to guess the value types for each column
- GuessTableTypes(String) - Constructor for class org.snpeff.fileIterator.GuessTableTypes
- guessType(String) - Method in class org.snpeff.fileIterator.GuessTableTypes
-
Guess data type for this value
- guessTypes() - Method in class org.snpeff.fileIterator.GuessTableTypes
-
Find column names form header and guess data types from values
- GZIP_EXTENTIONS - Static variable in class org.snpeff.util.Gpr
H
- has(String) - Method in class org.snpeff.ped.PedGenotype
-
Is 'genotype' in this one?
- hasAdditionalAnnotations() - Method in class org.snpeff.snpEffect.VariantEffect
-
Do we have an associated marker with additional annotations?
- hasAnnotations() - Method in class org.snpeff.interval.Custom
-
Do we have additional annotations?
- hasAnnotations() - Method in class org.snpeff.interval.GffMarker
-
When annotating a VCF file, add fields from this GFF
- hasAttr(String) - Method in class org.snpeff.interval.GffMarker
- hasCds() - Method in class org.snpeff.interval.Transcript
- hasChromosome(String) - Method in class org.snpeff.binseq.GenomicSequences
-
Do we have sequence information for this chromosome?
- hasChromosome(String) - Method in class org.snpeff.interval.Genome
-
Is this chromosome in this genome?
- hasCodingInfo() - Method in class org.snpeff.interval.Genome
- hasCount(String) - Method in class org.snpeff.stats.CountByType
- hasCvTerm() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- hasData() - Method in class org.snpeff.stats.AlleleCountStats
- hasData() - Method in class org.snpeff.stats.CountByType
- hasData() - Method in class org.snpeff.stats.GenotypeStats
- hasData() - Method in class org.snpeff.stats.HomHetStats
- hasData() - Method in interface org.snpeff.stats.SamplingStats
-
Does this statistic have any data?
- hasData() - Method in class org.snpeff.stats.TsTvStats
-
Does this stat have any data
- hasData() - Method in class org.snpeff.stats.VariantEffectStats
- hasData() - Method in class org.snpeff.stats.VariantStats
- hasData() - Method in class org.snpeff.stats.VariantTypeStats
- hasData() - Method in class org.snpeff.stats.VcfStats
- hasEffectImpact(VariantEffect.EffectImpact) - Method in class org.snpeff.snpEffect.VariantEffect
- hasEffectType(EffectType) - Method in class org.snpeff.snpEffect.VariantEffect
- hasEffectType(EffectType) - Method in class org.snpeff.vcf.VcfEffect
-
Does it have 'effType' ?
- hasError() - Method in class org.snpeff.interval.Transcript
-
Does this transcript have any errors?
- hasError() - Method in class org.snpeff.snpEffect.VariantEffect
- hasErrorOrWarning() - Method in class org.snpeff.interval.Transcript
-
Does this transcript have any errors?
- hasField(String) - Method in class org.snpeff.vcf.VcfEntry
- hasFormat(VcfHeaderFormat) - Method in class org.snpeff.vcf.VcfHeader
-
Do we already have this 'format' entry?
- hasGene(String) - Method in class org.snpeff.geneSets.GeneSet
- hasGene(String) - Method in class org.snpeff.geneSets.GeneSets
- hasGenotypes() - Method in class org.snpeff.vcf.VcfEntry
- hashCode() - Method in class org.snpeff.binseq.BinarySequence
- hashCode() - Method in class org.snpeff.binseq.DnaAndQualitySequence
- hashCode() - Method in class org.snpeff.binseq.DnaSequence
- hashCode() - Method in class org.snpeff.binseq.DnaSequenceByte
- hashCode() - Method in class org.snpeff.binseq.DnaSequencePe
- hashCode() - Method in class org.snpeff.collections.OpenBitSet
- hashCode() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- hashCode() - Method in class org.snpeff.interval.Interval
- hashCode() - Method in class org.snpeff.interval.Variant
- hashCode() - Method in class org.snpeff.nmer.Nmer
- hashCode() - Method in class org.snpeff.util.KeyValue
- hashCode() - Method in class org.snpeff.util.Tuple
- hashCode(byte[], int, int) - Static method in class org.snpeff.collections.ArrayUtil
-
Returns hash of chars in range start (inclusive) to end (inclusive)
- hashCode(char[], int, int) - Static method in class org.snpeff.collections.ArrayUtil
-
Returns hash of chars in range start (inclusive) to end (inclusive)
- HashLongLongArray - Class in org.snpeff.collections
-
A Hashinvalid input: '<'long, long[]> using primitive types instead or warped object The idea is to be able to add many long values for each key This could be implemented by simply doing HashMapinvalid input: '<'Long, Set
> (but it would consume much more memory) Note: We call each 'long[]' a bucket WARNING: This collection does NOT allow elements to be deleted! But you can replace values. - HashLongLongArray() - Constructor for class org.snpeff.collections.HashLongLongArray
- hasInfo(String) - Method in class org.snpeff.vcf.VcfEntry
- hasInfo(VcfHeaderInfo) - Method in class org.snpeff.vcf.VcfHeader
-
Do we already have this 'info' header?
- hasIUB(String) - Static method in class org.snpeff.util.IubString
-
Does the string have ANY IUB base?
- hasIUBMax(String) - Static method in class org.snpeff.util.IubString
-
Does the string have at most 'MAX_IUB_BASES' IUB bases?
- hasMapq() - Method in class org.snpeff.sam.SamEntry
-
Some aligners just use '255' in the mapping quality field (bowtie)
- hasMarker() - Method in class org.snpeff.snpEffect.VariantEffects
- hasMultipleCoordinates() - Method in class org.snpeff.genBank.Feature
- hasNext() - Method in class org.snpeff.fileIterator.BinSeqFileIterator
- hasNext() - Method in class org.snpeff.fileIterator.FastqFileIterator
- hasNext() - Method in class org.snpeff.fileIterator.FileIterator
- hasNext() - Method in class org.snpeff.fileIterator.VariantTxtFileIterator
- hasNext() - Method in class org.snpeff.genBank.FeaturesFile
- hasNext() - Method in class org.snpeff.interval.IntervalSetIterator
- hasNext() - Method in class org.snpeff.util.CombinatorialIterator
- hasNext() - Method in class org.snpeff.util.IubString
- hasOutput() - Method in class org.snpeff.reactome.Entity
- hasProteinId() - Method in class org.snpeff.interval.Transcript
- hasQuality() - Method in class org.snpeff.vcf.VcfEntry
- hasScore(String) - Method in class org.snpeff.stats.CountByType
- hasSeek() - Method in class org.snpeff.fileIterator.FileIterator
-
Is 'seek' operation supported?
- hasSequence() - Method in class org.snpeff.interval.MarkerSeq
-
Do we have a sequence for this exon?
- hasTag(String) - Method in class org.snpeff.interval.Transcript
-
Does this transcript have 'tag'?
- hasTags() - Method in class org.snpeff.interval.Transcript
- hasTitle - Variable in class org.snpeff.fileIterator.TableFile
- hasTranscriptSupportLevelInfo() - Method in class org.snpeff.interval.Genome
-
Do we have coding info from genes?
- hasTranscriptSupportLevelInfo() - Method in class org.snpeff.interval.Transcript
- hasTree(String) - Method in class org.snpeff.interval.tree.IntervalForest
-
Is the tree 'chromo' available?
- hasValidCoords() - Method in class org.snpeff.pdb.DistanceResult
- hasValue(String) - Method in class org.snpeff.geneSets.GeneSets
- hasWarning() - Method in class org.snpeff.interval.Transcript
-
Does this transcript have any errors?
- hasWarning() - Method in class org.snpeff.snpEffect.VariantEffect
- head - Variable in class org.snpeff.interval.tree.IntervalTree
- head - Variable in class org.snpeff.interval.tree.IntervalTreeOri
- head(Object) - Static method in class org.snpeff.util.Gpr
- HEAD_SIZE - Static variable in class org.snpeff.osCmd.StreamGobbler
- header - Variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
- heatMapColor(double, double, double, int, int) - Static method in class org.snpeff.util.GprHtml
-
Create a color (heat-map) based in a value and maximum possible value
- heatMapColor(long, long, long, int, int) - Static method in class org.snpeff.util.GprHtml
-
Create a color (heat-map) based in a value and maximum possible value
- help - Variable in class org.snpeff.SnpEff
- hgvs - Variable in class org.snpeff.SnpEff
- Hgvs - Class in org.snpeff.snpEffect
-
HGSV notation References: http://www.hgvs.org/
- Hgvs(VariantEffect) - Constructor for class org.snpeff.snpEffect.Hgvs
- HgvsDna - Class in org.snpeff.snpEffect
-
Coding DNA reference sequence References http://www.hgvs.org/mutnomen/recs.html Nucleotide numbering: - there is no nucleotide 0 - nucleotide 1 is the A of the ATG-translation initiation codon - the nucleotide 5' of the ATG-translation initiation codon is -1, the previous -2, etc.
- HgvsDna(VariantEffect) - Constructor for class org.snpeff.snpEffect.HgvsDna
- hgvsForce - Variable in class org.snpeff.SnpEff
- hgvsOld - Variable in class org.snpeff.SnpEff
- hgvsOneLetterAa - Variable in class org.snpeff.SnpEff
- HgvsProtein - Class in org.snpeff.snpEffect
-
Coding change in HGVS notation (amino acid changes) References: http://www.hgvs.org/mutnomen/recs.html
- HgvsProtein(VariantEffect) - Constructor for class org.snpeff.snpEffect.HgvsProtein
- hgvsShift - Variable in class org.snpeff.SnpEff
- hgvsTrId - Variable in class org.snpeff.SnpEff
- hgvsTrId - Variable in class org.snpeff.snpEffect.Hgvs
- HIGH - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.EffectImpact
- highestImpact(String) - Method in class org.snpeff.snpEffect.VariantEffects
-
Find the highest impact effect for transcript 'trId'
- HIGHLY_CONSERVED_AA_COUNT - Static variable in class org.snpeff.nextProt.NextProtSequenceConservation
- HIGHLY_CONSERVED_AA_PERCENT - Static variable in class org.snpeff.nextProt.NextProtSequenceConservation
- hline(int) - Method in class org.snpeff.svg.Svg
- HOME - Static variable in class org.snpeff.PromoterSequences
- HOME - Static variable in class org.snpeff.util.Gpr
- HomHetStats - Class in org.snpeff.stats
-
Count Hom/Het per sample From Pierre: For multiple ALT, I suggest to count the number of REF allele 0/1 => ALT1 0/2 => ALT1 1/1 => ALT2 2/2 => ALT2 1/2 => ALT2
- HomHetStats() - Constructor for class org.snpeff.stats.HomHetStats
- html() - Method in class org.snpeff.coverage.CountReadsOnMarkers
-
Show charts in html
- HTML_BG_COLOR - Static variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- HTML_BG_COLOR_TITLE - Static variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- HTML_HEIGHT - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- HTML_TD_GENES_MAX_LEN - Static variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- HTML_WIDTH - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- HTTP_PROTOCOL - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
- HUGE_DELETION_RATIO_THRESHOLD - Static variable in class org.snpeff.interval.Variant
- HUGE_DELETION_SIZE_THRESHOLD - Static variable in class org.snpeff.interval.Variant
- hypergeometric(int, int, int, int) - Method in class org.snpeff.probablility.Hypergeometric
-
See http://en.wikipedia.org/wiki/Hypergeometric_distribution
- Hypergeometric - Class in org.snpeff.probablility
-
Calculate hypergeometric distribution using an optimized algorithm that avoids problems with big factorials.
I
- id - Variable in class org.snpeff.fileIterator.MatrixEntry
- id - Variable in class org.snpeff.interval.Interval
- id - Variable in class org.snpeff.reactome.Entity
- id - Variable in class org.snpeff.vcf.VcfHeaderEntry
- id() - Static method in class org.snpeff.binseq.IdGenerator
- id() - Method in class org.snpeff.svg.Svg
- id() - Method in class org.snpeff.svg.SvgTranscript
- ID - Enum constant in enum class org.snpeff.genBank.Feature.Type
- idChain() - Method in class org.snpeff.interval.Marker
- idChain(String, String, boolean) - Method in class org.snpeff.interval.Marker
- idChain(String, String, boolean, VariantEffect) - Method in class org.snpeff.interval.Marker
-
A list of all IDs and parent IDs until chromosome
- IdGenerator - Class in org.snpeff.binseq
-
Generates Id
- IdGenerator() - Constructor for class org.snpeff.binseq.IdGenerator
- IdMap - Class in org.snpeff.gtex
-
Maps many IDs to many Names I.e.
- IdMap() - Constructor for class org.snpeff.gtex.IdMap
- IdMapper - Class in org.snpeff.pdb
-
Map protein ID to transcript ID and vice versa
- IdMapper() - Constructor for class org.snpeff.pdb.IdMapper
- IdMapperEntry - Class in org.snpeff.pdb
-
An entry in a ID mapping file
- IdMapperEntry(String, String) - Constructor for class org.snpeff.pdb.IdMapperEntry
- IG_C_gene - Enum constant in enum class org.snpeff.interval.BioType
- IG_C_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- IG_D_gene - Enum constant in enum class org.snpeff.interval.BioType
- IG_J_gene - Enum constant in enum class org.snpeff.interval.BioType
- IG_J_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- IG_V_gene - Enum constant in enum class org.snpeff.interval.BioType
- IG_V_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- ignoreChromosomeErrors - Variable in class org.snpeff.fileIterator.MarkerFileIterator
- ignoreProteinCodingAfter - Variable in class org.snpeff.snpEffect.LossOfFunction
- ignoreProteinCodingBefore - Variable in class org.snpeff.snpEffect.LossOfFunction
- implicit - Variable in class org.snpeff.vcf.VcfHeaderInfo
- imprecise - Variable in class org.snpeff.interval.Variant
- inc() - Method in class org.snpeff.stats.Counter
- inc() - Method in class org.snpeff.stats.CounterDouble
- inc() - Method in class org.snpeff.util.CombinatorialIterator
- inc(char) - Method in class org.snpeff.spliceSites.AcgtTree
-
Increment counter for a base
- inc(int, int) - Method in class org.snpeff.coverage.CoverageChr
-
Increment a region
- inc(String) - Method in class org.snpeff.stats.CountByType
- inc(String, int) - Method in class org.snpeff.stats.CountByType
-
Increment counter for a given type
- inc(String, int, int) - Method in class org.snpeff.coverage.CountFragments
-
Increment a region
- inc(String, int, int) - Method in class org.snpeff.coverage.Coverage
-
Increment a region
- inc(T) - Method in class org.snpeff.stats.CountByKey
-
Increment (by 1)
- inc(T, int) - Method in class org.snpeff.stats.CountByKey
-
Increment counter for a given type
- incCountFilesPass() - Method in class org.snpeff.pdb.ProteinInteractions
- incCountMapError() - Method in class org.snpeff.pdb.ProteinInteractions
- incCountMapOk() - Method in class org.snpeff.pdb.ProteinInteractions
- includes(Marker) - Method in class org.snpeff.interval.Marker
-
Is 'interval' completely included in 'this'?
- index() - Method in class org.snpeff.vcf.FileIndexChrPos
-
Index chromosomes in the whole file
- indexOf(String) - Method in class org.snpeff.binseq.DnaAndQualitySequence
-
Find the position of 'seq' in this sequence
- info - Variable in class org.snpeff.vcf.VcfEntry
- info(Object) - Static method in class org.snpeff.util.Log
-
Show absolute timer value and a message on STDERR
- INFO_KEY_PATTERN - Static variable in class org.snpeff.vcf.VcfEntry
- INFO_LINE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
- INFO_PREFIX - Static variable in class org.snpeff.vcf.VcfHeader
- INFO_REALIGN_3_PRIME - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- infoFieldName() - Method in enum class org.snpeff.vcf.EffFormatVersion
-
Get INF field name for corresponding format
- infoFieldName(EffFormatVersion) - Static method in class org.snpeff.vcf.VcfEffect
-
Get info field name based on format version
- infoln(Object) - Static method in class org.snpeff.util.Log
-
Show absolute timer value and a message on STDERR (prepend a newline)
- infoStr - Variable in class org.snpeff.vcf.VcfEntry
- init() - Method in class org.snpeff.fileIterator.VcfFileIterator
- init() - Method in class org.snpeff.sam.SamHeaderRecord
-
Initialize records before parsing
- init() - Method in class org.snpeff.sam.SamHeaderRecordSq
- init(String, int) - Method in class org.snpeff.fileIterator.FileIterator
-
Initialize
- init(String, int) - Method in class org.snpeff.fileIterator.MarkerFileIterator
-
Initialize
- initFields() - Method in class org.snpeff.fileIterator.TableFile
-
Map field names to Field objects
- INITIAL_BASES_EXTRA - Static variable in class org.snpeff.align.VariantRealign
- INITIAL_BASES_MULTIPLIER - Static variable in class org.snpeff.align.VariantRealign
- INITIAL_CAPACITY - Static variable in class org.snpeff.interval.tree.IntervalTreeArray
- initialize() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
-
Initialize SnpEff.
- initialize(Config) - Method in class org.snpeff.pdb.ProteinInteractions
-
Initialize class (deferred initialization) Note: This is not done at construction because we don't have a 'Config' object ready (loaded) at the time
- initSamples() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
-
Initialize samples (ranks: 1 to N)
- initStrand() - Method in class org.snpeff.snpEffect.Hgvs
- inOffset - Variable in class org.snpeff.fileIterator.MarkerFileIterator
- inputs - Variable in class org.snpeff.reactome.events.Reaction
- inputStream2StringBuffer(InputStream) - Static method in class org.snpeff.util.Gpr
- ins() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Insertions Insertions add one or more amino acid residues between two existing amino acids and this insertion is not a copy of a sequence immediately 5'-flanking (see Duplication).
- INS - Enum constant in enum class org.snpeff.interval.Variant.VariantType
- inSync - Variable in class org.snpeff.interval.tree.IntervalTree
- inSync - Variable in class org.snpeff.interval.tree.IntervalTreeArray
- inSync - Variable in class org.snpeff.interval.tree.IntervalTreeOri
- Integer - Enum constant in enum class org.snpeff.vcf.VcfInfoType
- interaction - Variable in class org.snpeff.SnpEff
- Intergenic - Class in org.snpeff.interval
-
Interval for in intergenic region
- Intergenic() - Constructor for class org.snpeff.interval.Intergenic
- Intergenic(Chromosome, int, int, boolean, String, String) - Constructor for class org.snpeff.interval.Intergenic
- INTERGENIC - Enum constant in enum class org.snpeff.snpEffect.EffectType
- INTERGENIC_CONSERVED - Enum constant in enum class org.snpeff.interval.GffType
- INTERGENIC_CONSERVED - Enum constant in enum class org.snpeff.snpEffect.EffectType
- IntergenicConserved - Class in org.snpeff.interval
-
Interval for a conserved intergenic region
- IntergenicConserved() - Constructor for class org.snpeff.interval.IntergenicConserved
- IntergenicConserved(Chromosome, int, int, boolean, String) - Constructor for class org.snpeff.interval.IntergenicConserved
- intersect() - Method in class org.snpeff.interval.Markers
-
Perform the intersection of all overlapping sub-intervals
- intersect(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
-
this = this AND other
- intersect(Marker) - Method in class org.snpeff.interval.Marker
-
Intersect of two markers
- intersect(Marker) - Method in class org.snpeff.interval.Markers
-
Intersection between 'marker' and all sub-intervals
- intersect(Markers) - Method in class org.snpeff.interval.tree.IntervalForest
-
Return the intersection of 'markers' and this IntervalForest For each marker 'm' in 'markers' - query the tree to get all markers intersecting 'm' - create a new interval which is the intersection of 'm' with all the resutls from the previous query.
- intersection(GoTerm) - Method in class org.snpeff.geneOntology.GoTerm
-
Intersects this term with 'goTerm' (intersects 'symbolIdSet' and 'interestingSymbolIdSet').
- intersection(GeneSet) - Method in class org.snpeff.geneSets.GeneSet
-
Intersects this term with 'geneSet' (intersects 'geneSet' and 'interestingGeneSet').
- intersectionCount(OpenBitSet, OpenBitSet) - Static method in class org.snpeff.collections.OpenBitSet
-
Returns the popcount or cardinality of the intersection of the two sets.
- intersectMarkers - Variable in class org.snpeff.interval.tree.IntervalTreeArray
- intersects(int, int) - Method in class org.snpeff.interval.Interval
-
Return true if this intersects '[iStart, iEnd]'
- intersects(long) - Method in class org.snpeff.interval.Interval
- intersects(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
-
returns true if the sets have any elements in common
- intersects(Interval) - Method in class org.snpeff.interval.Interval
-
Return true if this intersects 'interval'
- intersects(Marker) - Method in class org.snpeff.interval.Interval
-
Do the intervals intersect?
- intersectsCoreSpliceSite(Marker) - Method in class org.snpeff.interval.SpliceSite
-
Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins.
- intersectsCoreSpliceSite(Marker) - Method in class org.snpeff.interval.SpliceSiteAcceptor
- intersectsCoreSpliceSite(Marker) - Method in class org.snpeff.interval.SpliceSiteBranch
-
These are NOT core splice sites
- intersectsCoreSpliceSite(Marker) - Method in class org.snpeff.interval.SpliceSiteDonor
- intersectsCoreSpliceSite(Marker) - Method in class org.snpeff.interval.SpliceSiteRegion
- intersectsExons() - Method in class org.snpeff.interval.codonChange.CodonChange
-
Does the variant intersect any exons?
- intersectSize(Marker) - Method in class org.snpeff.interval.Interval
-
How much do intervals intersect?
- Interval - Class in org.snpeff.interval
-
A genomic interval.
- Interval() - Constructor for class org.snpeff.interval.Interval
- Interval(Interval, int, int, boolean, String) - Constructor for class org.snpeff.interval.Interval
- INTERVAL - Enum constant in enum class org.snpeff.interval.Variant.VariantType
- IntervalAndSubIntervals<T> - Class in org.snpeff.interval
-
Interval that contains sub intervals.
- IntervalAndSubIntervals() - Constructor for class org.snpeff.interval.IntervalAndSubIntervals
- IntervalAndSubIntervals(Marker, int, int, boolean, String) - Constructor for class org.snpeff.interval.IntervalAndSubIntervals
- IntervalComparatorByEnd - Class in org.snpeff.interval
-
Compare intervals by end position
- IntervalComparatorByEnd() - Constructor for class org.snpeff.interval.IntervalComparatorByEnd
- IntervalComparatorByEnd(boolean) - Constructor for class org.snpeff.interval.IntervalComparatorByEnd
- IntervalComparatorByStart - Class in org.snpeff.interval
-
Compare intervals by start position
- IntervalComparatorByStart() - Constructor for class org.snpeff.interval.IntervalComparatorByStart
- IntervalComparatorByStart(boolean) - Constructor for class org.snpeff.interval.IntervalComparatorByStart
- IntervalForest - Class in org.snpeff.interval.tree
-
A set of interval trees (e.g.
- IntervalForest() - Constructor for class org.snpeff.interval.tree.IntervalForest
- IntervalForest(Markers) - Constructor for class org.snpeff.interval.tree.IntervalForest
- IntervalNode - Class in org.snpeff.interval.tree
-
Node for interval tree structure
- IntervalNode() - Constructor for class org.snpeff.interval.tree.IntervalNode
- IntervalNode(Markers) - Constructor for class org.snpeff.interval.tree.IntervalNode
- IntervalNodeOri - Class in org.snpeff.interval.tree
-
The Node class contains the interval tree information for one single node
- IntervalNodeOri() - Constructor for class org.snpeff.interval.tree.IntervalNodeOri
- IntervalNodeOri(Markers) - Constructor for class org.snpeff.interval.tree.IntervalNodeOri
- intervals - Variable in class org.snpeff.interval.tree.IntervalTree
- intervals - Variable in class org.snpeff.interval.tree.IntervalTreeOri
- intervalsCenter - Variable in class org.snpeff.interval.tree.IntervalNode
- IntervalSetIterator - Class in org.snpeff.interval
-
Iterate over intervals.
- IntervalSetIterator(Markers) - Constructor for class org.snpeff.interval.IntervalSetIterator
- IntervalTree - Class in org.snpeff.interval.tree
-
An Interval Tree is essentially a map from intervals to objects, which can be queried for all data associated with a particular interval of point
- IntervalTree() - Constructor for class org.snpeff.interval.tree.IntervalTree
-
Instantiate a new interval tree with no intervals
- IntervalTree(Markers) - Constructor for class org.snpeff.interval.tree.IntervalTree
-
Instantiate an interval tree with a list of intervals
- IntervalTreeArray - Class in org.snpeff.interval.tree
-
Interval tree structure using arrays This is slightly faster than the new IntervalTree implementation
- IntervalTreeArray() - Constructor for class org.snpeff.interval.tree.IntervalTreeArray
- IntervalTreeArray(Markers) - Constructor for class org.snpeff.interval.tree.IntervalTreeArray
-
Instantiate an interval tree with a list of intervals
- IntervalTreeOri - Class in org.snpeff.interval.tree
-
An Interval Tree is essentially a map from intervals to objects, which can be queried for all data associated with a particular interval of point
- IntervalTreeOri() - Constructor for class org.snpeff.interval.tree.IntervalTreeOri
-
Instantiate a new interval tree with no intervals
- IntervalTreeOri(Markers) - Constructor for class org.snpeff.interval.tree.IntervalTreeOri
-
Instantiate an interval tree with a list of intervals
- IntHisto - Class in org.snpeff.snpEffect
-
Histogram of integer numbers
- IntHisto() - Constructor for class org.snpeff.snpEffect.IntHisto
- intLen(int) - Method in class org.snpeff.binseq.DnaSequencePe
-
Calculate the length of a sequence
- INTRAGENIC - Enum constant in enum class org.snpeff.snpEffect.EffectType
- intron() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
- intron() - Method in class org.snpeff.interval.codonChange.CodonChangeDup
-
Inversion does not intersect any exon
- intron() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
-
Variant affect one intron
- Intron - Class in org.snpeff.interval
-
Intron
- Intron() - Constructor for class org.snpeff.interval.Intron
- Intron(Transcript, int, int, boolean, String, Exon, Exon) - Constructor for class org.snpeff.interval.Intron
- INTRON - Enum constant in enum class org.snpeff.snpEffect.EffectType
- INTRON_CONSERVED - Enum constant in enum class org.snpeff.interval.GffType
- INTRON_CONSERVED - Enum constant in enum class org.snpeff.snpEffect.EffectType
- IntronConserved - Class in org.snpeff.interval
-
Interval for a conserved non-coding region in an intron
- IntronConserved() - Constructor for class org.snpeff.interval.IntronConserved
- IntronConserved(Transcript, int, int, boolean, String) - Constructor for class org.snpeff.interval.IntronConserved
- introns() - Method in class org.snpeff.interval.Transcript
-
Get all introns (lazy init)
- IntStats - Class in org.snpeff.stats
-
A simple class that does some basic statistics on integer numbers
- IntStats() - Constructor for class org.snpeff.stats.IntStats
- INV - Enum constant in enum class org.snpeff.interval.Variant.VariantType
- invalidateSorted() - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Invalidate sorted collections
- is() - Method in class org.snpeff.stats.BooleanMutable
- isAaCheck() - Method in class org.snpeff.interval.Transcript
- isAdjustIfParentDoesNotInclude(Marker) - Method in class org.snpeff.interval.Exon
- isAdjustIfParentDoesNotInclude(Marker) - Method in class org.snpeff.interval.Marker
-
Adjust parent if it does not include child?
- isAdjustIfParentDoesNotInclude(Marker) - Method in class org.snpeff.interval.Transcript
- isAlertDone() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- isAlertDone() - Method in class org.snpeff.osCmd.StreamGobbler
- isAmbiguous(String) - Static method in class org.snpeff.util.GprSeq
-
Are there any ambiguous bases in this sequence?
- isAnn() - Method in enum class org.snpeff.vcf.EffFormatVersion
-
Is this an 'ANN' format?
- isBefore() - Method in class org.snpeff.interval.VariantBnd
- isBiAllelic() - Method in class org.snpeff.vcf.VcfEntry
-
Is this bi-allelic (based ONLY on the number of ALTs) WARINIG: You should use 'calcHetero()' method for a more precise calculation.
- isBinary() - Method in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
-
Is the algorithm base on "interesting / not-interesting" binary clasification?
- isBinary() - Method in class org.snpeff.osCmd.StreamGobbler
- isBinaryStderr() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- isBinaryStdout() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- isBnd() - Method in class org.snpeff.interval.Variant
- isBnd() - Method in class org.snpeff.interval.VariantBnd
- isCanonical() - Method in class org.snpeff.interval.Transcript
- isCase() - Method in class org.snpeff.ped.TfamEntry
-
Is phenotype 'Case'?
- isChecked() - Method in class org.snpeff.interval.Transcript
-
Has this transcript been checked against CDS/DNA/AA sequences?
- isCircular() - Method in class org.snpeff.interval.Chromosome
- isCircular() - Method in class org.snpeff.interval.Interval
-
Is this interval part of a circular chromosome and it spans the 'chromosome zero / chromosome end' line?
- isComplement() - Method in class org.snpeff.genBank.Feature
- isCompressedGenotypes() - Method in class org.snpeff.vcf.VcfEntry
-
Do we have compressed genotypes in "HO,HE,NA" INFO fields?
- isConserved(int) - Method in class org.snpeff.motif.Pwm
-
Is position 'pos' conserved (only one base has non-zero counts)
- isControl() - Method in class org.snpeff.ped.TfamEntry
-
Is phenotype 'Control'?
- isCorrected() - Method in class org.snpeff.interval.CircularCorrection
- isCorrected() - Method in class org.snpeff.interval.Transcript
- isCustom() - Method in class org.snpeff.snpEffect.VariantEffect
- isDebug() - Method in class org.snpeff.fileIterator.FileIterator
- isDebug() - Method in class org.snpeff.interval.CircularCorrection
- isDebug() - Method in class org.snpeff.pdb.ProteinInteractions
- isDebug() - Method in class org.snpeff.snpEffect.Config
- isDeferredAnalysis() - Method in class org.snpeff.interval.Marker
-
Deferred analysis markers must be analyzed after 'standard' ones because their impact depends on other results For instance, a NextProt marker's impact would be different if the variant is synonymous or non-synonymous
- isDeferredAnalysis() - Method in class org.snpeff.interval.NextProt
-
Deferred analysis markers must be analyzed after 'standard' ones because their impact depends on other results For instance, a NextProt marker's impact would be different if the variant is synonymous or non-synonymous
- isDel() - Method in class org.snpeff.interval.Variant
- isDerived() - Method in class org.snpeff.vcf.PedigreeEntry
-
Is this an 'Original-Derived' entry type?
- isDnaCheck() - Method in class org.snpeff.interval.Transcript
- isDone() - Method in class org.snpeff.osCmd.OsCmdRunner
-
Has this runner finished?
- isDownstream(int) - Method in class org.snpeff.interval.Transcript
- isDup() - Method in class org.snpeff.interval.Variant
- isDuplicate() - Method in class org.snpeff.sam.SamEntry
-
PCR or optical duplicate
- isDuplication() - Method in class org.snpeff.snpEffect.HgvsDna
-
Is this a duplication?
- isDuplication() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Is this variant a duplication Reference: http://www.hgvs.org/mutnomen/disc.html#dupins ...the description "dup" (see Standards) may by definition only be used when the additional copy is directly 3'-flanking of the original copy (tandem duplication)
- isEff() - Method in enum class org.snpeff.vcf.EffFormatVersion
-
Id this an 'EFF' format?
- isEffectVcfInfoField(String) - Static method in enum class org.snpeff.vcf.EffFormatVersion
-
Is this one of the VCF INFO keys?
- isElongation() - Method in class org.snpeff.interval.Variant
- isEmpty() - Method in class org.snpeff.binseq.DnaSequence
-
Is this sequence empty?
- isEmpty() - Method in class org.snpeff.binseq.GenomicSequences
- isEmpty() - Method in class org.snpeff.collections.OpenBitSet
-
Returns true if there are no set bits
- isEmpty() - Method in class org.snpeff.genBank.Features
- isEmpty() - Method in class org.snpeff.geneSets.Result
- isEmpty() - Method in class org.snpeff.interval.CytoBands
- isEmpty() - Method in class org.snpeff.interval.Markers
- isEmpty() - Method in class org.snpeff.interval.tree.IntervalTree
- isEmpty() - Method in class org.snpeff.interval.tree.IntervalTreeArray
- isEmpty() - Method in class org.snpeff.interval.tree.IntervalTreeOri
- isEmpty() - Method in interface org.snpeff.interval.tree.Itree
- isEmpty() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- isEmpty() - Method in class org.snpeff.reactome.events.Complex
- isEmpty() - Method in class org.snpeff.reactome.events.Pathway
- isEmpty() - Method in class org.snpeff.snpEffect.VariantEffects
- isEmpty() - Method in class org.snpeff.stats.CountByKey
- isEmpty() - Method in class org.snpeff.stats.CountByType
-
Is this empty
- isEmpty(String) - Static method in class org.snpeff.vcf.VcfEntry
-
Does 'value' represent an EMPTY / MISSING value in a VCF field? (or multiple MISSING comma-separated values)
- isError() - Method in enum class org.snpeff.snpEffect.ErrorWarningType
- isErrorChromoHit() - Method in class org.snpeff.snpEffect.Config
- isErrorOnMissingChromo() - Method in class org.snpeff.snpEffect.Config
- isErrorProteinLength() - Method in class org.snpeff.interval.Transcript
-
Check if coding length is multiple of 3 in protein coding transcripts
- isErrorStartCodon() - Method in class org.snpeff.interval.Transcript
-
Is the first codon a START codon?
- isErrorStopCodonsInCds() - Method in class org.snpeff.interval.Transcript
-
Check if protein sequence has STOP codons in the middle of the coding sequence
- isExecuting() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- isExecuting() - Method in class org.snpeff.osCmd.OsCmdRunner
- isExon() - Method in class org.snpeff.snpEffect.VariantEffect
- isExonPart() - Method in class org.snpeff.interval.SpliceSiteRegion
- isExpandIub() - Method in class org.snpeff.fileIterator.VcfFileIterator
- isExpandIub() - Method in class org.snpeff.snpEffect.Config
- isFilterPass() - Method in class org.snpeff.vcf.VcfEntry
- isFirstFragment() - Method in class org.snpeff.sam.SamEntry
-
The first fragment in the template
- isFixed() - Method in class org.snpeff.reactome.Entity
- isFormat() - Method in class org.snpeff.vcf.VcfHeaderEntry
- isFormat() - Method in class org.snpeff.vcf.VcfHeaderFormat
- isFormatLine(String) - Static method in class org.snpeff.vcf.VcfHeader
- isFullVersion() - Method in enum class org.snpeff.vcf.EffFormatVersion
-
Is this format fully specified? I.e.
- isFusion() - Method in enum class org.snpeff.snpEffect.EffectType
- isGene(Marker) - Method in class org.snpeff.snpEffect.VariantEffectStructural
- isGeneGeneFusion() - Method in class org.snpeff.snpEffect.VariantEffectFusion
- isGreedy() - Method in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
-
Is this a greedy algorithm?
- isHeadeSection() - Method in class org.snpeff.fileIterator.VcfFileIterator
- isHeterozygous() - Method in class org.snpeff.vcf.VcfGenotype
-
Is the most likely genotype heterozygous?
- isHgvs() - Method in class org.snpeff.snpEffect.Config
- isHgvs1LetterAA() - Method in class org.snpeff.snpEffect.Config
- isHgvsOld() - Method in class org.snpeff.snpEffect.Config
- isHgvsShift() - Method in class org.snpeff.snpEffect.Config
- isHgvsTrId() - Method in class org.snpeff.snpEffect.Config
- isHighlyConservedAaSequence() - Method in class org.snpeff.interval.NextProt
- isHomozygous() - Method in class org.snpeff.ped.PedGenotype
-
Is this homozygous?
- isHomozygous() - Method in class org.snpeff.vcf.VcfGenotype
-
Is this genotype homozygous? (either REF or ALT)
- isHomozygousAlt() - Method in class org.snpeff.vcf.VcfGenotype
-
Is this genotype homozygous ALT?
- isIgnoreChromosomeErrors() - Method in class org.snpeff.fileIterator.MarkerFileIterator
- isImplicit() - Method in class org.snpeff.vcf.VcfHeaderInfo
- isImprecise() - Method in class org.snpeff.interval.Variant
- isInDel() - Method in class org.snpeff.interval.Variant
- isInfo() - Method in class org.snpeff.vcf.VcfHeaderEntry
- isInfo() - Method in class org.snpeff.vcf.VcfHeaderInfo
- isInfoLine(String) - Static method in class org.snpeff.vcf.VcfHeader
- isIns() - Method in class org.snpeff.interval.Variant
- isInSync() - Method in class org.snpeff.interval.tree.IntervalTree
-
Determine whether this interval tree is currently a reflection of all intervals in the interval list
- isInSync() - Method in class org.snpeff.interval.tree.IntervalTreeArray
- isInSync() - Method in class org.snpeff.interval.tree.IntervalTreeOri
-
Determine whether this interval tree is currently a reflection of all intervals in the interval list
- isInSync() - Method in interface org.snpeff.interval.tree.Itree
-
Is the tree 'in sync'? If false, the tree must be 'build()' before the next query
- isInteraction() - Method in class org.snpeff.nextProt.Location
- isInteraction() - Method in class org.snpeff.nextProt.LocationTargetIsoformInteraction
- isInteresting(String) - Method in class org.snpeff.geneSets.GeneSets
- isIntergenic() - Method in class org.snpeff.snpEffect.VariantEffect
- isInterval() - Method in class org.snpeff.interval.Variant
- isIntron() - Method in class org.snpeff.snpEffect.VariantEffect
- isIntron(int) - Method in class org.snpeff.interval.Transcript
- isIntronPart() - Method in class org.snpeff.interval.SpliceSiteRegion
- isInv() - Method in class org.snpeff.interval.Variant
- isIsoform() - Method in class org.snpeff.nextProt.Location
- isIsoform() - Method in class org.snpeff.nextProt.LocationTargetIsoform
- isLastFragment() - Method in class org.snpeff.sam.SamEntry
-
The last fragment in the template
- isLeave() - Method in class org.snpeff.geneOntology.GoTerm
-
Is this GOTerm a leave?
- isLeft() - Method in class org.snpeff.interval.VariantBnd
- isLof() - Method in class org.snpeff.snpEffect.LossOfFunction
-
Can this collection of effects produce a "Loss of function"
- isLof(VariantEffect) - Method in class org.snpeff.snpEffect.LossOfFunction
-
Is this single change a LOF? Criteria: 1) Core splice sites acceptors or donors (only CORE ones) 2) Stop gained (if this happens at the last part of the protein, we assume it has no effect) 3) Frame shifts
- isLofDeletion(VariantEffect) - Method in class org.snpeff.snpEffect.LossOfFunction
-
Is this deletion a LOF? Criteria: 1) First (coding) exon deleted 2) More than 50% of coding sequence deleted
- isMapped() - Method in class org.snpeff.sam.SamEntry
-
Is this entry mapped to the genome?
- isMissing() - Method in class org.snpeff.ped.TfamEntry
-
Is phenotype 'Missing'?
- isMissing() - Method in class org.snpeff.vcf.VcfGenotype
-
Is genotpye missing (e.g.
- isMixed() - Method in class org.snpeff.interval.Variant
- isMnp() - Method in class org.snpeff.interval.Variant
- isMostExonsHaveSequence() - Method in class org.snpeff.interval.Genome
-
Do most exons have sequence? This is an indicator that something went really bad building the database.
- isMotif() - Method in class org.snpeff.snpEffect.VariantEffect
- isMt() - Method in class org.snpeff.interval.Chromosome
-
Is this a mitochondrial chromosome? Note: This is a wild guess just by looking at the name
- isMultiallelic() - Method in class org.snpeff.vcf.VcfEntry
-
Is this multi-allelic (based ONLY on the number of ALTs) WARINIG: You should use 'calcHetero()' method for a more precise calculation.
- isMultipleFragments() - Method in class org.snpeff.sam.SamEntry
-
Template having multiple fragments in sequencing
- isMultipleGenes() - Method in class org.snpeff.snpEffect.VariantEffect
- isMultipleGenes() - Method in class org.snpeff.snpEffect.VariantEffectStructural
- isMultipleHits() - Method in class org.snpeff.sam.SamEntry
-
Is this read mapped to multiple genomic locations?
- isMultipleValues(String) - Method in class org.snpeff.fileIterator.GuessTableTypes
-
Has this field multiple values
- isMultipleValues(String) - Method in class org.snpeff.interval.GffMarker
-
Does the key have mutiple values
- isMultipleValues(String) - Method in class org.snpeff.interval.Gtf2Marker
-
Does the key have mutiple values
- isNewFeature(String) - Method in class org.snpeff.genBank.Embl
-
Has this line a new feature?
- isNewFeature(String) - Method in class org.snpeff.genBank.Features
-
Is there a new feature in this line?
- isNewFeature(String) - Method in class org.snpeff.genBank.GenBank
-
Has this line a new feature?
- isNewVersion() - Method in class org.snpeff.logStatsServer.VersionCheck
- isNextProt() - Method in class org.snpeff.snpEffect.VariantEffect
- isNextReverseWc() - Method in class org.snpeff.sam.SamEntry
-
SEQ of the next fragment in the template being reversed
- isNextUnmapped() - Method in class org.snpeff.sam.SamEntry
-
Next fragment in the template unmapped
- isNmd() - Method in class org.snpeff.snpEffect.LossOfFunction
-
Can this collection of effects produce a "Nonsense mediated decay"?
- isNmd(VariantEffect) - Method in class org.snpeff.snpEffect.LossOfFunction
-
Is this single change a LOF? Criteria: 1) Core splice sites acceptors or donors (only CORE ones) 2) Stop gained (if this happens at the last part of the protein, we assume it has no effect) 3) Frame shifts
- isNonRef() - Method in class org.snpeff.interval.Variant
- isNonRef() - Method in class org.snpeff.interval.VariantNonRef
- isNotQualityControl() - Method in class org.snpeff.sam.SamEntry
-
Not passing quality controls
- isNumberAllAlleles() - Method in class org.snpeff.vcf.VcfHeaderInfo
- isNumberNumber() - Method in class org.snpeff.vcf.VcfHeaderInfo
- isNumberOnePerAllele() - Method in class org.snpeff.vcf.VcfHeaderInfo
- isNumberOnePerGenotype() - Method in class org.snpeff.vcf.VcfHeaderInfo
- isNumberPerAllele() - Method in class org.snpeff.vcf.VcfHeaderInfo
- isOk(Apfloat) - Static method in class org.snpeff.probablility.RankSumPdf
-
Is the value OK? (i.e.
- isOnlyRegulation() - Method in class org.snpeff.snpEffect.Config
- isOpt(String) - Method in class org.snpeff.SnpEff
-
Is this a command line option (e.g.
- isPhased() - Method in class org.snpeff.vcf.VcfGenotype
- isPowerOfTwo(int) - Static method in class org.snpeff.collections.BitUtil
-
returns true if v is a power of two or zero
- isPowerOfTwo(long) - Static method in class org.snpeff.collections.BitUtil
-
returns true if v is a power of two or zero
- isProperlyAligned() - Method in class org.snpeff.sam.SamEntry
-
Each fragment properly aligned according to the aligner
- isProteinCoding() - Method in enum class org.snpeff.interval.BioType
- isProteinCoding() - Method in class org.snpeff.interval.Gene
-
Is any of the transcripts protein coding?
- isProteinCoding() - Method in class org.snpeff.interval.Transcript
- isProteingCoding() - Method in class org.snpeff.interval.GffMarker
-
Is biotType considered 'protein coding'?
- isQuiet() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- isQuiet() - Method in class org.snpeff.snpEffect.Config
- isRank() - Method in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
-
Does the algorithm need a rank statistic?
- isRanked() - Method in class org.snpeff.geneSets.GeneSets
- isRanked() - Method in class org.snpeff.geneSets.GeneSetsRanked
- isRanked(String) - Method in class org.snpeff.geneSets.GeneSetsRanked
- isReaction() - Method in class org.snpeff.reactome.Entity
- isReaction() - Method in class org.snpeff.reactome.events.Reaction
- isRef() - Method in class org.snpeff.vcf.VcfGenotype
-
Is any genotype different than REF? Note: This is calculated for the most likely genotype (GT field)
- isRegulation() - Method in class org.snpeff.snpEffect.VariantEffect
- isReverseWc() - Method in class org.snpeff.sam.SamEntry
-
SEQ being reverse complemented
- isRibosomalSlippage() - Method in class org.snpeff.genBank.Feature
- isRibosomalSlippage() - Method in class org.snpeff.interval.Transcript
- isRunning() - Method in class org.snpeff.osCmd.StreamGobbler
- isSameChromo(Marker) - Method in class org.snpeff.interval.Interval
- isSaveStd() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- isSecondaryAlignment() - Method in class org.snpeff.sam.SamEntry
-
Secondary alignment
- isShow(Result) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
-
Showld we show this result or should the output be filtered?
- isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.Chromosome
- isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.Downstream
-
Upstream sites are no included in transcript (by definition).
- isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.Gene
- isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.Marker
-
Show an error if parent does not include child?
- isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.SpliceSite
-
Splice sites are not included in Exons, by definition.
- isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.Upstream
-
Upstream sites are no included in transcript (by definition).
- isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.Variant
- isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.vcf.VcfEntry
- isSingleSnp() - Method in class org.snpeff.vcf.VcfEntry
-
Is thins a VCF entry with a single SNP?
- isSingleton() - Method in class org.snpeff.vcf.VcfEntry
-
Is this variant a singleton (appears only in one genotype)
- isSnp() - Method in class org.snpeff.interval.Variant
- isSpliceSite() - Method in class org.snpeff.snpEffect.VariantEffect
- isSpliceSiteCore() - Method in class org.snpeff.snpEffect.VariantEffect
- isSpliceSiteRegion() - Method in class org.snpeff.snpEffect.VariantEffect
- isStart(String) - Method in class org.snpeff.codons.CodonTable
-
Is 'codon' a start codon in this table?
- isStarted() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- isStartFirst(String) - Method in class org.snpeff.codons.CodonTable
-
Is the first codon a 'start' codon?
- isStdin(String) - Static method in class org.snpeff.util.Gpr
-
Empty or '-' means STDIN
- isStop(String) - Method in class org.snpeff.codons.CodonTable
-
Is 'codon' a stop codon in this table?
- isStopAa(String) - Method in class org.snpeff.codons.CodonTable
-
Is there a stop codon in this amino acid sequence
- isStrandMinus() - Method in class org.snpeff.interval.Interval
- isStrandPlus() - Method in class org.snpeff.interval.Interval
- isStructural() - Method in class org.snpeff.interval.Variant
- isStructural() - Method in class org.snpeff.interval.VariantBnd
- isStructuralHuge() - Method in class org.snpeff.interval.Variant
-
Is this a huge structural variant?
- isTranscript(Marker) - Method in class org.snpeff.snpEffect.VariantEffectStructural
- isTransition(String, String) - Method in class org.snpeff.stats.TsTvStats
-
Is this a transition?
- isTranversion(String, String) - Method in class org.snpeff.stats.TsTvStats
-
Is this a transversion?
- isTreatAllAsProteinCoding() - Method in class org.snpeff.snpEffect.Config
- isTruncation() - Method in class org.snpeff.interval.Variant
- isType(Marker, String) - Method in class org.snpeff.coverage.MarkerTypes
- isUIB(char) - Static method in class org.snpeff.util.IubString
- isUniqueHit() - Method in class org.snpeff.sam.SamEntry
-
Is this read mapped to only one genomic locations?
- isUnmapped() - Method in class org.snpeff.sam.SamEntry
-
Fragment unmapped
- isUpstream(int) - Method in class org.snpeff.interval.Transcript
- isUsed(String) - Method in class org.snpeff.geneSets.GeneSets
- isUsed(String) - Method in class org.snpeff.geneSets.GeneSetsRanked
- isUsed(GeneSet) - Method in class org.snpeff.geneSets.GeneSets
-
Is this gene set used? I.e.
- isUsed(GeneSet) - Method in class org.snpeff.geneSets.GeneSetsRanked
-
Is this gene set used? I.e.
- isUtr(int) - Method in class org.snpeff.interval.Transcript
- isUtr(Marker) - Method in class org.snpeff.interval.Transcript
- isUtr3() - Method in class org.snpeff.snpEffect.VariantEffect
- isUtr3(int) - Method in class org.snpeff.interval.Transcript
- isUtr3prime() - Method in class org.snpeff.interval.Utr
- isUtr3prime() - Method in class org.snpeff.interval.Utr3prime
- isUtr3prime() - Method in class org.snpeff.interval.Utr5prime
- isUtr5() - Method in class org.snpeff.snpEffect.VariantEffect
- isUtr5(int) - Method in class org.snpeff.interval.Transcript
- isUtr5prime() - Method in class org.snpeff.interval.Utr
- isUtr5prime() - Method in class org.snpeff.interval.Utr3prime
- isUtr5prime() - Method in class org.snpeff.interval.Utr5prime
- isValid() - Method in class org.snpeff.interval.Interval
- isValid() - Method in class org.snpeff.nextProt.Location
- isValid() - Method in class org.snpeff.ped.PedGenotype
- isValidData() - Method in class org.snpeff.stats.IntStats
-
Do we have any data
- isValidInfoKey(String) - Static method in class org.snpeff.vcf.VcfEntry
-
Make sure the INFO key matches the regular expression (as specified in VCF spec 4.3)
- isValidInfoValue(String) - Static method in class org.snpeff.vcf.VcfEntry
-
Check that this value can be added to an INFO field
- isValidIp(String) - Static method in class org.snpeff.util.Gpr
- isValidRid(int) - Static method in class org.snpeff.util.Gpr
-
Is this a valid Rid
- isVariant() - Method in class org.snpeff.interval.Variant
-
Is this a change or is ALT actually the same as the reference
- isVariant() - Method in class org.snpeff.vcf.VcfEntry
-
Is this a change or are the ALTs actually the same as the reference
- isVariant() - Method in class org.snpeff.vcf.VcfGenotype
-
Is any genotype different than REF? Note: This is calculated for the most likely genotype (GT field)
- isVariant(String) - Method in class org.snpeff.vcf.VcfEntry
-
Is this ALT string a variant?
- isVerbose() - Method in class org.snpeff.pdb.ProteinInteractions
- isVerbose() - Method in class org.snpeff.snpEffect.Config
- isWarning() - Method in enum class org.snpeff.snpEffect.ErrorWarningType
- isWarningStopCodon() - Method in class org.snpeff.interval.Transcript
-
Is the last codon a STOP codon?
- iterator() - Method in class org.snpeff.binseq.GenomicSequences
- iterator() - Method in class org.snpeff.binseq.indexer.SequenceIndexer
- iterator() - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
- iterator() - Method in class org.snpeff.codons.CodonTables
- iterator() - Method in class org.snpeff.fileIterator.BinSeqFileIterator
- iterator() - Method in class org.snpeff.fileIterator.FastqFileIterator
- iterator() - Method in class org.snpeff.fileIterator.FileIterator
- iterator() - Method in class org.snpeff.fileIterator.LineClassFileIterator
- iterator() - Method in class org.snpeff.fileIterator.LineFileIterator
- iterator() - Method in class org.snpeff.fileIterator.SamFileIterator
- iterator() - Method in class org.snpeff.genBank.Feature
- iterator() - Method in class org.snpeff.genBank.Features
- iterator() - Method in class org.snpeff.genBank.FeaturesFile
- iterator() - Method in class org.snpeff.geneOntology.GoTerm
- iterator() - Method in class org.snpeff.geneOntology.GoTerms
-
Iterate through each GOterm in this GOTerms
- iterator() - Method in class org.snpeff.geneSets.GeneSet
- iterator() - Method in class org.snpeff.geneSets.GeneSets
-
Iterate through each GeneSet in this GeneSets
- iterator() - Method in class org.snpeff.gtex.Gtex
- iterator() - Method in class org.snpeff.interval.Custom
- iterator() - Method in class org.snpeff.interval.Genes
- iterator() - Method in class org.snpeff.interval.Genome
- iterator() - Method in class org.snpeff.interval.GffMarker
- iterator() - Method in class org.snpeff.interval.IntervalAndSubIntervals
- iterator() - Method in class org.snpeff.interval.IntervalSetIterator
- iterator() - Method in class org.snpeff.interval.Markers
- iterator() - Method in class org.snpeff.interval.tree.IntervalForest
- iterator() - Method in class org.snpeff.interval.tree.IntervalNodeOri
- iterator() - Method in class org.snpeff.interval.tree.IntervalTree
- iterator() - Method in class org.snpeff.interval.tree.IntervalTreeArray
- iterator() - Method in class org.snpeff.interval.tree.IntervalTreeOri
- iterator() - Method in class org.snpeff.motif.Jaspar
- iterator() - Method in class org.snpeff.osCmd.OsCmdQueue
- iterator() - Method in class org.snpeff.ped.PedEntry
- iterator() - Method in class org.snpeff.ped.PedPedigree
- iterator() - Method in class org.snpeff.reactome.events.Complex
- iterator() - Method in class org.snpeff.reactome.events.Pathway
- iterator() - Method in class org.snpeff.reactome.Reactome
- iterator() - Method in class org.snpeff.sam.SamHeader
- iterator() - Method in class org.snpeff.snpEffect.Config
- iterator() - Method in class org.snpeff.snpEffect.VariantEffects
- iterator() - Method in class org.snpeff.spliceSites.TranscriptSet
- iterator() - Method in class org.snpeff.stats.GeneCountByTypeTable
- iterator() - Method in class org.snpeff.util.CombinatorialIterator
- iterator() - Method in class org.snpeff.util.Iterator2Iterable
- iterator() - Method in class org.snpeff.util.IubString
- iterator() - Method in class org.snpeff.vcf.Pedigree
- iterator() - Method in class org.snpeff.vcf.VcfEntry
- Iterator2Iterable<T> - Class in org.snpeff.util
-
Convert an iterator instance to a (fake) iterable
- Iterator2Iterable(Iterator<T>) - Constructor for class org.snpeff.util.Iterator2Iterable
- iteratorSorted() - Method in class org.snpeff.geneSets.GeneSets
-
Iterate through each GeneSet in this GeneSets
- Itree - Interface in org.snpeff.interval.tree
-
Interval tree interface
- iub2bases(char) - Static method in class org.snpeff.util.IubString
-
Convert a single IUB code to the corresponding bases IUB codes: M=A/C, R=A/G, W=A/T, S=C/G, Y=C/T, K=G/T and N=A/C/G/T
- IubString - Class in org.snpeff.util
-
Find all bases combinations from a string containing IUB codes
- IubString(String) - Constructor for class org.snpeff.util.IubString
J
- Jaspar - Class in org.snpeff.motif
-
Load PWM matrices from a Jaspar file
- Jaspar() - Constructor for class org.snpeff.motif.Jaspar
- JOIN - Static variable in class org.snpeff.genBank.Features
K
- K - Static variable in class org.snpeff.fastq.FastqSplit
- KB - Static variable in class org.snpeff.util.Gpr
- keepTranscripts(Set<String>) - Method in class org.snpeff.interval.Gene
-
Remove all transcripts in trIds
- keepTranscriptsProteinCoding() - Method in class org.snpeff.interval.Gene
-
Keep only protein coding transcripts
- keepTranscriptsProteinCoding() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Remove all transcripts that are NOT in the list
- key - Variable in class org.snpeff.util.KeyValue
- KEY_BUNDLE_SUFIX - Static variable in class org.snpeff.snpEffect.Config
- KEY_CODON_PREFIX - Static variable in class org.snpeff.snpEffect.Config
- KEY_CODONTABLE_SUFIX - Static variable in class org.snpeff.snpEffect.Config
- KEY_COORDINATES - Static variable in class org.snpeff.snpEffect.Config
- KEY_DATA_DIR - Static variable in class org.snpeff.snpEffect.Config
- KEY_DATABASE_LOCAL - Static variable in class org.snpeff.snpEffect.Config
- KEY_DATABASE_REPOSITORY - Static variable in class org.snpeff.snpEffect.Config
- KEY_DATABASE_REPOSITORY_KEY - Static variable in class org.snpeff.snpEffect.Config
- KEY_DBNSFP_FIELDS - Static variable in class org.snpeff.snpEffect.Config
- KEY_GENOME_SUFIX - Static variable in class org.snpeff.snpEffect.Config
- KEY_LOF_DELETE_PROTEIN_CODING_BASES - Static variable in class org.snpeff.snpEffect.Config
- KEY_LOF_IGNORE_PROTEIN_CODING_AFTER - Static variable in class org.snpeff.snpEffect.Config
- KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE - Static variable in class org.snpeff.snpEffect.Config
- KEY_REFERENCE_SUFIX - Static variable in class org.snpeff.snpEffect.Config
- KEY_SEPARATOR - Static variable in class org.snpeff.snpEffect.PurityChange
- KEY_VERSIONS_URL - Static variable in class org.snpeff.snpEffect.Config
- keys() - Method in class org.snpeff.collections.HashLongLongArray
-
Return an array with all the keys to this hash
- keys() - Method in class org.snpeff.snpEffect.Config
- keySet() - Method in class org.snpeff.geneOntology.GoTerms
- keySet() - Method in class org.snpeff.geneSets.GeneSets
- keySet() - Method in class org.snpeff.interval.tree.IntervalForest
- keySet() - Method in class org.snpeff.ped.PedPedigree
- keySet() - Method in class org.snpeff.stats.CountByKey
- keySet() - Method in class org.snpeff.stats.CountByType
- keysRanked(boolean) - Method in class org.snpeff.stats.CountByType
-
List all types (sorted by count)
- keysSorted() - Method in class org.snpeff.stats.CountByType
-
List all types (alphabetically sorted)
- KeyValue<A,
B> - Class in org.snpeff.util -
A "key = value" pair
- KeyValue(A, B) - Constructor for class org.snpeff.util.KeyValue
- kill() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- kill() - Method in class org.snpeff.osCmd.OsCmdQueue
-
Kill all commands
- KNOWN_FILE_EXTENSIONS - Static variable in class org.snpeff.util.GprSeq
- KNOWN_GENES - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
L
- LAST_BASE_IN_LONGWORD - Static variable in class org.snpeff.binseq.coder.DnaCoder
- lastBaseinWord() - Method in class org.snpeff.binseq.coder.Coder
-
Index of the last base coded in a word
- lastBaseinWord() - Method in class org.snpeff.binseq.coder.DnaCoder
- lastIdx - Variable in class org.snpeff.interval.tree.IntervalTreeArray
- lastIndexOf(String) - Method in class org.snpeff.binseq.DnaAndQualitySequence
-
Returns the index within this string of the rightmost occurrence of the specified substring
- lastNmdPos(Transcript) - Method in class org.snpeff.snpEffect.LossOfFunction
-
Find the last position where a nonsense mediated decay is supposed to occurr This is 50 bases (MND_BASES_BEFORE_LAST_JUNCTION bases) before the last exon-exon junction.
- LEADING_EDGE_FRACTION - Enum constant in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
- LeadingEdgeFractionAlgorithm - Class in org.snpeff.geneSets.algorithm
-
Leading edge fraction algorithm References: "Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits" http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001058 See page 12, "Step 4"
- LeadingEdgeFractionAlgorithm(GeneSets, int, boolean) - Constructor for class org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
- left - Variable in class org.snpeff.interval.tree.IntervalTreeArray
- leftNode - Variable in class org.snpeff.interval.tree.IntervalNode
- LEN_AFTER_TSS - Static variable in class org.snpeff.PromoterSequences
- LEN_UPSTREAM - Static variable in class org.snpeff.PromoterSequences
- length - Variable in class org.snpeff.fileIterator.BlastResultEntry
- length() - Method in class org.snpeff.binseq.BinarySequence
-
Get sequence length
- length() - Method in class org.snpeff.binseq.DnaAndQualitySequence
-
Sequence lenth
- length() - Method in class org.snpeff.binseq.DnaSequence
-
Sequence lenth
- length() - Method in class org.snpeff.binseq.DnaSequenceByte
-
Sequence lenth
- length() - Method in class org.snpeff.binseq.DnaSequencePe
- length() - Method in class org.snpeff.interval.Genome
-
Total genome length: add all chromosomes
- length() - Method in class org.snpeff.motif.Pwm
- length() - Method in class org.snpeff.nmer.Nmer
-
Get nmer's length
- length2words(int) - Method in class org.snpeff.binseq.coder.DnaCoder
-
Calculate the coded length of a sequence in 'words' (depends on coder)
- lengthChange() - Method in class org.snpeff.interval.Variant
-
Calculate the number of bases of change in length
- levels() - Method in class org.snpeff.geneOntology.GoTerms
-
Calculate each node's level (in DAG)
- LIGHT_ROW - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
- lincRNA - Enum constant in enum class org.snpeff.interval.BioType
- line - Variable in class org.snpeff.fileIterator.FileIterator
- line - Variable in class org.snpeff.vcf.FileIndexChrPos.LineAndPos
- line - Variable in class org.snpeff.vcf.VcfEntry
- line - Variable in class org.snpeff.vcf.VcfHeaderEntry
- LINE_COLOR_STROKE - Static variable in class org.snpeff.svg.Svg
- LINE_STROKE_WIDTH - Static variable in class org.snpeff.svg.Svg
- LineAndPos() - Constructor for class org.snpeff.vcf.FileIndexChrPos.LineAndPos
- LINEAR - Enum constant in enum class org.snpeff.reactome.Entity.TransferFunction
- lineChart - Variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
- LineChrPos - Class in org.snpeff.vcf
-
A simple chr:pos parser Stores using bytes instead of chars
- LineChrPos(String) - Constructor for class org.snpeff.vcf.LineChrPos
- LineClassFileIterator<T> - Class in org.snpeff.fileIterator
-
Iterate on each line.
- LineClassFileIterator(String, Class) - Constructor for class org.snpeff.fileIterator.LineClassFileIterator
- LineClassFileIterator(String, Class, String) - Constructor for class org.snpeff.fileIterator.LineClassFileIterator
- LineFileIterator - Class in org.snpeff.fileIterator
-
Iterate on each line in this file
- LineFileIterator(String) - Constructor for class org.snpeff.fileIterator.LineFileIterator
- LineFileIterator(String, boolean) - Constructor for class org.snpeff.fileIterator.LineFileIterator
- LineFilter - Interface in org.snpeff.osCmd
-
Filter a line before processing
- lineNum - Variable in class org.snpeff.fileIterator.FileIterator
- lineNum - Variable in class org.snpeff.vcf.VcfEntry
- LineSeqFileIterator - Class in org.snpeff.fileIterator
-
One line per sequence.
- LineSeqFileIterator(String) - Constructor for class org.snpeff.fileIterator.LineSeqFileIterator
- listTopTerms(int) - Method in class org.snpeff.geneOntology.GoTerms
-
Select a number of GOTerms
- listTopTerms(int) - Method in class org.snpeff.geneSets.GeneSets
-
Select a number of GeneSets
- load() - Method in class org.snpeff.binseq.GenomicSequences
-
Load sequences for all 'small chromosomes" (from "sequence.bin" file)
- load() - Method in class org.snpeff.fileIterator.FileIterator
-
Load all elements from a file into a list
- load() - Method in class org.snpeff.fileIterator.TableFile
-
Load all data into memory
- load() - Method in class org.snpeff.pdb.PdbFile
-
Opens filename, parses it and returns aStructure object .
- load() - Method in class org.snpeff.SnpEff
- load() - Method in class org.snpeff.Zzz
- load(String) - Method in class org.snpeff.binseq.GenomicSequences
-
Load sequences for a single chromosome (from "sequence.chr.bin" file)
- load(String) - Static method in class org.snpeff.genotypes.Genotypes
-
Read from a file
- load(String) - Method in class org.snpeff.interval.Markers
- load(String) - Method in class org.snpeff.motif.Jaspar
-
Load matrix file
- load(String) - Method in class org.snpeff.pdb.IdMapper
- load(String) - Method in class org.snpeff.ped.PedPedigree
-
Load a pedigree from a PED and MAP file pair
- load(String) - Method in class org.snpeff.reactome.GeneIds
-
Load data from file
- load(String) - Method in class org.snpeff.serializer.MarkerSerializer
-
Load data from file
- load(String) - Method in class org.snpeff.stats.ReadsOnMarkersModel
-
Load data from a file
- load(String, boolean) - Static method in class org.snpeff.fileIterator.BedFileIterator
- load(String, String) - Method in class org.snpeff.gtex.Gtex
- load(String, String) - Method in class org.snpeff.reactome.Reactome
- load(String, Genome) - Method in class org.snpeff.interval.Markers
- load(String, Genome) - Method in class org.snpeff.interval.tree.IntervalTree
- load(String, Genome) - Method in class org.snpeff.interval.tree.IntervalTreeArray
- load(String, Genome) - Method in class org.snpeff.interval.tree.IntervalTreeOri
- load(String, Genome) - Method in interface org.snpeff.interval.tree.Itree
-
Load intervals from file
- load(Config) - Static method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Load predictor from a binary file
- loadCatalystActivity() - Method in class org.snpeff.reactome.Reactome
-
Load catalyst activity to molecule mapping
- loadComplex2HasComponent() - Method in class org.snpeff.reactome.Reactome
-
Load complexes
- loadConfig() - Method in class org.snpeff.SnpEff
-
Read config file
- loadCustomFile(String) - Method in class org.snpeff.SnpEff
-
Read a custom interval file
- loadData(String) - Method in class org.snpeff.gtex.Gtex
-
Load data: Experimental (sometimes normalized) values
- loadDatabaseObjects() - Method in class org.snpeff.reactome.Reactome
-
Load objects table (populate objectType and objectName maps)
- loadDb() - Method in class org.snpeff.SnpEff
-
Load database
- loadExperimentalValues(String, boolean) - Method in class org.snpeff.geneSets.GeneSets
-
Reads a file with a list of genes and experimental values.
- loadExperimentalValues(String, boolean) - Method in class org.snpeff.geneSets.GeneSetsRanked
-
Reads a file with a list of genes and experimental values.
- loadGeneIds(String) - Method in class org.snpeff.reactome.Reactome
-
Load Gene IDs data, then map geneIDs invalid input: '<'-> Entities
- loadIdMapper() - Method in class org.snpeff.pdb.ProteinInteractions
- loadMap(String, String, HashMap<String, String>) - Method in class org.snpeff.reactome.Reactome
-
Load a two-column file into a Hash
- loadMarkers() - Method in class org.snpeff.fileIterator.MarkerFileIterator
- loadMarkers(String) - Method in class org.snpeff.SnpEff
-
Read markers file Supported formats: BED, TXT, BigBed, GFF
- loadMSigDb(String, boolean) - Method in class org.snpeff.geneSets.GeneSets
-
Read an MSigDBfile and add every Gene set (do not add relationships between nodes in DAG)
- loadOrCreateFromGenome(String) - Method in class org.snpeff.binseq.GenomicSequences
-
Load sequences from genomic sequence file or (if not file is available) generate some sequences from exons.
- loadPathway2HasEvent() - Method in class org.snpeff.reactome.Reactome
-
Load pathway events
- loadPhysicalEntity2Compartment() - Method in class org.snpeff.reactome.Reactome
-
Load compartment information
- loadReactionlikeEvent2CatalystActivity() - Method in class org.snpeff.reactome.Reactome
-
Load reaction catalyst
- loadReactionlikeEvent2Input() - Method in class org.snpeff.reactome.Reactome
-
Load reaction inputs
- loadReactionlikeEvent2Output() - Method in class org.snpeff.reactome.Reactome
-
Load reaction outputs
- loadRegulation() - Method in class org.snpeff.reactome.Reactome
-
Load reaction regulation
- loadSamples(String) - Method in class org.snpeff.gtex.Gtex
-
Load samples names
- loadSnpEffectPredictor() - Method in class org.snpeff.snpEffect.Config
-
Load a snpEff predictor WARNING: 'genome' object get replaced upon loading a snpEffectPredictor (this is a dangerous side effect)
- loadTfam(String) - Method in class org.snpeff.ped.PedPedigree
-
Load a TFAM file
- loadVcf() - Method in class org.snpeff.genotypes.Genotypes
-
Load data
- Location - Class in org.snpeff.nextProt
-
A location (i.e.
- Location() - Constructor for class org.snpeff.nextProt.Location
- Location(String) - Constructor for class org.snpeff.nextProt.Location
- Location(String, int, int) - Constructor for class org.snpeff.nextProt.Location
- locationBeginPos(Attributes) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- locationEnd() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
-
End of location tag
- locationEndPos(Attributes) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- locationIsoformStart(String) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- locationStart(Attributes) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- LocationTargetIsoform - Class in org.snpeff.nextProt
-
A location respect to an isoform
- LocationTargetIsoform(String) - Constructor for class org.snpeff.nextProt.LocationTargetIsoform
- LocationTargetIsoform(String, int, int) - Constructor for class org.snpeff.nextProt.LocationTargetIsoform
- LocationTargetIsoformInteraction - Class in org.snpeff.nextProt
-
A location respect to two locations within an isoform In this case "start" and "end" are not really an interval, but an interaction between two locations (e.g.
- LocationTargetIsoformInteraction(String, int, int) - Constructor for class org.snpeff.nextProt.LocationTargetIsoformInteraction
- LocationTargetIsoformInteraction(LocationTargetIsoform) - Constructor for class org.snpeff.nextProt.LocationTargetIsoformInteraction
- log - Variable in class org.snpeff.logStatsServer.LogStats
- log - Variable in class org.snpeff.SnpEff
- Log - Class in org.snpeff.util
-
Logging
- Log() - Constructor for class org.snpeff.util.Log
- LOG_THREAD_WAIT_TIME - Static variable in class org.snpeff.logStatsServer.LogStats
- LOG_THREAD_WAIT_TIME - Static variable in class org.snpeff.logStatsServer.VersionCheck
- LOG_THREAD_WAIT_TIME_REPEAT - Static variable in class org.snpeff.logStatsServer.LogStats
- LOG_THREAD_WAIT_TIME_REPEAT - Static variable in class org.snpeff.logStatsServer.VersionCheck
- Log.FatalErrorBehabiour - Enum Class in org.snpeff.util
- log2(double) - Static method in class org.snpeff.motif.MotifLogo
-
Log base 2
- LOG2 - Static variable in class org.snpeff.geneSets.GeneSets
- LOG2 - Static variable in class org.snpeff.spliceSites.AcgtTree
- LogStats - Class in org.snpeff.logStatsServer
-
Log basic usage information to a server (for feedback and stats) This information an always be suppressed (no info sent at all)
- LogStats(String, String, String) - Constructor for class org.snpeff.logStatsServer.LogStats
-
Constructor
- LogStats.RequestResult - Enum Class in org.snpeff.logStatsServer
- LossOfFunction - Class in org.snpeff.snpEffect
-
Analyze if a set of effects are can create a "Loss Of Function" and "Nonsense mediated decays" effects.
- LossOfFunction(Config, Collection<VariantEffect>) - Constructor for class org.snpeff.snpEffect.LossOfFunction
- LOW - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.EffectImpact
- LowFrequency - Enum constant in enum class org.snpeff.vcf.VcfEntry.AlleleFrequencyType
M
- M - Static variable in class org.snpeff.fastq.FastqSplit
- mac() - Method in class org.snpeff.vcf.VcfEntry
-
Calculate Minor allele count
- macro_lncRNA - Enum constant in enum class org.snpeff.interval.BioType
- maf() - Method in class org.snpeff.vcf.VcfEntry
-
Calculate Minor allele frequency
- main(String[]) - Static method in class org.snpeff.fastq.FastqSplit
-
Main
- main(String[]) - Static method in class org.snpeff.Fastq2Fastq
- main(String[]) - Static method in class org.snpeff.genotypes.Genotypes
- main(String[]) - Static method in class org.snpeff.probablility.Hypergeometric
- main(String[]) - Static method in class org.snpeff.probablility.RankSumNoReplacementSimulate
- main(String[]) - Static method in class org.snpeff.probablility.RankSumPdf
- main(String[]) - Static method in class org.snpeff.PromoterSequences
- main(String[]) - Static method in class org.snpeff.Qseq2Fastq
- main(String[]) - Static method in class org.snpeff.reactome.Reactome
-
Main
- main(String[]) - Static method in class org.snpeff.SnpEff
-
Main
- main(String[]) - Static method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
- main(String[]) - Static method in class org.snpeff.snpEffect.IntHisto
- main(String[]) - Static method in class org.snpeff.snpEffect.PurityChange
- main(String[]) - Static method in class org.snpeff.Zzz
- Male - Enum constant in enum class org.snpeff.ped.Sex
- mark(int) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- MARK - Static variable in class org.snpeff.genotypes.Genotypes
- MARK - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- marker - Variable in class org.snpeff.snpEffect.Hgvs
- marker - Variable in class org.snpeff.snpEffect.VariantEffect
- marker() - Method in class org.snpeff.svg.Svg
- Marker - Class in org.snpeff.interval
-
An interval intended as a mark (i.e.
- Marker() - Constructor for class org.snpeff.interval.Marker
- Marker(Marker, int, int) - Constructor for class org.snpeff.interval.Marker
- Marker(Marker, int, int, boolean, String) - Constructor for class org.snpeff.interval.Marker
- MarkerFileIterator<M> - Class in org.snpeff.fileIterator
-
Opens a Marker file and iterates over all markers
- MarkerFileIterator(BufferedReader, int) - Constructor for class org.snpeff.fileIterator.MarkerFileIterator
- MarkerFileIterator(String, int) - Constructor for class org.snpeff.fileIterator.MarkerFileIterator
- MarkerFileIterator(String, Genome, int) - Constructor for class org.snpeff.fileIterator.MarkerFileIterator
- markerId() - Method in class org.snpeff.svg.Svg
- MarkerParentId - Class in org.snpeff.interval
-
This is a marker used as a 'fake' parent during data serialization
- MarkerParentId(int) - Constructor for class org.snpeff.interval.MarkerParentId
- markers - Variable in class org.snpeff.interval.Markers
- markers - Variable in class org.snpeff.interval.tree.IntervalTreeArray
- markers() - Method in class org.snpeff.interval.Gene
- markers() - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
A list of all markers in this transcript
- markers() - Method in class org.snpeff.interval.Transcript
-
A list of all markers in this transcript
- Markers - Class in org.snpeff.interval
-
A collection of markers
- Markers() - Constructor for class org.snpeff.interval.Markers
- Markers(String) - Constructor for class org.snpeff.interval.Markers
- Markers(Collection) - Constructor for class org.snpeff.interval.Markers
- Markers(Markers) - Constructor for class org.snpeff.interval.Markers
- MarkerSeq - Class in org.snpeff.interval
-
Marker with a DNA sequence
- MarkerSeq() - Constructor for class org.snpeff.interval.MarkerSeq
- MarkerSeq(Marker, int, int, boolean, String) - Constructor for class org.snpeff.interval.MarkerSeq
- MarkerSeq(Marker, int, int, String) - Constructor for class org.snpeff.interval.MarkerSeq
- MarkerSerializer - Class in org.snpeff.serializer
-
Serialize markers to (and from) file
- MarkerSerializer(Genome) - Constructor for class org.snpeff.serializer.MarkerSerializer
- MarkerTypes - Class in org.snpeff.coverage
-
Create a list of marker types (names or labels for markers)
- MarkerTypes() - Constructor for class org.snpeff.coverage.MarkerTypes
- markerTypesClass() - Method in class org.snpeff.coverage.MarkerTypes
-
List of markers whose types are based on class names
- MarkerUtil - Class in org.snpeff.interval
-
Generic utility methods for Markers
- MarkerUtil() - Constructor for class org.snpeff.interval.MarkerUtil
- MarkerWithFrame - Interface in org.snpeff.interval
-
A Marker that has 'frame' information (Exon and Cds)
- markSupported() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- mask - Static variable in class org.snpeff.genotypes.GenotypeVector
- mask(int) - Method in class org.snpeff.binseq.coder.Coder
-
Bitmask for a base in a word
- mask(int) - Method in class org.snpeff.binseq.coder.DnaCoder
- MASK - Static variable in class org.snpeff.binseq.DnaSequenceByte
- MASK_ALL_WORD - Static variable in class org.snpeff.binseq.coder.DnaCoder
- MASK_BASE - Variable in class org.snpeff.binseq.coder.DnaCoder
- MASK_FIRST_BASE - Static variable in class org.snpeff.binseq.coder.DnaCoder
- MASK_HIGH - Variable in class org.snpeff.binseq.coder.DnaCoder
- MASK_LOW - Variable in class org.snpeff.binseq.coder.DnaCoder
- MAT_PEPTIDE - Enum constant in enum class org.snpeff.genBank.Feature.Type
- matrix - Variable in class org.snpeff.fileIterator.MatrixEntry
- MatrixEntry - Class in org.snpeff.fileIterator
-
A simple entry in a 'Matrix' file
- MatrixEntry() - Constructor for class org.snpeff.fileIterator.MatrixEntry
- MatrixEntryFileIterator - Class in org.snpeff.fileIterator
-
Iterate on each line of a file, creating a MatrixEntry
- MatrixEntryFileIterator(String) - Constructor for class org.snpeff.fileIterator.MatrixEntryFileIterator
- max() - Method in class org.snpeff.gsa.ScoreList
-
Get minimum pvalue
- max() - Method in class org.snpeff.nmer.NmerCount
-
Max nmer count
- max() - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
- max() - Method in class org.snpeff.stats.CountByKey
-
Maximum count
- max() - Method in class org.snpeff.stats.CountByType
-
Maximum count
- max(double) - Method in class org.snpeff.stats.CounterDouble
- max(NmerCount) - Method in class org.snpeff.nmer.NmerCount
-
Max nmer count
- MAX - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
- MAX_ALIGN_LENGTH - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
- MAX_CODON_SEQUENCE_LEN - Static variable in class org.snpeff.snpEffect.VariantEffect
- MAX_CONVERGENCE_DIFFERENCE - Static variable in class org.snpeff.reactome.Reactome
- MAX_DATA_POINTS - Static variable in class org.snpeff.stats.plot.GooglePlot
- MAX_DATA_POINTS - Static variable in class org.snpeff.stats.plot.GooglePlotInt
- MAX_ENTROPY - Static variable in class org.snpeff.spliceSites.AcgtTree
- MAX_ERROR_RATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
- MAX_ERROR_RATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- MAX_ERRORS - Static variable in class org.snpeff.util.Log
- MAX_EXONS - Static variable in class org.snpeff.interval.ExonSpliceCharacterizer
- MAX_EXONS_CHART - Static variable in class org.snpeff.coverage.CountReadsOnMarkers
- MAX_ITERATIONS - Static variable in class org.snpeff.align.VariantRealign
- MAX_ITERATIONS - Static variable in class org.snpeff.binseq.GenomicSequences
- MAX_ITERATIONS - Static variable in class org.snpeff.reactome.Reactome
- MAX_IUB_BASES - Static variable in class org.snpeff.util.IubString
- MAX_LEN_TO_SHOW - Static variable in class org.snpeff.genBank.Features
- MAX_MAC - Static variable in class org.snpeff.stats.AlleleCountStats
- MAX_MAC - Static variable in class org.snpeff.stats.VariantTypeStats
- MAX_NMER_SIZE - Static variable in class org.snpeff.nmer.Nmer
- MAX_NORM_DOUBLE - Static variable in class org.snpeff.probablility.NormalDistribution
- MAX_QUALITY - Static variable in class org.snpeff.binseq.coder.DnaQualityCoder
- MAX_SEQUENCE_LEN_HGVS - Static variable in class org.snpeff.snpEffect.Hgvs
- MAX_SIZE - Static variable in class org.snpeff.align.VcfRefAltAlign
- MAX_SPLICE_SIZE - Static variable in class org.snpeff.spliceSites.SpliceTypes
- MAX_TRANSCRIPTS_PER_GENE - Static variable in class org.snpeff.spliceSites.TranscriptSet
- MAX_WARNINGS - Static variable in class org.snpeff.util.Log
- MAX_WARNS - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
- MAX_WEIGHT_SUM - Static variable in class org.snpeff.reactome.events.Reaction
- maxPvalue - Variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- maxPvalueAjusted - Variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- maxRankSum(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Maximum possible rank sum
- maxRankSum(int, int) - Static method in class org.snpeff.probablility.RankSumPdf
-
Maximum possible rank sum
- maxTranscriptSupportLevel - Variable in class org.snpeff.SnpEff
- MB - Static variable in class org.snpeff.util.Gpr
- mean(int) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
- mean(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Mean value for a given N and N_T
- mean(int, int) - Static method in class org.snpeff.probablility.RankSumPdf
-
Mean value for a given N and N_T
- mean(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
-
Calculate the mean References: http://en.wikipedia.org/wiki/Hypergeometric_distribution
- merge() - Method in class org.snpeff.interval.Markers
-
Merge overlapping intervals This is the same as 'union()' method, but the algorithm is more efficient
- message - Variable in class org.snpeff.snpEffect.VariantEffect
- method - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- MICRO_RNA - Enum constant in enum class org.snpeff.snpEffect.EffectType
- MicroCosmEntry - Class in org.snpeff.fileIterator.microCosm
-
Entry in a MicroCosm (miRNA target prediction) file
- MicroCosmEntry() - Constructor for class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- MicroCosmFileIterator - Class in org.snpeff.fileIterator.microCosm
-
Iterate on each line of a MicroCosm predictions References: http://www.ebi.ac.uk/enright-srv/microcosm/
- MicroCosmFileIterator(String) - Constructor for class org.snpeff.fileIterator.microCosm.MicroCosmFileIterator
- MicroRnaBindingSite - Class in org.snpeff.interval
-
miRna binding site (usually this was predicted by some algorithm)
- MicroRnaBindingSite() - Constructor for class org.snpeff.interval.MicroRnaBindingSite
- MicroRnaBindingSite(Marker, int, int, boolean, String, double) - Constructor for class org.snpeff.interval.MicroRnaBindingSite
- mid - Variable in class org.snpeff.interval.tree.IntervalTreeArray
- min() - Method in class org.snpeff.gsa.ScoreList
-
Get minimum pvalue
- min() - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
- min() - Method in class org.snpeff.stats.CountByKey
-
Minimum count
- min() - Method in class org.snpeff.stats.CountByType
-
Minimum count
- min(double) - Method in class org.snpeff.stats.CounterDouble
- MIN - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
- MIN_COUNT_CODON - Static variable in class org.snpeff.snpEffect.PurityChange
- MIN_LINES - Static variable in class org.snpeff.fileIterator.GuessTableTypes
- MIN_MARKERS_PER_LEAF - Static variable in class org.snpeff.interval.tree.IntervalTreeArray
- MIN_QUALITY - Static variable in class org.snpeff.binseq.coder.DnaQualityCoder
- MIN_TOTAL_FRAME_COUNT - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- MineMarkerIntervals - Class in org.snpeff.stats
-
Mine marker intervals: I.e.
- MineMarkerIntervals(Markers) - Constructor for class org.snpeff.stats.MineMarkerIntervals
- MineTwoMarkerIntervals - Class in org.snpeff.stats
-
Mine marker intervals: I.e.
- MineTwoMarkerIntervals(Markers, Markers) - Constructor for class org.snpeff.stats.MineTwoMarkerIntervals
- minRankSum(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Minimum possible rank sum
- minRankSum(int, int) - Static method in class org.snpeff.probablility.RankSumPdf
-
Minimum possible rank sum
- minus(Marker) - Method in class org.snpeff.interval.Marker
-
Return the difference between two markers
- minus(Marker) - Method in class org.snpeff.interval.Markers
-
Calculate 'set minus' using one interval
- minus(Markers) - Method in class org.snpeff.interval.Markers
-
Returns the result of this set minus 'intervals'
- miRNA - Enum constant in enum class org.snpeff.interval.BioType
- miRnaName - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- MISC_FEATURE - Enum constant in enum class org.snpeff.genBank.Feature.Type
- misc_RNA - Enum constant in enum class org.snpeff.interval.BioType
- MISC_RNA - Enum constant in enum class org.snpeff.genBank.Feature.Type
- mismatch - Variable in class org.snpeff.fileIterator.BlastResultEntry
- MISSENSE - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.FunctionalClass
- MISSING - Static variable in class org.snpeff.fileIterator.VcfFileIterator
- MIXED - Enum constant in enum class org.snpeff.interval.Variant.VariantType
- MND_BASES_BEFORE_LAST_JUNCTION - Static variable in class org.snpeff.snpEffect.LossOfFunction
-
Number of bases before last exon-exon junction that nonsense mediated decay is supposed to occur
- MNP - Enum constant in enum class org.snpeff.interval.Variant.VariantType
- MODERATE - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.EffectImpact
- MODIFIER - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.EffectImpact
- Monitor - Class in org.snpeff.reactome
- Monitor() - Constructor for class org.snpeff.reactome.Monitor
- mother - Variable in class org.snpeff.vcf.PedigreeEntry
- motherNum - Variable in class org.snpeff.vcf.PedigreeEntry
- motif - Variable in class org.snpeff.SnpEff
- Motif - Class in org.snpeff.interval
-
Regulatory elements
- Motif() - Constructor for class org.snpeff.interval.Motif
- Motif(Marker, int, int, boolean, String, String, String) - Constructor for class org.snpeff.interval.Motif
- MOTIF - Enum constant in enum class org.snpeff.snpEffect.EffectType
- MOTIF_DELETED - Enum constant in enum class org.snpeff.snpEffect.EffectType
- MotifFileIterator - Class in org.snpeff.fileIterator
-
Opens a regulation file and create Motif elements.
- MotifFileIterator(String, Genome, Jaspar) - Constructor for class org.snpeff.fileIterator.MotifFileIterator
- MotifLogo - Class in org.snpeff.motif
-
Create a DNA logo for a PWM References: - See WebLogo http://weblogo.berkeley.edu/ - "WebLogo: A Sequence Logo Generator"
- MotifLogo(Pwm) - Constructor for class org.snpeff.motif.MotifLogo
- mRna() - Method in class org.snpeff.interval.Transcript
-
Retrieve coding sequence AND the UTRs (mRNA = 5'UTR + CDS + 3'UTR) I.e.
- MRNA - Enum constant in enum class org.snpeff.genBank.Feature.Type
- msg - Variable in class org.snpeff.logStatsServer.LogStats
- Mt_rRNA - Enum constant in enum class org.snpeff.interval.BioType
- Mt_tRNA - Enum constant in enum class org.snpeff.interval.BioType
- MULTIPLE_VALUES_SEPARATOR - Static variable in class org.snpeff.interval.GffMarker
- multiThreaded - Variable in class org.snpeff.SnpEff
- MultivalueHashMap<K,
V> - Class in org.snpeff.collections -
A Hash that can hold multiple values for each key
- MultivalueHashMap() - Constructor for class org.snpeff.collections.MultivalueHashMap
- MUTUALLY_EXCLUSIVE - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
N
- NA_VALUE - Static variable in class org.snpeff.gtex.Gtex
- name - Variable in class org.snpeff.interval.Markers
- name - Variable in class org.snpeff.reactome.Entity
- name - Variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
- name() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
-
Return an annotation "name" Clean up characters to make them compatible with VCF annotations
- NCACTIVITY - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
- NCCAT - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
- NCCONS - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
- NCELEMENT - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
- NCFACTOR - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
- NCMARK - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
- NeedlemanWunsch - Class in org.snpeff.align
-
Needleman-Wunsch (global sequence alignment) algorithm for sequence alignment (short strings, since it's not memory optimized)
- NeedlemanWunsch(String, String) - Constructor for class org.snpeff.align.NeedlemanWunsch
- NeedlemanWunschOverlap - Class in org.snpeff.align
-
Needleman-Wunsch algorithm for string alignment (short strings, since it's not memory optimized)
- NeedlemanWunschOverlap(String, String) - Constructor for class org.snpeff.align.NeedlemanWunschOverlap
- NegativeRegulation - Enum constant in enum class org.snpeff.reactome.events.Reaction.RegulationType
- netCdsChange() - Method in class org.snpeff.interval.codonChange.CodonChange
-
We may have to calculate 'netCdsChange', which is the effect on the CDS Note: A deletion or a MNP might affect several exons
- netCdsChange() - Method in class org.snpeff.interval.codonChange.CodonChangeMnp
-
We may have to calculate 'netCdsChange', which is the effect on the CDS Note: A deletion or a MNP might affect several exons
- netChange(boolean) - Method in class org.snpeff.interval.Variant
-
Return the change (always compared to 'referenceStrand')
- netChange(Marker) - Method in class org.snpeff.interval.Variant
-
Only the part of the change that overlaps with a marker Return the change (always in positive strand)
- newItree() - Method in class org.snpeff.interval.tree.IntervalForest
-
Create new tree.
- newNode(Markers) - Method in class org.snpeff.interval.tree.IntervalNode
-
Create a new node
- next - Variable in class org.snpeff.fileIterator.FileIterator
- next() - Method in class org.snpeff.fileIterator.BinSeqFileIterator
- next() - Method in class org.snpeff.fileIterator.FastqFileIterator
- next() - Method in class org.snpeff.fileIterator.FileIterator
- next() - Method in class org.snpeff.fileIterator.VariantTxtFileIterator
- next() - Method in class org.snpeff.genBank.FeaturesFile
- next() - Method in class org.snpeff.interval.IntervalSetIterator
- next() - Method in class org.snpeff.util.CombinatorialIterator
- next() - Method in class org.snpeff.util.IubString
- NEXT_PROT - Enum constant in enum class org.snpeff.snpEffect.EffectType
- nextHighestPowerOfTwo(int) - Static method in class org.snpeff.collections.BitUtil
-
returns the next highest power of two, or the current value if it's already a power of two or zero
- nextHighestPowerOfTwo(long) - Static method in class org.snpeff.collections.BitUtil
-
returns the next highest power of two, or the current value if it's already a power of two or zero
- nextLine - Variable in class org.snpeff.fileIterator.FileIterator
- nextProt - Variable in class org.snpeff.SnpEff
- nextProt(Transcript, String, String, int, int) - Method in class org.snpeff.nextProt.NextProtMarkerFactory
-
Create a single NextProt marker
- nextProt(Transcript, NextProtXmlAnnotation, Location) - Method in class org.snpeff.nextProt.NextProtMarkerFactory
-
Create a list of NextProt markers according to this annotation
- NextProt - Class in org.snpeff.interval
-
NextProt annotation marker
- NextProt() - Constructor for class org.snpeff.interval.NextProt
- NextProt(Transcript, int, int, String) - Constructor for class org.snpeff.interval.NextProt
- NextProt(Transcript, int, int, String, String) - Constructor for class org.snpeff.interval.NextProt
- NextProtDb - Class in org.snpeff.nextProt
-
Parse NetxProt XML file and build a database
- NextProtDb(String, Config) - Constructor for class org.snpeff.nextProt.NextProtDb
- NextProtHandler - Class in org.snpeff.nextProt
-
Handler used in XML parsing for NextProt database It keeps track of the tags and saves state data to create Markers using NextProtMarkerFactory http://www.nextprot.org/
- NextProtHandler(NextProtMarkerFactory) - Constructor for class org.snpeff.nextProt.NextProtHandler
- nextProtKeepAllTrs - Variable in class org.snpeff.SnpEff
- NextProtMarkerFactory - Class in org.snpeff.nextProt
-
Creates Markers from nextprot XML annotations
- NextProtMarkerFactory(Config) - Constructor for class org.snpeff.nextProt.NextProtMarkerFactory
- NextProtSequenceConservation - Class in org.snpeff.nextProt
-
A simple analysis of sequence conservation for each entry type Why? Many NextProt annotations are only a few amino acids long (or only 1 AA) and often they only involve very specific sequences If the sequence is highly conserved and a non-synonymous mutation occurs, then this might be disruptive (i.e.
- NextProtSequenceConservation() - Constructor for class org.snpeff.nextProt.NextProtSequenceConservation
- NextProtXmlAnnotation - Class in org.snpeff.nextProt
-
Mimics the 'annotation' tag in a NextProt XML file
- NextProtXmlAnnotation(NextProtXmlEntry, String) - Constructor for class org.snpeff.nextProt.NextProtXmlAnnotation
- NextProtXmlEntry - Class in org.snpeff.nextProt
-
Mimics the 'entry' in a NextProt XML file
- NextProtXmlEntry(String, NextProtHandler) - Constructor for class org.snpeff.nextProt.NextProtXmlEntry
- NextProtXmlIsoform - Class in org.snpeff.nextProt
-
Mimics the 'isoform-mapping' in a NextProt XML file
- NextProtXmlIsoform(String) - Constructor for class org.snpeff.nextProt.NextProtXmlIsoform
- NextProtXmlNode - Class in org.snpeff.nextProt
-
Mimics a node in NextProt XML file
- NextProtXmlNode(String) - Constructor for class org.snpeff.nextProt.NextProtXmlNode
- nextSetBit(int) - Method in class org.snpeff.collections.OpenBitSet
-
Returns the index of the first set bit starting at the index specified.
- nextSetBit(long) - Method in class org.snpeff.collections.OpenBitSet
-
Returns the index of the first set bit starting at the index specified.
- Nmer - Class in org.snpeff.nmer
-
Binary packed N-mer (i.e.
- Nmer(int) - Constructor for class org.snpeff.nmer.Nmer
- Nmer(String) - Constructor for class org.snpeff.nmer.Nmer
- NmerCount - Class in org.snpeff.nmer
-
Mark if an Nmer has been 'seen' It only count up to 255 (one byte per counter)
- NmerCount(int) - Constructor for class org.snpeff.nmer.NmerCount
- NmerCountWc - Class in org.snpeff.nmer
-
Create a counter that can count Nmers as well as their WC complements That means that given an Nmer, the nmer and the Watson-Crick complement are counted the same.
- NmerCountWc(int) - Constructor for class org.snpeff.nmer.NmerCountWc
- NO_VARIANT - Static variable in class org.snpeff.interval.Variant
- noGenome - Variable in class org.snpeff.SnpEff
- NOINFO - Enum constant in enum class org.snpeff.logStatsServer.LogStats.RequestResult
- non_coding - Enum constant in enum class org.snpeff.interval.BioType
- NON_CODING - Enum constant in enum class org.snpeff.interval.Gene.GeneType
- NON_CODING - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.Coding
- non_stop_decay - Enum constant in enum class org.snpeff.interval.BioType
- NON_SYNONYMOUS_CODING - Enum constant in enum class org.snpeff.snpEffect.EffectType
- NON_SYNONYMOUS_START - Enum constant in enum class org.snpeff.snpEffect.EffectType
- NON_SYNONYMOUS_STOP - Enum constant in enum class org.snpeff.snpEffect.EffectType
- NONE - Enum constant in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
- NONE - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
- NONE - Enum constant in enum class org.snpeff.snpEffect.EffectType
- NONE - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.FunctionalClass
- NoneAlgorithm - Class in org.snpeff.geneSets.algorithm
-
An algorithm that does nothing
- NoneAlgorithm(GeneSets) - Constructor for class org.snpeff.geneSets.algorithm.NoneAlgorithm
- NONSENSE - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.FunctionalClass
- nonsense_mediated_decay - Enum constant in enum class org.snpeff.interval.BioType
- NormalDistribution - Class in org.snpeff.probablility
-
Calculate Normal distribution (PDF invalid input: '&' CDF) using more precision if required
- NormalDistribution() - Constructor for class org.snpeff.probablility.NormalDistribution
- noSpaces(String) - Static method in class org.snpeff.util.Gpr
-
Remove spaces and tabs from string.
- ntz(int) - Static method in class org.snpeff.collections.BitUtil
-
Returns number of trailing zeros in a 32 bit int value.
- ntz(long) - Static method in class org.snpeff.collections.BitUtil
-
Returns number of trailing zeros in a 64 bit long value.
- ntz2(long) - Static method in class org.snpeff.collections.BitUtil
-
returns 0 based index of first set bit (only works for x!=0)
This is an alternate implementation of ntz() - ntz3(long) - Static method in class org.snpeff.collections.BitUtil
-
returns 0 based index of first set bit
This is an alternate implementation of ntz() - ntzTable - Static variable in class org.snpeff.collections.BitUtil
-
table of number of trailing zeros in a byte
- NullReader - Class in org.snpeff.fileIterator
-
A buffered reader for a file.
- NullReader() - Constructor for class org.snpeff.fileIterator.NullReader
- NUM_CORES - Static variable in class org.snpeff.util.Gpr
- number - Variable in class org.snpeff.vcf.VcfHeaderInfo
- number(String) - Static method in class org.snpeff.interval.Chromosome
-
Convert to chromosome number (return '0' if it cannot be converted)
- NUMBER - Enum constant in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
- numberOfInterestingSymbols() - Method in class org.snpeff.geneOntology.GoTerms
-
Calculate how many interesting symbol-IDs in are there in all these GOTerms
- numberOfNodes() - Method in class org.snpeff.geneOntology.GoTerms
-
Number of nodes in this DAG
- numberOfNodesWithOneInterestingSymbol() - Method in class org.snpeff.geneOntology.GoTerms
-
Calculate the number of nodes in that have at least one interesting symbol
- numberOfNodesWithOneSymbol() - Method in class org.snpeff.geneOntology.GoTerms
-
Calculate the number of nodes in that have at least one annotated symbol
- numberOfSymbols() - Method in class org.snpeff.geneOntology.GoTerms
-
Calculate how many symbol-IDs in are there in all these GOTerms
- numChilds() - Method in class org.snpeff.interval.IntervalAndSubIntervals
- numWorkers - Variable in class org.snpeff.SnpEff
O
- observed(String) - Method in class org.snpeff.stats.ObservedOverExpected
- observed(String) - Method in class org.snpeff.stats.ObservedOverExpectedCHG
-
Count the number of CHH in this sequence
- observed(String) - Method in class org.snpeff.stats.ObservedOverExpectedCHH
-
Count the number of CHH in this sequence
- observed(String) - Method in class org.snpeff.stats.ObservedOverExpectedCpG
-
Count the number of CpG in this sequence
- observed(Exon) - Method in class org.snpeff.stats.ObservedOverExpected
-
Observed sequence (average between plus and minus strand)
- observed(Gene) - Method in class org.snpeff.stats.ObservedOverExpected
-
Observed sequence (average between plus and minus strand)
- observed(Transcript) - Method in class org.snpeff.stats.ObservedOverExpected
-
Observed sequence (average between plus and minus strand)
- observedChg(String) - Method in class org.snpeff.stats.ObservedOverExpected
-
Count the number of CHG in this sequence
- ObservedOverExpected - Class in org.snpeff.stats
-
Observed over expected values (o/e) ratios E.g.: CpG dinucleotides in a sequence
- ObservedOverExpected() - Constructor for class org.snpeff.stats.ObservedOverExpected
- ObservedOverExpectedCHG - Class in org.snpeff.stats
-
Observed over expected values (o/e) of CHG in a sequence
- ObservedOverExpectedCHG() - Constructor for class org.snpeff.stats.ObservedOverExpectedCHG
- ObservedOverExpectedCHH - Class in org.snpeff.stats
-
Observed over expected values (o/e) of CHH in a sequence
- ObservedOverExpectedCHH() - Constructor for class org.snpeff.stats.ObservedOverExpectedCHH
- ObservedOverExpectedCpG - Class in org.snpeff.stats
-
Observed over expected values (o/e) of CpG in a sequence
- ObservedOverExpectedCpG() - Constructor for class org.snpeff.stats.ObservedOverExpectedCpG
- oe(String) - Method in class org.snpeff.stats.ObservedOverExpected
-
Observed over expected ratio
- oe(Exon) - Method in class org.snpeff.stats.ObservedOverExpected
-
Observed over expected ratio
- oe(Gene) - Method in class org.snpeff.stats.ObservedOverExpected
-
Observed over expected ratio
- oe(Transcript) - Method in class org.snpeff.stats.ObservedOverExpected
-
Observed over expected ratio
- OFFSET - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
- OK - Enum constant in enum class org.snpeff.logStatsServer.LogStats.RequestResult
- ONE - Static variable in class org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
- onlyOneError - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
- onlyOneError - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- onlyProtein - Variable in class org.snpeff.SnpEff
- onlyRegulation - Variable in class org.snpeff.SnpEff
- onlyTranscriptsFile - Variable in class org.snpeff.SnpEff
- open() - Method in class org.snpeff.svg.Svg
- open() - Method in class org.snpeff.vcf.FileIndexChrPos
-
Open file and initiate mappings
- open(String) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- open(String) - Method in class org.snpeff.genBank.Features
-
Open a file
- open(String) - Method in class org.snpeff.genBank.FeaturesFile
-
Open a file
- OpenBitSet - Class in org.snpeff.collections
-
An "open" BitSet implementation that allows direct access to the array of words storing the bits.
- OpenBitSet() - Constructor for class org.snpeff.collections.OpenBitSet
- OpenBitSet(long) - Constructor for class org.snpeff.collections.OpenBitSet
-
Constructs an OpenBitSet large enough to hold numBits.
- OpenBitSet(long[], int) - Constructor for class org.snpeff.collections.OpenBitSet
-
Constructs an OpenBitSet from an existing long[].
- opposite() - Method in enum class org.snpeff.ped.Sex
-
Return the opposite sex
- or(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
- ORDER - Static variable in class org.snpeff.genBank.Features
- org.snpeff - package org.snpeff
- org.snpeff.align - package org.snpeff.align
- org.snpeff.binseq - package org.snpeff.binseq
- org.snpeff.binseq.coder - package org.snpeff.binseq.coder
- org.snpeff.binseq.comparator - package org.snpeff.binseq.comparator
- org.snpeff.binseq.indexer - package org.snpeff.binseq.indexer
- org.snpeff.codons - package org.snpeff.codons
- org.snpeff.collections - package org.snpeff.collections
- org.snpeff.complexity - package org.snpeff.complexity
- org.snpeff.coverage - package org.snpeff.coverage
- org.snpeff.fastq - package org.snpeff.fastq
- org.snpeff.fileIterator - package org.snpeff.fileIterator
- org.snpeff.fileIterator.microCosm - package org.snpeff.fileIterator.microCosm
- org.snpeff.fileIterator.parser - package org.snpeff.fileIterator.parser
- org.snpeff.filter - package org.snpeff.filter
- org.snpeff.genBank - package org.snpeff.genBank
- org.snpeff.geneOntology - package org.snpeff.geneOntology
- org.snpeff.geneSets - package org.snpeff.geneSets
- org.snpeff.geneSets.algorithm - package org.snpeff.geneSets.algorithm
- org.snpeff.genotypes - package org.snpeff.genotypes
- org.snpeff.gsa - package org.snpeff.gsa
- org.snpeff.gtex - package org.snpeff.gtex
- org.snpeff.interval - package org.snpeff.interval
- org.snpeff.interval.codonChange - package org.snpeff.interval.codonChange
- org.snpeff.interval.tree - package org.snpeff.interval.tree
- org.snpeff.logStatsServer - package org.snpeff.logStatsServer
- org.snpeff.motif - package org.snpeff.motif
- org.snpeff.nextProt - package org.snpeff.nextProt
- org.snpeff.nmer - package org.snpeff.nmer
- org.snpeff.osCmd - package org.snpeff.osCmd
- org.snpeff.outputFormatter - package org.snpeff.outputFormatter
- org.snpeff.overlap - package org.snpeff.overlap
- org.snpeff.pdb - package org.snpeff.pdb
- org.snpeff.ped - package org.snpeff.ped
- org.snpeff.probablility - package org.snpeff.probablility
- org.snpeff.probablility.bootstrap - package org.snpeff.probablility.bootstrap
- org.snpeff.reactome - package org.snpeff.reactome
- org.snpeff.reactome.events - package org.snpeff.reactome.events
- org.snpeff.sam - package org.snpeff.sam
- org.snpeff.serializer - package org.snpeff.serializer
- org.snpeff.snpEffect - package org.snpeff.snpEffect
- org.snpeff.snpEffect.commandLine - package org.snpeff.snpEffect.commandLine
- org.snpeff.snpEffect.factory - package org.snpeff.snpEffect.factory
- org.snpeff.spliceSites - package org.snpeff.spliceSites
- org.snpeff.stats - package org.snpeff.stats
- org.snpeff.stats.plot - package org.snpeff.stats.plot
- org.snpeff.svg - package org.snpeff.svg
- org.snpeff.util - package org.snpeff.util
- org.snpeff.vcf - package org.snpeff.vcf
- OsCmdQueue - Class in org.snpeff.osCmd
-
A queue of commands to be run.
- OsCmdQueue() - Constructor for class org.snpeff.osCmd.OsCmdQueue
- OsCmdRunner - Class in org.snpeff.osCmd
-
Run an OS command as a thread
- OsCmdRunner(String, String[]) - Constructor for class org.snpeff.osCmd.OsCmdRunner
- output - Variable in class org.snpeff.reactome.Entity
- output - Variable in class org.snpeff.SnpEff
- OutputFormatter - Class in org.snpeff.outputFormatter
-
Formats output How is this used: - newSection(); // Create a new 'section' on the output format (e.g.
- OutputFormatter() - Constructor for class org.snpeff.outputFormatter.OutputFormatter
- outputs - Variable in class org.snpeff.reactome.events.Reaction
- overlap(BinarySequence, int) - Method in class org.snpeff.binseq.BinarySequence
-
Creates a new sequence by overlapping 'this' and 'sequence' E.g.
- overlap(BinarySequence, int) - Method in class org.snpeff.binseq.DnaAndQualitySequence
-
Creates a new sequence by overlapping 'this' and 'sequence' E.g.
- overlap(BinarySequence, int) - Method in class org.snpeff.binseq.DnaSequence
-
Creates a new sequence by overlapping 'this' and 'sequence' E.g.
- overlap(DnaSequence, DnaSequence) - Method in class org.snpeff.overlap.OverlapDnaSeq
- overlap(S, S) - Method in class org.snpeff.overlap.Overlap
-
Calculate the best overlap between two sequences
- overlap(T) - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
-
Find the best possible overlap and join the sequences or just add add the sequence to the index
- Overlap<S> - Class in org.snpeff.overlap
-
Calculates the best overlap between two sequences Note: An overlap is a simple 'alignment' which can only contain gaps at the beginning or at the end of the sequences.
- Overlap() - Constructor for class org.snpeff.overlap.Overlap
- OverlapDnaSeq - Class in org.snpeff.overlap
- OverlapDnaSeq() - Constructor for class org.snpeff.overlap.OverlapDnaSeq
- OverlapFilter<T> - Interface in org.snpeff.binseq.indexer
-
Indicate whether an overlap between two sequences should be considered or not
- OverlapFilterCompareAllAll - Class in org.snpeff.binseq.indexer
-
Only allow overlaps between sequences mapped to same/different partition
- OverlapFilterCompareAllAll() - Constructor for class org.snpeff.binseq.indexer.OverlapFilterCompareAllAll
- OverlapFilterDnaId - Class in org.snpeff.binseq.indexer
-
Only allow sequences with different IDs to be overlapped
- OverlapFilterDnaId() - Constructor for class org.snpeff.binseq.indexer.OverlapFilterDnaId
- OverlapRessult<T> - Class in org.snpeff.binseq.indexer
-
An object used to store overlap parameters
- OverlapRessult() - Constructor for class org.snpeff.binseq.indexer.OverlapRessult
P
- p(int[], int[], double[]) - Method in class org.snpeff.probablility.CochranArmitageTest
- P - Static variable in class org.snpeff.fastq.FastqSplit
- P_VALUE_THRESHOLD - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- padN(String, int) - Static method in class org.snpeff.util.GprSeq
- pAll(int) - Method in class org.snpeff.spliceSites.AcgtTree
- pAll(int, List<Double>) - Method in class org.snpeff.spliceSites.AcgtTree
- parent - Variable in class org.snpeff.interval.Interval
- parse() - Method in class org.snpeff.nextProt.NextProtDb
-
Parse all XML files in a directory
- parse() - Method in class org.snpeff.vcf.VcfEntry
-
Parse a 'line' from a 'vcfFileIterator'
- parse() - Method in class org.snpeff.vcf.VcfHeader
-
Parse header lines
- parse(String) - Method in interface org.snpeff.fileIterator.parser.Parser
- parse(String) - Method in class org.snpeff.fileIterator.VcfFileIterator
- parse(String) - Static method in enum class org.snpeff.genBank.Feature.Type
-
Parse a string into a Feature.Type
- parse(String) - Method in class org.snpeff.gtex.GtexExperiment
- parse(String) - Static method in enum class org.snpeff.interval.BioType
-
Parse a BioType
- parse(String) - Static method in enum class org.snpeff.interval.GffType
- parse(String) - Static method in enum class org.snpeff.interval.TranscriptSupportLevel
- parse(String) - Method in class org.snpeff.logStatsServer.VersionCheck
-
Parse versions page Format: One entry per line Line format: "softwareName \t version \t date \t URL \n"
- parse(String) - Method in class org.snpeff.ped.PedEntry
- parse(String) - Method in class org.snpeff.ped.TfamEntry
-
Parse a line form a TFAM file
- parse(String) - Method in class org.snpeff.sam.SamHeaderRecord
-
Parse a line for this record type
- parse(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Parse a line
- parse(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22
- parse(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
- parse(String) - Static method in enum class org.snpeff.vcf.VcfInfoType
- parse(String[]) - Method in class org.snpeff.genotypes.Genotypes
-
Parse command line arguments
- parse(String[]) - Method in class org.snpeff.ped.PedEntry
- parse(String[]) - Method in class org.snpeff.ped.TfamEntry
-
Parse fields form a line
- parse(Genome, String) - Method in class org.snpeff.interval.GffMarker
-
Parse an entry (line) from a GFF file
- parse(EffFormatVersion, String) - Static method in enum class org.snpeff.snpEffect.EffectType
-
Parse a string to an EffectType
- parse(VcfConsequenceHeader, String) - Static method in class org.snpeff.vcf.VcfConsequence
- parse(VcfConsequenceHeader, VcfEntry) - Static method in class org.snpeff.vcf.VcfConsequence
- parseArgs(String[]) - Method in class org.snpeff.fastq.FastqSplit
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.SnpEff
-
Parse command line arguments
- parseArgs(String[]) - Method in interface org.snpeff.snpEffect.commandLine.CommandLine
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuildNextProt
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCount
-
Parse
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDownload
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDump
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdLen
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdSeq
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdShow
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
- parseArgs(String[]) - Method in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- parseAttributes(String) - Method in class org.snpeff.interval.GffMarker
-
Parse attributes (key-value pairs) from a line in a GFF file
- parseAttributes(String) - Method in class org.snpeff.interval.Gtf2Marker
-
Parse attributes
- parseBoolSafe(String) - Static method in class org.snpeff.util.Gpr
-
Equivalent to Boolean.parseBoolean, except it returns 0 on invalid integer (NumberFormatException)
- parsedHeader() - Method in class org.snpeff.fileIterator.GuessTableTypes
- parseDoubleSafe(String) - Static method in class org.snpeff.util.Gpr
-
Equivalent to Double.parseDouble(), except it returns 0 on invalid double (NumberFormatException)
- parseFeatures() - Method in class org.snpeff.genBank.Features
-
Parse features
- parseField(String, String) - Method in class org.snpeff.sam.SamHeaderRecord
-
Parse a field for this record
- parseField(String, String) - Method in class org.snpeff.sam.SamHeaderRecordSq
- parseFieldLine(String, String, int) - Method in class org.snpeff.genBank.Embl
-
Parse a feature line Line types: ID - identification (begins each entry; 1 per entry) AC - accession number (>=1 per entry) PR - project identifier (0 or 1 per entry) DT - date (2 per entry) DE - description (>=1 per entry) KW - keyword (>=1 per entry) OS - organism species (>=1 per entry) OC - organism classification (>=1 per entry) OG - organelle (0 or 1 per entry) RN - reference number (>=1 per entry) RC - reference comment (>=0 per entry) RP - reference positions (>=1 per entry) RX - reference cross-reference (>=0 per entry) RG - reference group (>=0 per entry) RA - reference author(s) (>=0 per entry) RT - reference title (>=1 per entry) RL - reference location (>=1 per entry) DR - database cross-reference (>=0 per entry) CC - comments or notes (>=0 per entry) AH - assembly header (0 or 1 per entry) AS - assembly information (0 or >=1 per entry) FH - feature table header (2 per entry) FT - feature table data (>=2 per entry) XX - spacer line (many per entry) SQ - sequence header (1 per entry) CO - contig/construct line (0 or >=1 per entry) bb - (blanks) sequence data (>=1 per entry) // - termination line (ends each entry; 1 per entry)
- parseFieldLine(String, String, int, int) - Method in class org.snpeff.genBank.GenBank
-
Parse a feature line
- parseFloatSafe(String) - Static method in class org.snpeff.util.Gpr
-
Equivalent to Float.parseFloat(), except it returns 0 on invalid double (NumberFormatException)
- parseId() - Method in class org.snpeff.interval.GffMarker
-
Obtain or create an ID
- parseInt(char[]) - Static method in class org.snpeff.collections.ArrayUtil
-
Parses the string argument as if it was an int value and returns the result.
- parseInt(char[], int, int) - Static method in class org.snpeff.collections.ArrayUtil
-
Parses a char array into an int.
- parseInt(char[], int, int, int) - Static method in class org.snpeff.collections.ArrayUtil
-
Parses the string argument as if it was an int value and returns the result.
- parseIntSafe(String) - Static method in class org.snpeff.util.Gpr
-
Equivalent to Integer.parseInt, except it returns 0 on invalid integer (NumberFormatException)
- parseLof() - Method in class org.snpeff.vcf.VcfEntry
-
Parse LOF from VcfEntry
- parseLongSafe(String) - Static method in class org.snpeff.util.Gpr
-
Equivalent to Integer.parseInt, except it returns 0 on invalid integer (NumberFormatException)
- parseNmd() - Method in class org.snpeff.vcf.VcfEntry
-
Parse NMD from VcfEntry
- parsePosition(String) - Method in class org.snpeff.fileIterator.MarkerFileIterator
-
Parse a string as a 'position'.
- parsePosition(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Parse a string as a 'position'.
- Parser<T> - Interface in org.snpeff.fileIterator.parser
-
Parse a string and return a collection of objects.
- parseSampleNames() - Method in class org.snpeff.vcf.VcfHeader
- parseSampleNum() - Method in class org.snpeff.vcf.VcfHeader
- parseTranscript(String) - Static method in class org.snpeff.snpEffect.Hgvs
- parseVcfLine(String) - Method in class org.snpeff.fileIterator.VcfFileIterator
-
Parse a line from a VCF file
- Pathway - Class in org.snpeff.reactome.events
-
A Reactome pathway
- Pathway(int, String) - Constructor for class org.snpeff.reactome.events.Pathway
- Pcingola - Class in org.snpeff
-
Author's data
- Pcingola() - Constructor for class org.snpeff.Pcingola
- pdb() - Method in class org.snpeff.pdb.ProteinInteractions
-
PDB analysis
- PDB_ENT_EXT - Static variable in class org.snpeff.pdb.PdbFile
- PDB_ENT_EXT_GZ - Static variable in class org.snpeff.pdb.PdbFile
- PDB_EXT - Static variable in class org.snpeff.pdb.PdbFile
- PDB_EXT_GZ - Static variable in class org.snpeff.pdb.PdbFile
- PDB_EXTS - Static variable in class org.snpeff.pdb.PdbFile
- PDB_RESOLUTION_UNSET - Static variable in class org.snpeff.pdb.PdbFile
- pdbAaLen - Variable in class org.snpeff.pdb.IdMapperEntry
- pdbAnalysis() - Method in class org.snpeff.pdb.PdbFile
-
Analyze a PDB file
- pdbAnalysis() - Method in class org.snpeff.pdb.ProteinInteractions
-
Check that protein sequences form PDB matches sequences from Genome Return an IdMapped of confirmed entries (i.e.
- pdbChainId - Variable in class org.snpeff.pdb.IdMapperEntry
- pdbChainId1 - Variable in class org.snpeff.pdb.DistanceResult
- pdbChainId2 - Variable in class org.snpeff.pdb.DistanceResult
- PdbFile - Class in org.snpeff.pdb
-
A structure that reads PDB files
- PdbFile(ProteinInteractions, String) - Constructor for class org.snpeff.pdb.PdbFile
- PdbUtil - Class in org.snpeff.pdb
- PdbUtil() - Constructor for class org.snpeff.pdb.PdbUtil
- pdf(double, double, double) - Static method in class org.snpeff.probablility.NormalDistribution
- pdf(double, int, int) - Method in class org.snpeff.probablility.Binomial
-
Probability density function
- pdf(int, int, int) - Static method in class org.snpeff.probablility.RankSumPdf
-
Probability density function (pdf)
- pdf(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Probability of getting a rank sum equal to 'r' when adding the ranks of 'nt' selected items.
- pdfApfloat(double, double, double) - Static method in class org.snpeff.probablility.NormalDistribution
- pdfExact(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Probability of getting a rank sum equal to 'r' when adding the ranks of 'nt' selected items.
- pdfExact(int, int, long, long, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Probability density function (pdf): Exact calculation
- pdfLog(double, int, int) - Method in class org.snpeff.probablility.Binomial
- pdfNormal(int, int, int) - Static method in class org.snpeff.probablility.RankSumPdf
-
Normal approximation to rank sum statistic
- pdfNormal(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Normal approximation to rank sum statistic
- pdfTriangle(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Uniform 'approximation' to rank sum statistic
- pdfUniform(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Uniform 'approximation' to rank sum statistic
- PedEntry - Class in org.snpeff.ped
-
An entry in a PED table.
- PedEntry(PlinkMap, String) - Constructor for class org.snpeff.ped.PedEntry
- PedEntry(PlinkMap, String, String, String, String, Sex, double, String[]) - Constructor for class org.snpeff.ped.PedEntry
- PedFamily - Class in org.snpeff.ped
-
A family: A group of Tfams with the same familyId
- PedFamily() - Constructor for class org.snpeff.ped.PedFamily
- PedFileIterator - Class in org.snpeff.ped
-
PED file iterator (PED file from PLINK) Reference: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
- PedFileIterator(String, String) - Constructor for class org.snpeff.ped.PedFileIterator
- PedGenotype - Class in org.snpeff.ped
-
A Simple genotype implementation for PED files
- PedGenotype(String[]) - Constructor for class org.snpeff.ped.PedGenotype
- PedGenotype(String[], String, int) - Constructor for class org.snpeff.ped.PedGenotype
- Pedigree - Class in org.snpeff.vcf
-
A pedigree for cancer samples
- Pedigree(VcfFileIterator) - Constructor for class org.snpeff.vcf.Pedigree
- Pedigree(VcfFileIterator, String) - Constructor for class org.snpeff.vcf.Pedigree
- PEDIGREE_PREFIX - Static variable in class org.snpeff.vcf.VcfHeader
- PedigreeEntry - Class in org.snpeff.vcf
-
Pedigree entry in a VCF file header E.g.: ##PEDIGREE=invalid input: '<'Derived=Patient_01_Somatic,Original=Patient_01_Germline> or ##PEDIGREE=invalid input: '<'Child=CHILD-GENOME-ID,Mother=MOTHER-GENOME-ID,Father=FATHER-GENOME-ID>
- PedigreeEntry(String, String) - Constructor for class org.snpeff.vcf.PedigreeEntry
- PedigreeEntry(String, String, String) - Constructor for class org.snpeff.vcf.PedigreeEntry
- PedPedigree - Class in org.snpeff.ped
-
A pedigree of PedEntries
- PedPedigree() - Constructor for class org.snpeff.ped.PedPedigree
- PedPedigree(String) - Constructor for class org.snpeff.ped.PedPedigree
- percent(String) - Method in class org.snpeff.stats.CountByType
-
Percentage by type
- percentColumns() - Method in class org.snpeff.stats.plot.GoogleBarChart
-
Scale columns to their respective counts
- percentColumns(ArrayList<String>) - Method in class org.snpeff.stats.plot.GoogleBarChart
-
Scale column to total sum
- Performance Results - Search tag in class org.snpeff.collections.OpenBitSet
- Section
- phase - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- PHASE - Enum constant in enum class org.snpeff.interval.FrameType
- PHENOTYPE_CASE - Static variable in class org.snpeff.ped.TfamEntry
-
From PLINK's manual: Affection status, by default, should be coded: -9 missing 0 missing 1 unaffected 2 affected
- PHENOTYPE_CONTROL - Static variable in class org.snpeff.ped.TfamEntry
- PHENOTYPE_MISSING - Static variable in class org.snpeff.ped.TfamEntry
- pident - Variable in class org.snpeff.fileIterator.BlastResultEntry
- PlinkMap - Class in org.snpeff.ped
-
PLINK MAP file References: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
- PlinkMap() - Constructor for class org.snpeff.ped.PlinkMap
- PlinkMap(String) - Constructor for class org.snpeff.ped.PlinkMap
- plodity() - Method in class org.snpeff.vcf.VcfGenotype
-
Genotype plodity (i.e.
- Polymerisation - Class in org.snpeff.reactome.events
-
A polymerization event
- Polymerisation(int, String) - Constructor for class org.snpeff.reactome.events.Polymerisation
- polymorphic_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- pop(long) - Static method in class org.snpeff.collections.BitUtil
-
Returns the number of bits set in the long
- pop_andnot(long[], long[], int, int) - Static method in class org.snpeff.collections.BitUtil
-
Returns the popcount or cardinality of A invalid input: '&' ~B Neither array is modified.
- pop_array(long[], int, int) - Static method in class org.snpeff.collections.BitUtil
-
Returns the number of set bits in an array of longs.
- pop_intersect(long[], long[], int, int) - Static method in class org.snpeff.collections.BitUtil
-
Returns the popcount or cardinality of the two sets after an intersection.
- pop_union(long[], long[], int, int) - Static method in class org.snpeff.collections.BitUtil
-
Returns the popcount or cardinality of the union of two sets.
- pop_xor(long[], long[], int, int) - Static method in class org.snpeff.collections.BitUtil
- pos - Variable in class org.snpeff.fileIterator.MatrixEntry
- pos() - Method in class org.snpeff.snpEffect.HgvsDna
-
Genomic position for exonic variants
- pos(int) - Method in class org.snpeff.snpEffect.HgvsDna
-
HGVS position base on genomic coordinates (chr is assumed to be the same as in transcript/marker).
- pos(int) - Method in class org.snpeff.snpEffect.HgvsProtein
-
Protein position
- pos(int, int) - Method in class org.snpeff.snpEffect.HgvsProtein
- pos(String) - Method in class org.snpeff.vcf.FileIndexChrPos
-
The position argument of a line (second column in tab-separated format).
- pos(Transcript, int) - Method in class org.snpeff.snpEffect.HgvsProtein
-
Protein position
- pos(Transcript, int, int) - Method in class org.snpeff.snpEffect.HgvsProtein
-
Position string given two coordinates
- POS_OFFSET - Static variable in class org.snpeff.vcf.FileIndexChrPos
- pos1 - Variable in class org.snpeff.pdb.DistanceResult
- pos2 - Variable in class org.snpeff.pdb.DistanceResult
- posArray() - Method in class org.snpeff.stats.ChrPosStats
- posDel() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Position for deletions
- posDelIns() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Position for 'delins'
- posDownstream(int) - Method in class org.snpeff.snpEffect.HgvsDna
-
Position downstream of the transcript
- posDup() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Position for 'duplications' (a special kind of insertion)
- posExon(int) - Method in class org.snpeff.snpEffect.HgvsDna
-
Convert genomic position to HGVS compatible (DNA) position
- posFs() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Frame shifts ....are described using ...
- posIns() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Position for insertions
- posIntron(int, Intron) - Method in class org.snpeff.snpEffect.HgvsDna
-
Intronic position
- position - Variable in class org.snpeff.vcf.FileIndexChrPos.LineAndPos
- PositiveRegulation - Enum constant in enum class org.snpeff.reactome.events.Reaction.RegulationType
- posSnpOrMnp() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Position: SNP or NMP
- PosStats - Class in org.snpeff.stats
-
How many changes per position do we have in a chromosome.
- PosStats() - Constructor for class org.snpeff.stats.PosStats
- PosStats(String) - Constructor for class org.snpeff.stats.PosStats
- PosStats(String, int) - Constructor for class org.snpeff.stats.PosStats
- posUpstream(int) - Method in class org.snpeff.snpEffect.HgvsDna
-
Position upstream of the transcript Note: How to calculate Upstream position: If strand is '-' as for NM_016176.3, "genomicTxStart" being the rightmost tx coord: cDotUpstream = -(cdsStart + variantPos - genomicTxStart) Instead of "-(variantPos - genomicCdsStart)": The method that stays in transcript space until extending beyond the transcript is correct because of these statements on http://varnomen.hgvs.org/bg-material/numbering/: * nucleotides upstream (5') of the ATG-translation initiation codon (start) are marked with a "-" (minus) and numbered c.-1, c.-2, c.-3, etc.
- posUtr3(int) - Method in class org.snpeff.snpEffect.HgvsDna
-
Position within 3'UTR
- posUtr5(int) - Method in class org.snpeff.snpEffect.HgvsDna
-
Position within 5'UTR
- PREFERRED_CONFIG_FILE - Static variable in class org.snpeff.snpEffect.Config
- prefixTranslocation() - Method in class org.snpeff.snpEffect.HgvsDna
-
Translocation nomenclature.
- prependEachLine(String, Object) - Static method in class org.snpeff.util.Gpr
-
Prepend a message to each line
- prime3_overlapping_ncrna - Enum constant in enum class org.snpeff.interval.BioType
- print() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Dump to sdtout
- print(String) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- print(String) - Method in class org.snpeff.outputFormatter.OutputFormatter
-
Print a "raw" string to a file
- PRINT_SOMETHING_TIME - Static variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- PRINT_SOMETHING_TIME - Static variable in class org.snpeff.geneSets.GeneSets
- printSection(Marker) - Method in class org.snpeff.outputFormatter.OutputFormatter
-
End this section and print results
- printSequences() - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
- probabilityTable(CountByType) - Method in class org.snpeff.coverage.CountReadsOnMarkers
-
Show probabilities
- processed_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- processed_transcript - Enum constant in enum class org.snpeff.interval.BioType
- progress() - Method in class org.snpeff.osCmd.ExecuteOsCommand
-
Report progress
- progress() - Method in interface org.snpeff.osCmd.Progress
- Progress - Interface in org.snpeff.osCmd
- PROGRESSIVE_BASES_EXTRA - Static variable in class org.snpeff.align.VariantRealign
- PROGRESSIVE_BASES_MULTIPLIER - Static variable in class org.snpeff.align.VariantRealign
- PromoterSequences - Class in org.snpeff
-
Get promoter sequences from genes
- PromoterSequences(String, String, List<String>) - Constructor for class org.snpeff.PromoterSequences
- propertyToStringArray(String) - Method in class org.snpeff.snpEffect.Config
-
Parse a comma separated property as a string array
- protein() - Method in class org.snpeff.interval.Transcript
-
Protein sequence (amino acid sequence produced by this transcripts)
- protein_coding - Enum constant in enum class org.snpeff.interval.BioType
- PROTEIN_INTERACTION_FILE - Static variable in class org.snpeff.pdb.ProteinInteractions
- PROTEIN_PROTEIN_INTERACTION_LOCUS - Enum constant in enum class org.snpeff.snpEffect.EffectType
- PROTEIN_STRUCTURAL_INTERACTION_LOCUS - Enum constant in enum class org.snpeff.snpEffect.EffectType
- proteinId - Variable in class org.snpeff.pdb.DistanceResult
- proteinId - Variable in class org.snpeff.pdb.IdMapperEntry
- ProteinInteractionLocus - Class in org.snpeff.interval
-
Protein interaction: An amino acid that is "in contact" with another amino acid.
- ProteinInteractionLocus() - Constructor for class org.snpeff.interval.ProteinInteractionLocus
- ProteinInteractionLocus(Transcript, int, int, String) - Constructor for class org.snpeff.interval.ProteinInteractionLocus
- ProteinInteractions - Class in org.snpeff.pdb
-
This class reads a set of protein structure (PDB) files, analyzes the structures, and creates a interactions file for a SnpEff genome database (interactions.bin)
- ProteinInteractions() - Constructor for class org.snpeff.pdb.ProteinInteractions
- ProteinProteinInteractionLocus - Class in org.snpeff.interval
-
Protein interaction: An amino acid that is "in contact" with another amino acid within the same protein.
- ProteinProteinInteractionLocus() - Constructor for class org.snpeff.interval.ProteinProteinInteractionLocus
- ProteinProteinInteractionLocus(Transcript, int, int, Transcript, String) - Constructor for class org.snpeff.interval.ProteinProteinInteractionLocus
- ProteinStructuralInteractionLocus - Class in org.snpeff.interval
-
Protein interaction: An amino acid that is "in contact" with another amino acid.
- ProteinStructuralInteractionLocus() - Constructor for class org.snpeff.interval.ProteinStructuralInteractionLocus
- ProteinStructuralInteractionLocus(Transcript, int, int, String) - Constructor for class org.snpeff.interval.ProteinStructuralInteractionLocus
- pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- PurityChange - Class in org.snpeff.snpEffect
-
Analize purity changes in codons and amino acids
- PurityChange(CodonTable) - Constructor for class org.snpeff.snpEffect.PurityChange
- put(long, long) - Method in class org.snpeff.collections.HashLongLongArray
-
Insert a invalid input: '<'key, value> pair How does it work? - bucket_number = hash.get( key ) - bu = bucket[ bucket_number ] - append 'value' to 'bu'
- pValue - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- pValueBonferroni() - Method in class org.snpeff.gsa.ScoreList
-
Minimum p-value corrected using Bonferroni
- pValueDown(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
- pValueDown(int, int, int, int, double) - Method in class org.snpeff.probablility.FisherExactTest
-
Pvalue for 'k' or less Note: Includes 'k' It also compares to a 'threshold' value to speedup the process.
- pValueFdr(double) - Method in class org.snpeff.gsa.ScoreList
-
Combine p-values using FDR procedure References: http://en.wikipedia.org/wiki/False_discovery_rate
- pValueFisherChi2() - Method in class org.snpeff.gsa.ScoreList
-
Combine p-values using Fisher's method References: http://en.wikipedia.org/wiki/Fisher's_method
- pValueSimes() - Method in class org.snpeff.gsa.ScoreList
-
Combine p-values using Simes's procedure References: http://biomet.oxfordjournals.org/content/73/3/751
- PvaluesList - Class in org.snpeff.gsa
-
A list of pvalues (i.e.
- PvaluesList() - Constructor for class org.snpeff.gsa.PvaluesList
- pValueUp(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
- pValueUp(int, int, int, int, double) - Method in class org.snpeff.probablility.FisherExactTest
-
Fisher's exact test for more than 'k' It also compares to a 'threshold' value to speedup the process.
- pValueZScore() - Method in class org.snpeff.gsa.ScoreList
-
Combine p-values using Stouffer's Z-score method References: http://en.wikipedia.org/wiki/Fisher's_method (scroll down to Stouffer's method)
- Pwm - Class in org.snpeff.motif
-
Create a DNA motif count matrix Refrence http://en.wikipedia.org/wiki/Position-specific_scoring_matrix
- Pwm(int) - Constructor for class org.snpeff.motif.Pwm
- Pwm(String) - Constructor for class org.snpeff.motif.Pwm
- PwmAndSeqs - Class in org.snpeff.motif
-
Create a DNA motif count matrix and also count the number of sequences in that contribute to this motif.
- PwmAndSeqs(int) - Constructor for class org.snpeff.motif.PwmAndSeqs
Q
- qend - Variable in class org.snpeff.fileIterator.BlastResultEntry
- Qseq2Fastq - Class in org.snpeff
-
Convert qseq file to fastq
- Qseq2Fastq() - Constructor for class org.snpeff.Qseq2Fastq
- qseqid - Variable in class org.snpeff.fileIterator.BlastResultEntry
- qstart - Variable in class org.snpeff.fileIterator.BlastResultEntry
- quality - Variable in class org.snpeff.vcf.VcfEntry
- qualityToBits(int) - Method in class org.snpeff.binseq.coder.Coder
-
Encode a quality using a binary representation
- qualityToBits(int) - Method in class org.snpeff.binseq.coder.DnaQualityCoder
-
WARNING: This implementation transforms the quality to a range [0, ..., 63] (in order to use 6 bits)
- qualtityArray(Fastq) - Static method in class org.snpeff.fastq.FastqTools
-
Create an array of integers describing quality
- quantile(double) - Method in class org.snpeff.gsa.ScoreList
-
Get pvalue quantile
- quantile(double) - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
-
Smallest number whose CDF is larger than a given quantile.
- query(Interval) - Method in class org.snpeff.interval.tree.IntervalNode
-
Perform an interval intersection query on the node
- query(Interval) - Method in class org.snpeff.interval.tree.IntervalNodeOri
-
Perform an interval intersection query on the node
- query(Interval) - Method in class org.snpeff.interval.tree.IntervalTree
-
Perform an interval query, returning the intervals that intersect with 'interval'
- query(Interval) - Method in class org.snpeff.interval.tree.IntervalTreeArray
-
Query index to find all VCF entries intersecting 'marker' Store VCF entries in 'results'
- query(Interval) - Method in class org.snpeff.interval.tree.IntervalTreeOri
-
Perform an interval query, returning the intervals that intersect with 'interval'
- query(Interval) - Method in interface org.snpeff.interval.tree.Itree
-
Perform an interval query, returning the intervals that intersect with 'interval'
- query(Interval, int, Markers) - Method in class org.snpeff.interval.tree.IntervalTreeArray
-
Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF entries in 'results'
- query(Marker) - Method in class org.snpeff.interval.CytoBands
- query(Marker) - Method in class org.snpeff.interval.Exon
-
Query all genomic regions that intersect 'marker'
- query(Marker) - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Query all genomic regions that intersect 'marker'
- query(Marker) - Method in class org.snpeff.interval.Intron
-
Query all genomic regions that intersect 'marker'
- query(Marker) - Method in class org.snpeff.interval.Marker
-
Query all genomic regions that intersect 'marker' (this makes sense in Gene, Transcript, Exon, etc.)
- query(Marker) - Method in class org.snpeff.interval.Transcript
-
Query all genomic regions that intersect 'marker'
- query(Marker) - Method in class org.snpeff.interval.tree.IntervalForest
-
Query all intervals that intersect with 'interval'
- query(Marker) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Return a collection of intervals that intersect 'marker'
- query(Markers) - Method in class org.snpeff.interval.tree.IntervalForest
-
Query all intervals that intersect with any interval in 'intervals'
- query(IntervalForest) - Method in class org.snpeff.interval.Marker
-
Return a collection of intervals that intersect this marker
- query(IntervalForest) - Method in class org.snpeff.interval.VariantBnd
-
Return a collection of intervals that intersect both ends of this variant
- queryClosestGene(Marker) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Find closest gene to this marker
- queryDeep(Marker) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Return a collection of intervals that intersect 'marker' Query resulting genes, transcripts and exons to get ALL types of intervals possible
- queryExon(Marker) - Method in class org.snpeff.interval.Transcript
-
Return the first exon that intersects 'interval' (null if not found)
- queryIntersects(Interval, int, Markers) - Method in class org.snpeff.interval.tree.IntervalTreeArray
-
Query entries intersecting 'marker' at node 'idx'
- queryMarkerSequence(Marker) - Method in class org.snpeff.binseq.GenomicSequences
-
Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form database
- querySequence(Marker) - Method in class org.snpeff.binseq.GenomicSequences
-
Get sequence for a marker
- queryUnique(Markers) - Method in class org.snpeff.interval.tree.IntervalForest
-
Query unique intervals that intersect with any interval in 'markers' I.e.: Return a set of intervals that intersects (at least once) with any interval in 'markers'
- quiet - Variable in class org.snpeff.SnpEff
R
- rand() - Method in class org.snpeff.interval.Markers
-
Return a random interval within this collection
- rand(int) - Method in class org.snpeff.probablility.RandMarker
-
Create a random marker of size readLen
- rand(int, int) - Method in class org.snpeff.stats.PosStats
-
Create random counts (used for debugging)
- rand(Random) - Static method in enum class org.snpeff.ped.Sex
-
Random sex
- randBase(Random) - Static method in class org.snpeff.util.GprSeq
-
Random base
- RandMarker - Class in org.snpeff.probablility
-
Create random markers using a uniform distribution
- RandMarker(Genome) - Constructor for class org.snpeff.probablility.RandMarker
- RandMarker(Genome, int) - Constructor for class org.snpeff.probablility.RandMarker
- random(int) - Method in class org.snpeff.nmer.NmerCount
-
Create random sequences and count nmers This is used to create a null distribution
- randomizeSamples() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
-
Shufle samples (random ranks)
- randomSampling(int, int, int) - Method in class org.snpeff.stats.ReadsOnMarkersModel
-
Sample and calculate the probability of hitting each type of marker (marker.class).
- randSequence(Random, int) - Static method in class org.snpeff.util.GprSeq
-
Random sequence
- rankByValue(boolean) - Method in class org.snpeff.geneSets.GeneSetsRanked
-
Rank genes by value
- rankExons() - Method in class org.snpeff.interval.Transcript
-
Assign ranks to exons
- ranks(boolean) - Method in class org.snpeff.stats.CountByType
-
A map: key -> rank(counts)
- rankSum() - Method in class org.snpeff.geneSets.GeneSet
-
Calculate rankSum, rankedSymbols and maxRank
- rankSum() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
-
Calculate rankSums
- RANKSUM - Enum constant in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
- RANKSUM_GREEDY - Enum constant in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
- RankSumNoReplacementPdf - Class in org.snpeff.probablility
-
Calculate rank sum probability distribution function (pdf) and cumulative distribution function (cdf).
- RankSumNoReplacementSimulate - Class in org.snpeff.probablility
-
Calculate rank sum probability distribution function (pdf) and cumulative distribution function (cdf).
- RankSumNoReplacementSimulate(int, int) - Constructor for class org.snpeff.probablility.RankSumNoReplacementSimulate
- RankSumPdf - Class in org.snpeff.probablility
-
Calculate rank sum probability distribution function (pdf) and cumulative distribution function (cdf).
- RankSumPdf() - Constructor for class org.snpeff.probablility.RankSumPdf
- RankSumPValueAlgorithm - Class in org.snpeff.geneSets.algorithm
- RankSumPValueAlgorithm(GeneSetsRanked, int) - Constructor for class org.snpeff.geneSets.algorithm.RankSumPValueAlgorithm
- RankSumPValueGreedyAlgorithm - Class in org.snpeff.geneSets.algorithm
- RankSumPValueGreedyAlgorithm(GeneSetsRanked, int) - Constructor for class org.snpeff.geneSets.algorithm.RankSumPValueGreedyAlgorithm
- Rare - Enum constant in enum class org.snpeff.vcf.VcfEntry.AlleleFrequencyType
- RARE_AMINO_ACID - Enum constant in enum class org.snpeff.snpEffect.EffectType
- RARE_THRESHOLD - Static variable in class org.snpeff.codons.FindRareAaIntervals
- RareAminoAcid - Class in org.snpeff.interval
-
Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.
- RareAminoAcid() - Constructor for class org.snpeff.interval.RareAminoAcid
- RareAminoAcid(Marker, int, int, String) - Constructor for class org.snpeff.interval.RareAminoAcid
- ratio(String) - Method in class org.snpeff.complexity.SequenceComplexity
-
Measure string's complexity ratio.
- Reaction - Class in org.snpeff.reactome.events
-
A reaction
- Reaction(int, String) - Constructor for class org.snpeff.reactome.events.Reaction
- Reaction.RegulationType - Enum Class in org.snpeff.reactome.events
-
Reaction regulation types
- Reactome - Class in org.snpeff.reactome
-
Load reactome data from TXT files
- Reactome() - Constructor for class org.snpeff.reactome.Reactome
- read() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- read(char[]) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- read(char[], int, int) - Method in class org.snpeff.fileIterator.NullReader
- read(char[], int, int) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- read(DataInputStream) - Method in class org.snpeff.binseq.BinarySequence
-
Read a sequence from a data stream
- read(DataInputStream) - Method in class org.snpeff.binseq.DnaAndQualitySequence
-
Read data in binary format
- read(DataInputStream) - Method in class org.snpeff.binseq.DnaNSequence
-
Read data in binary format
- read(DataInputStream) - Method in class org.snpeff.binseq.DnaSequence
-
Read data in binary format
- read(DataInputStream) - Method in class org.snpeff.binseq.DnaSequenceId
-
Read data in binary format
- read(DataInputStream) - Method in class org.snpeff.binseq.DnaSequencePe
-
Read data in binary format
- read(InputStream) - Method in class org.snpeff.nmer.Nmer
- read(InputStream) - Static method in class org.snpeff.util.Gpr
-
Read an input stream
- read(String) - Method in class org.snpeff.ped.PlinkMap
-
Reads MAP file MAP file format (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) Space separated or tab columns: chromosome (1-22, X, Y or 0 if unplaced) rs# or snp identifier Genetic distance (morgans) Base-pair position (bp units)
- read(CharBuffer) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- READ_INPUT_SHOW_EVERY - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
- readCacheFile() - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Read cache file
- readDataStream(DataInputStream) - Method in class org.snpeff.binseq.BinarySequence
- readDataStream(DataInputStream) - Method in class org.snpeff.binseq.DnaAndQualitySequence
-
Read data in binary format
- readDataStream(DataInputStream) - Method in class org.snpeff.binseq.DnaAndQualitySequenceWithId
-
Read data in binary format
- readDataStream(DataInputStream) - Method in class org.snpeff.binseq.DnaNSequence
-
Read data in binary format
- readDataStream(DataInputStream) - Method in class org.snpeff.binseq.DnaSequence
-
Read data in binary format
- readDataStream(DataInputStream) - Method in class org.snpeff.binseq.DnaSequenceId
-
Read data in binary format
- readDataStream(DataInputStream) - Method in class org.snpeff.binseq.DnaSequencePe
-
Read data in binary format
- reader - Variable in class org.snpeff.fileIterator.FileIterator
- reader(String) - Static method in class org.snpeff.util.Gpr
-
Try to open a file (BufferedReader) using either the file or a gzip file (appending '.gz' to fileName)
- reader(String, boolean) - Static method in class org.snpeff.util.Gpr
-
Try to open a file (BufferedReader) using either the file or a gzip file (appending '.gz' to fileName)
- readExonSequences() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Read exon sequences from a FASTA file
- readExonSequences() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
- readExonSequencesGff(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Read chromosome sequence from GFF3 file and extract exons' sequences
- readField(String[], int) - Method in class org.snpeff.fileIterator.VcfFileIterator
-
Read a field an return a value
- readFile() - Method in class org.snpeff.genBank.Embl
-
Load and parse the contents of a data file
- readFile() - Method in class org.snpeff.genBank.Features
-
Load and parse the contents of a data file previously opened by 'open()' method.
- readFile() - Method in class org.snpeff.genBank.GenBank
-
Load and parse the contents of a data file
- readFile(String) - Static method in class org.snpeff.util.Gpr
-
Read a file as a String.
- readFile(String, boolean) - Static method in class org.snpeff.util.Gpr
-
Read a file as a String.
- readFile(RegulationFileIterator) - Method in class org.snpeff.RegulationFileConsensus
-
Read a file and add all regulation intervals
- readFileSerialized(String) - Static method in class org.snpeff.util.Gpr
-
Read an object from a file (supposing an object was previously serialized to that file)
- readFileSerializedGz(String) - Static method in class org.snpeff.util.Gpr
-
Read an object from a file (supposing an object was previously serialized to that file) Note: The file is compressed using GZIP
- readFileSerializedGzThrow(String) - Static method in class org.snpeff.util.Gpr
-
Read an object from a file (supposing an object was previously serialized to that file) Note: Same as 'readFileSerializedGz' but it throws all the exceptions
- readGeneAssocFile(String, boolean) - Method in class org.snpeff.geneOntology.GoTerms
-
Reads a file containing every gene (names and ids) associated GO terms
- readGenomeSequence(String) - Method in class org.snpeff.interval.Genome
-
Read the whole genome sequence into memory
- readGff() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
-
Read GFF file from the beginning looking for 'typeToRead' elements
- readHeader() - Method in class org.snpeff.fileIterator.VcfFileIterator
-
Read only header info
- readId(String) - Static method in class org.snpeff.util.GprSeq
-
Create an ID: Remove everything after the first space char.
- readInterestingSymbolIdsFile(String) - Method in class org.snpeff.geneOntology.GoTerms
-
Reads a file with a list of 'interesting' genes (one per line)
- readLine() - Method in class org.snpeff.fileIterator.FileIterator
-
Read a line from reader
- readLine() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- readMarkers(String) - Static method in class org.snpeff.interval.Markers
-
Read markers from a file Supported formats: BED, BigBed, VCF, TXT
- readNext() - Method in class org.snpeff.fileIterator.BedFileIterator
- readNext() - Method in class org.snpeff.fileIterator.BigBedFileIterator
- readNext() - Method in class org.snpeff.fileIterator.FastaFileIterator
-
Read a sequence from the file
- readNext() - Method in class org.snpeff.fileIterator.FileIterator
-
Read next element
- readNext() - Method in class org.snpeff.fileIterator.GenericMarkerFileIterator
- readNext() - Method in class org.snpeff.fileIterator.Gff3FileIterator
- readNext() - Method in class org.snpeff.fileIterator.LineClassFileIterator
-
Read a sequence from the file
- readNext() - Method in class org.snpeff.fileIterator.LineFileIterator
-
Read a sequence from the file
- readNext() - Method in class org.snpeff.fileIterator.MotifFileIterator
- readNext() - Method in class org.snpeff.fileIterator.RegulationBedFileIterator
- readNext() - Method in class org.snpeff.fileIterator.RegulationGffFileIterator
- readNext() - Method in class org.snpeff.fileIterator.SamFileIterator
-
Read a sequence from the file
- readNext() - Method in class org.snpeff.fileIterator.VariantTxtFileIterator
- readNext() - Method in class org.snpeff.fileIterator.VcfFileIterator
- readNext() - Method in class org.snpeff.fileIterator.VcfHapMapFileIterator
- readNext() - Method in class org.snpeff.ped.PedFileIterator
- readOboFile(String, boolean) - Method in class org.snpeff.geneOntology.GoTerms
-
Read an OBO file
- readRefSeqFile() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene
-
Read and parse genes file
- readRefSeqFile() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRefSeq
-
Read and parse RefSeq file
- ReadsOnMarkersModel - Class in org.snpeff.stats
-
Calculate the maximum interval length by type, for all markers in a genome Create a probability model based on binomial ditribution.
- ReadsOnMarkersModel(SnpEffectPredictor) - Constructor for class org.snpeff.stats.ReadsOnMarkersModel
- readTxt(String, int, Genome, int) - Method in class org.snpeff.interval.Marker
-
Parse a line (form a file) Format: "chromosome \t start \t end \t id \n"
- readTxt(String, Genome, int) - Static method in class org.snpeff.interval.MarkerUtil
-
Read intervals from a file using a simplt TXT format Format: chr \t start \t end \t id Note: Zero-based positions
- ready() - Method in class org.snpeff.fileIterator.FileIterator
-
Is reader ready? I.e.
- ready() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- realign() - Method in class org.snpeff.align.VariantRealign
-
Realign variant
- realignLeft() - Method in class org.snpeff.interval.Variant
-
Create a new variant realigning it towards the leftmost position
- realignLeft() - Method in class org.snpeff.interval.VariantBnd
- realignLeft() - Method in class org.snpeff.interval.VariantNonRef
- realignSeqs() - Method in class org.snpeff.align.VariantRealign
-
Realignment
- RECT_COLOR_FILL - Static variable in class org.snpeff.svg.Svg
- RECT_COLOR_STROKE - Static variable in class org.snpeff.svg.Svg
- RECT_HEIGHT - Static variable in class org.snpeff.svg.Svg
- RECT_STROKE_WIDTH - Static variable in class org.snpeff.svg.Svg
- rectangle() - Method in class org.snpeff.svg.Svg
- rectangle(double, double, double, double, boolean) - Method in class org.snpeff.svg.Svg
- redundant(Collection<? extends Marker>) - Static method in class org.snpeff.interval.MarkerUtil
-
Redundant markers in a list: Find intervals that are totally included in other intervals in the list
- ref - Variable in class org.snpeff.fileIterator.MatrixEntry
- ref - Variable in class org.snpeff.interval.Variant
- ref - Variable in class org.snpeff.vcf.VcfEntry
- ref() - Method in class org.snpeff.snpEffect.HgvsDna
- REFSEQ - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
- regions(Marker, boolean, boolean) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Name of the regions hit by a marker
- regions(Marker, boolean, boolean, String) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Name of the regions hit by a marker
- Regulation - Class in org.snpeff.interval
-
Regulatory elements
- Regulation() - Constructor for class org.snpeff.interval.Regulation
- Regulation(Marker, int, int, boolean, String, String, String) - Constructor for class org.snpeff.interval.Regulation
- REGULATION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- RegulationBedFileIterator - Class in org.snpeff.fileIterator
-
Opens a GFF3 file and create regulatory elements.
- RegulationBedFileIterator(String, String, String) - Constructor for class org.snpeff.fileIterator.RegulationBedFileIterator
- RegulationBedFileIterator(String, Genome, String, String) - Constructor for class org.snpeff.fileIterator.RegulationBedFileIterator
- RegulationConsensusMultipleBed - Class in org.snpeff
-
Create a regulation consensus from multiple BED files
- RegulationConsensusMultipleBed(String, String) - Constructor for class org.snpeff.RegulationConsensusMultipleBed
- RegulationFileConsensus - Class in org.snpeff
-
Create a regulation consensus from a regulation file.
- RegulationFileConsensus() - Constructor for class org.snpeff.RegulationFileConsensus
- RegulationFileIterator - Class in org.snpeff.fileIterator
-
Opens a regulation file and create Regulation elements.
- RegulationFileIterator(String, int) - Constructor for class org.snpeff.fileIterator.RegulationFileIterator
- RegulationFileIterator(String, Genome, int) - Constructor for class org.snpeff.fileIterator.RegulationFileIterator
- RegulationFileSplitBytType - Class in org.snpeff
-
Split regulation files into smaller files (one per 'regulation type') Regulation files can be quite large and we cannot read them into memory.
- RegulationFileSplitBytType() - Constructor for class org.snpeff.RegulationFileSplitBytType
- RegulationGffFileIterator - Class in org.snpeff.fileIterator
-
Opens a GFF3 file and create regulatory elements.
- RegulationGffFileIterator(String) - Constructor for class org.snpeff.fileIterator.RegulationGffFileIterator
- RegulationGffFileIterator(String, Genome) - Constructor for class org.snpeff.fileIterator.RegulationGffFileIterator
- regulationTracks - Variable in class org.snpeff.SnpEff
- regulator - Variable in class org.snpeff.reactome.events.Reaction
- remove() - Method in class org.snpeff.fileIterator.BinSeqFileIterator
- remove() - Method in class org.snpeff.fileIterator.FastqFileIterator
- remove() - Method in class org.snpeff.fileIterator.FileIterator
- remove() - Method in class org.snpeff.genBank.FeaturesFile
- remove() - Method in class org.snpeff.interval.IntervalSetIterator
- remove() - Method in class org.snpeff.util.CombinatorialIterator
- remove() - Method in class org.snpeff.util.IubString
- remove(Object) - Method in class org.snpeff.interval.Markers
- remove(String) - Method in class org.snpeff.stats.CountByType
-
Remove this entry type
- remove(String) - Method in class org.snpeff.vcf.VcfHeader
-
Remove header line starting with a prefix
- remove(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
-
Remove all elements set in other.
- remove(GeneSet) - Method in class org.snpeff.geneSets.GeneSets
- remove(Chromosome) - Method in class org.snpeff.interval.Genome
-
Remove a chromosome WARINIG: Doesn't check any dependencies!
- remove(T) - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Remove a subinterval
- removeAll(Collection<?>) - Method in class org.snpeff.interval.Markers
- removeBackslashR(String) - Static method in class org.snpeff.util.Gpr
-
Remove trailing '\r'
- removeExt(String) - Static method in class org.snpeff.util.Gpr
- removeExt(String) - Static method in class org.snpeff.util.GprSeq
- removeExt(String, String[]) - Static method in class org.snpeff.util.Gpr
-
Remove extension from a file (if matches one of 'fileExtensions[]')
- removeGeneSet(String) - Method in class org.snpeff.geneSets.GeneSets
-
Remove a GeneSet
- removeGOTerm(String) - Method in class org.snpeff.geneOntology.GoTerms
-
Remove a GOTerm
- removeInfo(String) - Method in class org.snpeff.vcf.VcfEntry
-
Remove INFO field
- removeInfo(String) - Method in class org.snpeff.vcf.VcfHeader
-
Remove header line matching an INFO field
- removeNonCanonical(String) - Method in class org.snpeff.interval.Gene
-
Remove all non-canonical transcripts
- removeNonCanonical(String) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Remove all non-canonical transcripts If a file is provided, read "Gene => canonical_transcript" mapping from file
- removeTranscript(String) - Static method in class org.snpeff.snpEffect.Hgvs
- removeUnusedSets() - Method in class org.snpeff.geneSets.GeneSets
-
Remove unused gene sets
- removeUnverified() - Method in class org.snpeff.interval.Gene
-
Remove unverified or corrected transcripts
- removeUnverified() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Remove all unverified transcripts
- repeat(char, int) - Static method in class org.snpeff.util.Gpr
-
Create a string of n time 'c'
- REPEAT_REGION - Enum constant in enum class org.snpeff.genBank.Feature.Type
- REPEAT_UNIT - Enum constant in enum class org.snpeff.genBank.Feature.Type
- replace(long, long, long) - Method in class org.snpeff.collections.HashLongLongArray
-
Replace a value with newValue
- replaceBase(long, int, char) - Method in class org.snpeff.binseq.coder.DnaCoder
-
Decode bits from a given position
- replaceQuality(byte, int) - Method in class org.snpeff.binseq.coder.DnaQualityCoder
-
Replace quality value in a given code
- replaceSeq(String) - Method in class org.snpeff.sam.SamEntry
-
Replace a sequence WARNING: Doing this might invalidate the CIGAR field
- replaceTranscript(Transcript, Transcript) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- report(String, String, String, boolean, boolean, String[], String, HashMap<String, String>) - Static method in class org.snpeff.logStatsServer.LogStats
-
Report stats to server
- REPORT_TEMPLATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
- reportValues() - Method in class org.snpeff.SnpEff
-
Additional values to be reported
- reportValues() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- Requirement - Enum constant in enum class org.snpeff.reactome.events.Reaction.RegulationType
- resample(int) - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
-
Re-sample 'iterations' times
- ReSampleInt - Class in org.snpeff.probablility.bootstrap
-
Re-sample statistic Statistic is a sum of a set of integer numbers (e.g.
- ReSampleInt(int[], int) - Constructor for class org.snpeff.probablility.bootstrap.ReSampleInt
- ReSampleMap - Class in org.snpeff.probablility.bootstrap
-
Resample statistic
- ReSampleMap(HashMap<String, Integer>, int) - Constructor for class org.snpeff.probablility.bootstrap.ReSampleMap
- ReSampleMapRank - Class in org.snpeff.probablility.bootstrap
-
Re-sample statistic using ranks of scores (scores are double)
- ReSampleMapRank(HashMap<String, Double>, int) - Constructor for class org.snpeff.probablility.bootstrap.ReSampleMapRank
- reset() - Method in class org.snpeff.binseq.GenomicSequences
- reset() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- reset() - Method in class org.snpeff.geneSets.GeneSets
-
Reset every 'interesting' gene or ranked gene (on every single GeneSet in this GeneSets)
- reset() - Method in class org.snpeff.geneSets.GeneSetsRanked
-
Reset every 'interesting' gene or ranked gene (on every single GeneSet in this GeneSets)
- reset() - Method in class org.snpeff.interval.Exon
- reset() - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Remove all intervals
- reset() - Method in class org.snpeff.interval.Intron
- reset() - Method in class org.snpeff.interval.Transcript
- reset() - Method in class org.snpeff.interval.tree.IntervalTreeArray
- reset() - Method in class org.snpeff.reactome.Entity
- reset() - Method in class org.snpeff.reactome.Reactome
-
Reset all nodes in the circuit
- reset() - Static method in class org.snpeff.snpEffect.Config
- reset() - Method in class org.snpeff.stats.Average
- reset() - Method in class org.snpeff.stats.AverageInt
- reset() - Method in class org.snpeff.stats.Counter
- reset() - Method in class org.snpeff.stats.CounterDouble
- reset() - Static method in class org.snpeff.util.Log
-
Reset all parameters, warning counters, silenced warningis, etc.
- resetBuffer() - Method in class org.snpeff.osCmd.StreamGobbler
- resetBuffers() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- resetCache() - Method in class org.snpeff.interval.Transcript
- resetExons() - Method in class org.snpeff.interval.Transcript
- resetInterestingSymbolIds() - Method in class org.snpeff.geneOntology.GoTerms
-
Reset every 'interesting' symbolId (on every single GOTerm in this GOTerms)
- Result - Class in org.snpeff.geneSets
-
Store a result form a greedy search algorithm
- Result() - Constructor for class org.snpeff.geneSets.Result
- Result(List<GeneSet>, double) - Constructor for class org.snpeff.geneSets.Result
- Result(GeneSet, Apfloat, int) - Constructor for class org.snpeff.geneSets.Result
- Result(Result) - Constructor for class org.snpeff.geneSets.Result
- retainAll(Collection<?>) - Method in class org.snpeff.interval.Markers
- retainAllTranscripts(Set<String>) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Remove all transcripts that are NOT in the list
- RETAINED - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
- retained_intron - Enum constant in enum class org.snpeff.interval.BioType
- reverse() - Method in class org.snpeff.interval.Variant
-
Reverse variant (e.g.
- reverse(String) - Static method in class org.snpeff.util.GprSeq
-
Reverse of a string (sequence)
- reverseBases(long) - Method in class org.snpeff.binseq.coder.DnaCoder
-
Reverse all bases in 'code'
- reverseMask - Static variable in class org.snpeff.genotypes.GenotypeVector
- reverseWc() - Method in class org.snpeff.binseq.BinarySequence
-
Reverse Watson-Cricks complement
- reverseWc() - Method in class org.snpeff.binseq.DnaAndQualitySequence
- reverseWc() - Method in class org.snpeff.binseq.DnaNSequence
- reverseWc() - Method in class org.snpeff.binseq.DnaSequence
- reverseWc() - Method in class org.snpeff.binseq.DnaSequencePe
- reverseWc(String) - Static method in class org.snpeff.util.GprSeq
-
Reverse Watson-Cricks complement
- reverseWC - Variable in class org.snpeff.binseq.indexer.OverlapRessult
- REVISION - Static variable in class org.snpeff.SnpEff
- ribozyme - Enum constant in enum class org.snpeff.interval.BioType
- right - Variable in class org.snpeff.interval.tree.IntervalTreeArray
- rightNode - Variable in class org.snpeff.interval.tree.IntervalNode
- rmInfo(String) - Method in class org.snpeff.vcf.VcfEntry
-
Parse INFO fields
- rol(char) - Method in class org.snpeff.nmer.Nmer
-
Rotate sequence left and append a base at the end Note: The first base is dropped, so the total length is still 'n'
- rootNode() - Method in class org.snpeff.geneOntology.GoTerm
-
Get the root node
- rootNodes() - Method in class org.snpeff.geneOntology.GoTerms
- rotate(int) - Method in class org.snpeff.overlap.SequenceRotator
-
Rotate left
- rRNA - Enum constant in enum class org.snpeff.interval.BioType
- RRNA - Enum constant in enum class org.snpeff.genBank.Feature.Type
- run() - Method in class org.snpeff.fastq.FastqSplit
-
Run command
- run() - Method in class org.snpeff.logStatsServer.LogStats
-
Run thread in background
- run() - Method in class org.snpeff.logStatsServer.VersionCheck
-
Run thread in background
- run() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- run() - Method in class org.snpeff.osCmd.OsCmdQueue
-
Run commands
- run() - Method in class org.snpeff.osCmd.OsCmdRunner
- run() - Method in class org.snpeff.osCmd.StreamGobbler
- run() - Method in class org.snpeff.pdb.ProteinInteractions
-
Run analysis.
- run() - Method in class org.snpeff.PromoterSequences
- run() - Method in class org.snpeff.RegulationConsensusMultipleBed
-
Main method: Creates the consensus from multiple files
- run() - Method in class org.snpeff.SnpEff
-
Run according to command line options
- run() - Method in interface org.snpeff.snpEffect.commandLine.CommandLine
-
Run the command
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
-
Run command
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
-
Build database
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuildNextProt
-
Run main analysis
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
-
Run command
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
-
Run command
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCount
-
Run
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDownload
-
Download database from server
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDump
-
Run according to command line options
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
-
Run according to command line options
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
-
Run command
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdLen
-
Run
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
-
Run command
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdSeq
-
Run according to command line options
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdShow
-
Run according to command line options
- run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
- run() - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
- run() - Method in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- run() - Method in class org.snpeff.stats.ReadsOnMarkersModel
-
Run
- run(boolean) - Method in class org.snpeff.pdb.ProteinInteractions
- run(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
-
Run according to command line options
- run(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
- run(GtexExperiment) - Method in class org.snpeff.reactome.Reactome
-
Run some simulations
- run(Gtex, String) - Method in class org.snpeff.reactome.Reactome
-
Run all experiments on gtex
- run(SnpEff, String[], StringBuilder) - Method in class org.snpeff.SnpEff
-
Run a SnpEff (usually a sub-class)
- runAnalisis() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
-
Run command
- runAnalisisRand() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
-
Run enrichment analysis using random scores
- runCommands() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
-
Read "command" lines from file.
- runIfNotExists(String[], String, boolean) - Static method in class org.snpeff.osCmd.OsCmdRunner
-
Run an OS command only if the output files does not exists.
- runIfNotExists(String, boolean) - Method in class org.snpeff.osCmd.OsCmdRunner
-
Run a command only if 'outputFile' does not exist
S
- SamEntry - Class in org.snpeff.sam
-
An entry in a SAM file References: http://samtools.sourceforge.net/SAM-1.3.pdf
- SamEntry(String) - Constructor for class org.snpeff.sam.SamEntry
-
Create an entry give a line from a file
- SamFileIterator - Class in org.snpeff.fileIterator
-
Reads a SAM file Note: This is a very 'rustic' reader (we should use Picard's API instead)
- SamFileIterator(String) - Constructor for class org.snpeff.fileIterator.SamFileIterator
- SamHeader - Class in org.snpeff.sam
-
Sam header
- SamHeader() - Constructor for class org.snpeff.sam.SamHeader
- SamHeaderRecord - Class in org.snpeff.sam
-
Sam header record
- SamHeaderRecord(String, String) - Constructor for class org.snpeff.sam.SamHeaderRecord
- SamHeaderRecordSq - Class in org.snpeff.sam
-
SQ header: Reference sequence dictionary.
- SamHeaderRecordSq(String) - Constructor for class org.snpeff.sam.SamHeaderRecordSq
- samLine2Id(String) - Static method in class org.snpeff.sam.SamEntry
-
Get an ID from a SAM line
- sample(double) - Method in class org.snpeff.stats.FloatStats
- sample(int) - Method in class org.snpeff.stats.ChrPosStats
-
Use 'num' as a sample
- sample(int) - Method in class org.snpeff.stats.IntStats
-
Use 'num' as a sample
- sample(Gene, Transcript, String, VariantEffect) - Method in class org.snpeff.stats.GeneCountByTypeTable
-
Sample this invalid input: '<'gene, marker, type, variant> tuple to update statistics
- sample(Marker, Marker) - Method in class org.snpeff.stats.PosStats
-
Use 'num' as a sample
- sample(Variant) - Method in class org.snpeff.stats.VariantStats
-
Use this sample to perform statistics
- sample(VariantEffect) - Method in class org.snpeff.stats.VariantEffectStats
- sample(VcfEntry) - Method in class org.snpeff.stats.AlleleCountStats
-
Update MAC counters
- sample(VcfEntry) - Method in class org.snpeff.stats.GenotypeStats
-
Update counters
- sample(VcfEntry) - Method in class org.snpeff.stats.HomHetStats
-
Update Hom/Het counters
- sample(VcfEntry) - Method in class org.snpeff.stats.TsTvStats
-
Update Ts and Tv counters Only for SNPs
- sample(VcfEntry) - Method in class org.snpeff.stats.VariantTypeStats
-
Update MAC counters
- sample(VcfEntry) - Method in class org.snpeff.stats.VcfStats
- sample(T) - Method in interface org.snpeff.stats.SamplingStats
-
Analyze one sample
- sampleMean(int) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
-
Calculate the mean rankSum for a given 'N_T' (number of ranks to add)
- sampleNumbers(List<String>) - Method in class org.snpeff.vcf.PedigreeEntry
-
Find sample numbers in a list of sample names
- sampleVariance(int) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
-
Calculate the variance of rankSum for a given 'N_T' (number of ranks to add)
- SamplingStats<T> - Interface in org.snpeff.stats
-
Perform stats by analyzing some samples
- sanityCheck() - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
-
Perform consistency checks
- sanityCheck(Variant) - Method in class org.snpeff.interval.Exon
-
Check that the base in the exon corresponds with the one in the SNP
- sanityCheck(Variant) - Method in class org.snpeff.interval.Transcript
-
Perfom some baseic chekcs, return error type, if any
- sanityCheckChromo(String, Chromosome) - Method in class org.snpeff.fileIterator.MarkerFileIterator
-
Sanity check
- sanityzeFileName(String) - Static method in class org.snpeff.util.Gpr
- sanityzeName(String) - Static method in class org.snpeff.util.Gpr
- save() - Method in class org.snpeff.RegulationFileConsensus
-
Save databases (one file per regType)
- save(Iterable<Marker>) - Method in class org.snpeff.serializer.MarkerSerializer
-
Save all markers
- save(String) - Method in class org.snpeff.fileIterator.TableFile
-
Save this object to a binary file (using Java serialization)
- save(String) - Method in class org.snpeff.genotypes.Genotypes
-
Save to file
- save(String) - Method in class org.snpeff.interval.Genome
-
Save genome to file
- save(String) - Method in class org.snpeff.interval.Markers
-
Save to a file using a serializer
- save(String) - Method in class org.snpeff.reactome.Monitor
- save(String) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Save predictor to a binary file
- save(String) - Method in class org.snpeff.stats.ReadsOnMarkersModel
-
Save model to file
- save(String, String) - Method in class org.snpeff.interval.Markers
-
Save to a file using a serializer Only save one chromosome ('chr') Note: This is used to save only markers related to one chromosome (e.g.
- save(String, Markers) - Method in class org.snpeff.serializer.MarkerSerializer
-
Save data to file
- save(List<DistanceResult>) - Method in class org.snpeff.pdb.ProteinInteractions
-
Save results
- save(Marker) - Method in class org.snpeff.serializer.MarkerSerializer
-
Save a marker
- save(Config) - Method in class org.snpeff.binseq.GenomicSequences
-
Save genomic sequence into separate files (per chromosome)
- save(Config) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Save predictor to a binary file (specified by the configuration)
- saveDatabase() - Method in class org.snpeff.nextProt.NextProtDb
- saveDatabase() - Method in class org.snpeff.nextProt.NextProtMarkerFactory
-
Save nextprot markers as databases
- saveGseaGeneSets(String) - Method in class org.snpeff.geneOntology.GoTerms
-
Save gene sets file for GSEA analysis Format specification: http://www.broad.mit.edu/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29
- saveGseaGeneSets(String) - Method in class org.snpeff.geneSets.GeneSets
-
Save gene sets file for GSEA analysis Format specification: http://www.broad.mit.edu/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29
- saveOutput - Variable in class org.snpeff.SnpEff
- saveTfam(String) - Method in class org.snpeff.ped.PedPedigree
-
Save pedigree as a TFAM file
- SCALE - Static variable in class org.snpeff.motif.Pwm
- SCALE_HEIGHT - Static variable in class org.snpeff.svg.SvgScale
- SCALE_TICK_HEIGHT - Static variable in class org.snpeff.svg.SvgScale
- scaleWeights() - Method in class org.snpeff.reactome.events.Reaction
-
Scale weights so that they add to 1
- scaRNA - Enum constant in enum class org.snpeff.interval.BioType
- score - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- score(long[], long[], int, int, int) - Method in class org.snpeff.binseq.coder.DnaCoder
-
Calculate a 'score' for a sequence (dst) and a sub-sequence (src).
- score(String) - Method in class org.snpeff.motif.Pwm
-
Calculate PWM score for a string
- score(Collection<String>) - Method in class org.snpeff.probablility.bootstrap.ReSampleMap
- score(Collection<String>) - Method in class org.snpeff.probablility.bootstrap.ReSampleMapRank
- score(DnaAndQualitySequence, int, DnaAndQualitySequence, int) - Method in class org.snpeff.binseq.comparator.DnaQualSubsequenceComparator
- score(DnaSequence, int, DnaSequence, int) - Method in class org.snpeff.binseq.comparator.DnaSubsequenceComparator
- score(ScoreList.ScoreSummary) - Method in class org.snpeff.gsa.ScoreList
-
Create a single pValue representing the gene
- score(T, int, T, int) - Method in class org.snpeff.binseq.comparator.SubsequenceComparator
- SCORE_CUTOFF_QUANTILE_DEFAULT - Static variable in class org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
- SCORE_THRESHOLD - Static variable in class org.snpeff.interval.Motif
- ScoreList - Class in org.snpeff.gsa
-
A list of scores
- ScoreList() - Constructor for class org.snpeff.gsa.ScoreList
- ScoreList.ScoreSummary - Enum Class in org.snpeff.gsa
- scoreSlow(DnaSequence, int, DnaSequence, int) - Method in class org.snpeff.binseq.comparator.DnaSubsequenceComparator
-
This method is used when none of the indexes is zero.
- scRNA - Enum constant in enum class org.snpeff.interval.BioType
- second - Variable in class org.snpeff.util.Tuple
- seek(long) - Method in class org.snpeff.fileIterator.FileIterator
-
Seek to 'pos' (jump to byte number 'pos' in the file
- seek(long) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
-
Seek to a position in the file
- SeekableBufferedReader - Class in org.snpeff.fileIterator
-
A buffered reader for a file.
- SeekableBufferedReader(String) - Constructor for class org.snpeff.fileIterator.SeekableBufferedReader
- SeekableBufferedReader(String, int) - Constructor for class org.snpeff.fileIterator.SeekableBufferedReader
- select() - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
-
Select the 'best' gene sets
- select() - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
-
Select the 'best' gene sets
- send - Variable in class org.snpeff.fileIterator.BlastResultEntry
- sense_intronic - Enum constant in enum class org.snpeff.interval.BioType
- sense_overlapping - Enum constant in enum class org.snpeff.interval.BioType
- separator - Variable in class org.snpeff.fileIterator.LineClassFileIterator
- separator - Variable in class org.snpeff.fileIterator.TableFile
- separator() - Method in enum class org.snpeff.vcf.EffFormatVersion
-
Multiple effect separator
- separatorSplit() - Method in enum class org.snpeff.vcf.EffFormatVersion
-
Multiple effect separator: Split regex
- seqConservation() - Method in class org.snpeff.spliceSites.AcgtTree
- SEQUENCE - Enum constant in enum class org.snpeff.snpEffect.EffectType
- SequenceComplexity - Class in org.snpeff.complexity
-
Measures the complexity of a sequence Ideally we'd like to measure the Kolmogorov complexity of the sequence.
- SequenceComplexity() - Constructor for class org.snpeff.complexity.SequenceComplexity
- SequenceIndexer<T> - Class in org.snpeff.binseq.indexer
-
A collection of sequences that are indexed using some algorithm Note: The ID is just the position in the array.
- SequenceIndexer(SubsequenceComparator<T>) - Constructor for class org.snpeff.binseq.indexer.SequenceIndexer
- SequenceReference - Class in org.snpeff.binseq.comparator
-
A reference to a sequence.
- SequenceReference() - Constructor for class org.snpeff.binseq.comparator.SequenceReference
- SequenceRotator - Class in org.snpeff.overlap
-
Rotates a binary packed sequence WARNING: We only rotate up to Coder.basesPerWord() because after that the sequences are the same (with an integer offset) NOTE: Left rotation 'n' is the same as a right rotation 'Coder.basesPerWord() - n'
- SequenceRotator(DnaSequence) - Constructor for class org.snpeff.overlap.SequenceRotator
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Cds
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Chromosome
-
Parse a line from a serialized file
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Exon
-
Parse a line from a serialized file
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Gene
-
Parse a line from a serialized file
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Genome
-
Parse a line from a serialized file
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Parse a line from a serialized file
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Intron
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Marker
-
Parse a line from a serialized file
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.MarkerSeq
-
Parse a line from a serialized file
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Motif
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.NextProt
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Regulation
-
Parse a line from a serialized file
- serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Transcript
-
Parse a line from a serialized file
- serializeParse(MarkerSerializer) - Method in interface org.snpeff.serializer.TxtSerializable
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Cds
-
Create a string to serialize to a file
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Chromosome
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Exon
-
Create a string to serialize to a file
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Gene
-
Create a string to serialize to a file
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Genome
-
Create a string to serialize to a file
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Create a string to serialize to a file
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Intron
-
Create a string to serialize to a file
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Marker
-
Create a string to serialize to a file
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.MarkerSeq
-
Create a string to serialize to a file
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Motif
-
Create a string to serialize to a file
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.NextProt
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Regulation
-
Create a string to serialize to a file
- serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Transcript
-
Create a string to serialize to a file
- serializeSave(MarkerSerializer) - Method in interface org.snpeff.serializer.TxtSerializable
- set(boolean) - Method in class org.snpeff.stats.BooleanMutable
- set(char, AcgtTree) - Method in class org.snpeff.spliceSites.AcgtTree
-
Set a node
- set(double) - Method in class org.snpeff.stats.CounterDouble
- set(int, int) - Method in class org.snpeff.genotypes.GenotypeVector
-
Set genotype code Codes {0, 1, 2, 3} => Genotypes { 0/0, 0/1, 1/0, 1/1 }
- set(int, int, int) - Method in class org.snpeff.util.CombinatorialIterator
- set(int, int, VcfGenotype) - Method in class org.snpeff.genotypes.Genotypes
-
Set an entry
- set(int, VcfGenotype) - Method in class org.snpeff.genotypes.GenotypeVector
-
Set genotype
- set(long) - Method in class org.snpeff.collections.OpenBitSet
-
sets a bit, expanding the set size if necessary
- set(long) - Method in class org.snpeff.stats.Counter
- set(long, long) - Method in class org.snpeff.collections.OpenBitSet
-
Sets a range of bits, expanding the set size if necessary
- set(String) - Method in class org.snpeff.binseq.BinarySequence
-
Set sequence from a string
- set(String) - Method in class org.snpeff.binseq.DnaAndQualitySequence
-
Set sequence
- set(String) - Method in class org.snpeff.binseq.DnaNSequence
- set(String) - Method in class org.snpeff.binseq.DnaSequence
-
Set sequence
- set(String) - Method in class org.snpeff.binseq.DnaSequenceByte
-
Set sequence
- set(String) - Method in class org.snpeff.binseq.DnaSequencePe
- set(String) - Method in class org.snpeff.motif.Pwm
-
Set PWM as a perfect match to a dna sequence
- set(String) - Method in class org.snpeff.nmer.Nmer
-
Set nmer's sequence
- set(String, boolean) - Method in class org.snpeff.binseq.DnaSequence
- set(String, String) - Method in class org.snpeff.vcf.VcfGenotype
-
Set a genotype field value
- set(String, String, FastqVariant) - Method in class org.snpeff.binseq.DnaAndQualitySequence
-
Set sequence
- set(List<GeneSet>, Apfloat) - Method in class org.snpeff.geneSets.Result
-
Ser a new list and pvalue
- set(Genome, CodonTable) - Method in class org.snpeff.codons.CodonTables
-
Set a codon table for a all chromosomes in a genome I.e.: Default genome-wide chromosome table
- set(Genome, Chromosome, CodonTable) - Method in class org.snpeff.codons.CodonTables
-
Set a codon table for a given genome invalid input: '&' chromosome
- set(Marker, EffectType, VariantEffect.EffectImpact, String) - Method in class org.snpeff.snpEffect.VariantEffect
- setAa(String) - Method in class org.snpeff.vcf.VcfEffect
- setAa1(AminoAcid) - Method in class org.snpeff.pdb.DistanceResult
- setAa2(AminoAcid) - Method in class org.snpeff.pdb.DistanceResult
- setAaCheck(boolean) - Method in class org.snpeff.interval.Transcript
- setAaIdx(int, int) - Method in class org.snpeff.interval.Exon
- setAaLen(int) - Method in class org.snpeff.vcf.VcfEffect
- setAaMinSeparation(int) - Method in class org.snpeff.pdb.ProteinInteractions
- setAcc(String) - Method in class org.snpeff.geneOntology.GoTerm
- setAddUtrs(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
- setAdjustedPvalue(boolean) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- setAlert(String) - Method in class org.snpeff.osCmd.StreamGobbler
- setAlertNotify(Object) - Method in class org.snpeff.osCmd.StreamGobbler
- setAlignLeft() - Method in class org.snpeff.align.VariantRealign
- setAlignRight() - Method in class org.snpeff.align.VariantRealign
- setAutoClose(boolean) - Method in class org.snpeff.fileIterator.FileIterator
- setBarSpace(int) - Method in class org.snpeff.stats.plot.GooglePlotInt
- setBarWidth(int) - Method in class org.snpeff.stats.plot.GooglePlotInt
- setBase(int, char) - Method in class org.snpeff.binseq.DnaNSequence
-
Replace a base in the sequence
- setBase(int, char) - Method in class org.snpeff.binseq.DnaSequence
-
Replace a base in the sequence
- setBaseY(int) - Method in class org.snpeff.svg.Svg
- setBinary(boolean) - Method in class org.snpeff.osCmd.StreamGobbler
- setBinaryStderr(boolean) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setBinaryStdout(boolean) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setBioType(BioType) - Method in class org.snpeff.interval.Gene
- setBioType(BioType) - Method in class org.snpeff.interval.Transcript
- setBioType(BioType) - Method in class org.snpeff.vcf.VcfEffect
- setBits(long[]) - Method in class org.snpeff.collections.OpenBitSet
-
Expert: sets a new long[] to use as the bit storage
- setCacheFile(String) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
- setCanonical(boolean) - Method in class org.snpeff.interval.Transcript
- setCanonical(boolean) - Method in class org.snpeff.SnpEff
- setCellType(String) - Method in class org.snpeff.RegulationConsensusMultipleBed
- setCheckNumOk(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
- setCheckNumOk(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
- setCheckNumOk(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- setChilds(HashSet<GoTerm>) - Method in class org.snpeff.geneOntology.GoTerm
- setChromo(Chromosome) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
- setChromosomeNameOri(String) - Method in class org.snpeff.interval.Interval
- setChrStr(String) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setCircular(boolean) - Method in class org.snpeff.interval.Chromosome
- setCircularCorrectLargeGap(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- setCodes(long[]) - Method in class org.snpeff.binseq.DnaSequence
- setCoding(VariantEffect.Coding) - Method in class org.snpeff.vcf.VcfEffect
- setCodon(String) - Method in class org.snpeff.vcf.VcfEffect
- setCodons(String, String, int, int) - Method in class org.snpeff.snpEffect.VariantEffect
-
Set codon change.
- setCodonsAround(String, String) - Method in class org.snpeff.snpEffect.VariantEffect
-
Set values for codons around change.
- setColumnSeparator(String) - Method in class org.snpeff.fileIterator.GuessTableTypes
- setCommandArgs(String[]) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setCommandLineStr(String) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setCompartment(Compartment) - Method in class org.snpeff.reactome.Entity
- setConfig(Config) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setConfig(Config) - Method in class org.snpeff.pdb.ProteinInteractions
- setConfig(Config) - Method in class org.snpeff.SnpEff
- setConfig(Config) - Method in interface org.snpeff.snpEffect.VcfAnnotator
-
Set configuration
- setConfig(Config) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
- setConfigFile(String) - Method in class org.snpeff.SnpEff
- setCorrectLargeGap(boolean) - Method in class org.snpeff.interval.CircularCorrection
- setCounts(char, int[]) - Method in class org.snpeff.motif.Pwm
-
Set counts for one base
- setCreateChromos(boolean) - Method in class org.snpeff.fileIterator.MarkerFileIterator
- setCreateChromos(boolean) - Method in class org.snpeff.fileIterator.VcfFileIterator
- setCreateRandSequences(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- setCvTerm(CvTerm) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- setDebug(boolean) - Method in class org.snpeff.align.VariantRealign
- setDebug(boolean) - Method in class org.snpeff.fileIterator.FileIterator
- setDebug(boolean) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- setDebug(boolean) - Method in class org.snpeff.interval.CircularCorrection
- setDebug(boolean) - Method in class org.snpeff.interval.tree.IntervalForest
- setDebug(boolean) - Method in class org.snpeff.interval.tree.IntervalTreeArray
- setDebug(boolean) - Method in class org.snpeff.nextProt.NextProtDb
- setDebug(boolean) - Method in class org.snpeff.pdb.ProteinInteractions
- setDebug(boolean) - Method in class org.snpeff.SnpEff
- setDebug(boolean) - Method in class org.snpeff.snpEffect.Config
- setDebug(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- setDebug(boolean) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- setDebug(boolean) - Method in interface org.snpeff.snpEffect.VcfAnnotator
-
Set debug mode
- setDebug(boolean) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
- setDebug(boolean) - Method in class org.snpeff.spliceSites.SpliceTypes
- setDebug(boolean) - Method in class org.snpeff.spliceSites.TranscriptSet
- setDebug(boolean) - Method in class org.snpeff.util.Download
- setDebug(boolean) - Method in class org.snpeff.vcf.FileIndexChrPos
- setDebug(boolean) - Method in class org.snpeff.vcf.Pedigree
- setDefaultWaitTime(long) - Method in class org.snpeff.osCmd.OsCmdRunner
- setDeletion(int) - Method in class org.snpeff.align.NeedlemanWunsch
- setDeletion(int) - Method in class org.snpeff.align.NeedlemanWunschOverlap
- setDescription(String) - Method in class org.snpeff.geneSets.GeneSet
- setDescription(String) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- setDisableLoad(boolean) - Method in class org.snpeff.binseq.GenomicSequences
- setDistance(int) - Method in class org.snpeff.snpEffect.VariantEffect
- setDistanceThreshold(double) - Method in class org.snpeff.pdb.ProteinInteractions
- setDistanceThresholdNon(double) - Method in class org.snpeff.pdb.ProteinInteractions
- setDnaCheck(boolean) - Method in class org.snpeff.interval.Transcript
- setDoNotAddIfNotInGeneSet(boolean) - Method in class org.snpeff.geneSets.GeneSets
- setEffect(EffectType) - Method in class org.snpeff.snpEffect.VariantEffect
-
Set effect using default impact
- setEffectDetails(String) - Method in class org.snpeff.vcf.VcfEffect
- setEffectImpact(VariantEffect.EffectImpact) - Method in class org.snpeff.snpEffect.VariantEffect
- setEffectType(EffectType) - Method in class org.snpeff.snpEffect.VariantEffect
- setEffectType(EffectType) - Method in class org.snpeff.vcf.VcfEffect
- setEnd(int) - Method in class org.snpeff.interval.Interval
- setErrorChromoHit(boolean) - Method in class org.snpeff.snpEffect.Config
- setErrorIfUnsorted(boolean) - Method in class org.snpeff.fileIterator.VcfFileIterator
- setErrorOnMissingChromo(boolean) - Method in class org.snpeff.snpEffect.Config
- setExonId(String) - Method in class org.snpeff.vcf.VcfEffect
- setExpandIub(boolean) - Method in class org.snpeff.fileIterator.VcfFileIterator
- setExpandIub(boolean) - Method in class org.snpeff.snpEffect.Config
- setFalse() - Method in class org.snpeff.stats.BooleanMutable
- setFastaFile(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- setFatalErrorBehabiour(Log.FatalErrorBehabiour) - Static method in class org.snpeff.util.Log
- setFileName(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- setFilter(String) - Method in class org.snpeff.vcf.VcfEntry
- setFilterOutputGeneSets(Set<String>) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- setFixedOutput(double) - Method in class org.snpeff.reactome.Entity
- setForceNegativeStrand(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
- setForcePositiveStrand(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
- setFormat(String) - Method in class org.snpeff.vcf.VcfEntry
- setFormatVersion(EffFormatVersion) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
- setFormatVersion(EffFormatVersion) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- setFormatVersion(EffFormatVersion) - Method in class org.snpeff.vcf.VcfEffect
- setFrame(int) - Method in class org.snpeff.interval.Cds
-
Frame can be {-1, 0, 1, 2}, where '-1' means unknown
- setFrame(int) - Method in class org.snpeff.interval.Exon
-
Frame can be {-1, 0, 1, 2}, where '-1' means unknown
- setFrame(int) - Method in interface org.snpeff.interval.MarkerWithFrame
- setFunClass(VariantEffect.FunctionalClass) - Method in class org.snpeff.vcf.VcfEffect
- setGap(int) - Method in class org.snpeff.binseq.DnaSequencePe
- setGatk(boolean) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
- setGeneId(String) - Method in class org.snpeff.gsa.ScoreList
- setGeneId(String) - Method in class org.snpeff.vcf.VcfEffect
- setGeneName(String) - Method in class org.snpeff.vcf.VcfEffect
- setGeneSetByName(HashMap<String, GeneSet>) - Method in class org.snpeff.geneSets.GeneSets
- setGeneSetCount(List<Integer>) - Method in class org.snpeff.geneSets.Result
- setGeneSetCountLast(int) - Method in class org.snpeff.geneSets.Result
- setGeneSets(List<GeneSet>) - Method in class org.snpeff.geneSets.Result
-
Assign geneSets
- setGeneSets(GeneSets) - Method in class org.snpeff.geneSets.GeneSet
- setGenesSet(HashSet<String>) - Method in class org.snpeff.geneOntology.GoTerm
- setGenomeFasta(String) - Method in class org.snpeff.spliceSites.SpliceTypes
- setGenomeVer(String) - Method in class org.snpeff.pdb.ProteinInteractions
- setGenomeVer(String) - Method in class org.snpeff.SnpEff
- setGenotype(String) - Method in class org.snpeff.interval.Variant
- setGenotype(String) - Method in class org.snpeff.vcf.VcfEffect
- setGenotype(String) - Method in class org.snpeff.vcf.VcfGenotype
-
Set genotype value
- setGenotypeStr(String) - Method in class org.snpeff.vcf.VcfEntry
- setGoTerms(GoTerms) - Method in class org.snpeff.geneOntology.GoTerm
- sethAxis(String) - Method in class org.snpeff.stats.plot.GoogleLineChart
- setHeight(int) - Method in class org.snpeff.stats.plot.GoogleLineChart
- setHgvsOld(boolean) - Method in class org.snpeff.snpEffect.Config
- setHgvsOneLetterAA(boolean) - Method in class org.snpeff.snpEffect.Config
- setHgvsShift(boolean) - Method in class org.snpeff.snpEffect.Config
- setHgvsTrId(boolean) - Method in class org.snpeff.snpEffect.Config
- setHighlyConservedAaSequence(boolean) - Method in class org.snpeff.interval.NextProt
- setHtmlTable(boolean) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- setId(String) - Method in class org.snpeff.interval.Interval
- setId(String) - Method in class org.snpeff.motif.Pwm
- setId(String) - Method in class org.snpeff.vcf.VcfHeaderEntry
- setIdMapFile(String) - Method in class org.snpeff.pdb.ProteinInteractions
- setIgnoreCase(boolean) - Method in class org.snpeff.util.Diff
- setIgnoreChromosomeErrors(boolean) - Method in class org.snpeff.fileIterator.MarkerFileIterator
- setIgnoreSpaces(boolean) - Method in class org.snpeff.util.Diff
- setImpact(VariantEffect.EffectImpact) - Method in class org.snpeff.vcf.VcfEffect
- setImplicit(boolean) - Method in class org.snpeff.vcf.VcfHeaderInfo
- setImprecise(boolean) - Method in class org.snpeff.interval.Variant
- setInitialSize(int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
- setInOffset(int) - Method in class org.snpeff.fileIterator.MarkerFileIterator
- setInOffset(int) - Method in class org.snpeff.fileIterator.VcfFileIterator
- setInterestingGenes(HashSet<String>) - Method in class org.snpeff.geneSets.GeneSets
- setInterestingSymbolIdSet(HashSet<String>) - Method in class org.snpeff.geneOntology.GoTerm
- setLabel(String) - Method in class org.snpeff.geneOntology.GoTerms
- setLabel(String) - Method in class org.snpeff.interval.Custom
- setLength(int) - Method in class org.snpeff.interval.Chromosome
- setLength(int) - Method in class org.snpeff.nmer.Nmer
-
Set nmer's length
- setLevel(int) - Method in class org.snpeff.geneOntology.GoTerm
- setLine(String) - Method in class org.snpeff.interval.GenericMarker
- setLineFilter(LineFilter) - Method in class org.snpeff.osCmd.StreamGobbler
- setLineNum(int) - Method in class org.snpeff.vcf.VcfEntry
- setLog(boolean) - Method in class org.snpeff.SnpEff
- setLossOfFunction(boolean) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
- setMarker(Marker) - Method in class org.snpeff.snpEffect.VariantEffect
-
Set marker.
- setMarker(Marker) - Method in class org.snpeff.snpEffect.VariantEffects
- setMarkerTypes(MarkerTypes) - Method in class org.snpeff.coverage.CountReads
- setMarkerTypes(MarkerTypes) - Method in class org.snpeff.stats.ReadsOnMarkersModel
- setMaskDownloadException(boolean) - Method in class org.snpeff.util.Download
- setMatch(int) - Method in class org.snpeff.align.NeedlemanWunsch
- setMatch(int) - Method in class org.snpeff.align.NeedlemanWunschOverlap
- setMaxBins(int) - Method in class org.snpeff.stats.IntStats
- setMaxBins(int) - Method in class org.snpeff.stats.plot.GoogleHistogram
- setMaxErrorRate(double) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
- setMaxErrorRate(double) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- setMaxGeneSetSize(int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- setMaxGeneSetSize(int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- setMaxMismatchRate(double) - Method in class org.snpeff.pdb.ProteinInteractions
- setMaxPvalue(double) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- setMaxPValue(double) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- setMaxPvalueAdjusted(double) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- setMaxPvalueAjusted(double) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- setMaxRank(int) - Method in class org.snpeff.geneOntology.GoTerm
- setMaxRank(int) - Method in class org.snpeff.geneSets.GeneSet
- setMinExons(int) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
- setMinGeneSetSize(int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- setMinGeneSetSize(int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- setMinOverlap(int) - Method in class org.snpeff.overlap.OverlapDnaSeq
- setMinus(GoTerm) - Method in class org.snpeff.geneOntology.GoTerm
-
Perform a 'set minus' between this term and 'goTerm' (set minus for 'symbolIdSet' and 'interestingSymbolIdSet').
- setMinus(GeneSet) - Method in class org.snpeff.geneSets.GeneSet
-
Perform a 'set minus' between this term and 'geneSet' (set minus for 'geneSet' and 'interestingGeneSet').
- setMissMatch(int) - Method in class org.snpeff.align.NeedlemanWunsch
- setMissMatch(int) - Method in class org.snpeff.align.NeedlemanWunschOverlap
- setMonitorTrace(Monitor) - Method in class org.snpeff.reactome.Reactome
- setN(int) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
- setName(String) - Method in class org.snpeff.geneSets.GeneSet
- setName(String) - Method in class org.snpeff.interval.Markers
- setName(String) - Method in class org.snpeff.interval.tree.IntervalForest
- setName(String) - Method in class org.snpeff.motif.Pwm
- setNameSpace(String) - Method in class org.snpeff.geneOntology.GoTerm
- setNextProt(boolean) - Method in class org.snpeff.SnpEff
- setNextProtKeepAllTrs(boolean) - Method in class org.snpeff.SnpEff
- setNmer(long) - Method in class org.snpeff.nmer.Nmer
-
Set nmer (binary coded)
- setNumber(int) - Method in class org.snpeff.vcf.VcfHeaderInfo
- setNumber(String) - Method in class org.snpeff.vcf.VcfHeaderInfo
- setNumberLabelsXaxis(int) - Method in class org.snpeff.stats.plot.GooglePlotInt
- setNumberOfSamples(int) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
- setNumGenes(int) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
- setNumIterations(int) - Method in class org.snpeff.stats.ReadsOnMarkersModel
- setNumReads(int) - Method in class org.snpeff.stats.ReadsOnMarkersModel
- setNumThreads(int) - Method in class org.snpeff.osCmd.OsCmdQueue
- setNumWords(int) - Method in class org.snpeff.collections.OpenBitSet
-
Expert: sets the number of longs in the array that are in use
- setObjetcToNotify(Object) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setOnlyOneTranscript(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
- setOnlyRegulation(boolean) - Method in class org.snpeff.snpEffect.Config
- setOrderDescending(boolean) - Method in class org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
- setOutOffset(int) - Method in class org.snpeff.outputFormatter.BedOutputFormatter
- setOutOffset(int) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setOutOffset(int) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
- setOutputDir(String) - Method in class org.snpeff.RegulationFileConsensus
- setOutputFile(String) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setOverlapFilter(OverlapFilter<T>) - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
- setParent(Interval) - Method in class org.snpeff.interval.Interval
- setParents(HashSet<GoTerm>) - Method in class org.snpeff.geneOntology.GoTerm
- setParseNow(boolean) - Method in class org.snpeff.fileIterator.VcfFileIterator
-
Should we parse vcfEntries later? (lazy parsing)
- setPdbDir(String) - Method in class org.snpeff.pdb.ProteinInteractions
- setPdbOrganismCommon(String) - Method in class org.snpeff.pdb.ProteinInteractions
- setPdbOrganismScientific(String) - Method in class org.snpeff.pdb.ProteinInteractions
- setPdbResolution(double) - Method in class org.snpeff.pdb.ProteinInteractions
- setPlotMaxData(int) - Method in class org.snpeff.stats.plot.GooglePlotInt
- setPlotSizeX(int) - Method in class org.snpeff.stats.plot.GooglePlotInt
- setPlotSizeY(int) - Method in class org.snpeff.stats.plot.GooglePlotInt
- setProgress(Progress) - Method in class org.snpeff.osCmd.StreamGobbler
- setProteinByTrId(Map<String, String>) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- setProteinCoding(boolean) - Method in class org.snpeff.interval.Transcript
- setProteinId(String) - Method in class org.snpeff.interval.Transcript
- setPvalue(double) - Method in class org.snpeff.geneSets.Result
- setPvalue(Apfloat) - Method in class org.snpeff.geneSets.Result
- setpValueCutOffQuantile(double) - Method in class org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
- setPwd(String) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setPwm(Pwm) - Method in class org.snpeff.interval.Motif
- setQuality(int, int) - Method in class org.snpeff.binseq.BinarySequence
-
Set the quality at position 'index'
- setQuiet(boolean) - Method in class org.snpeff.snpEffect.Config
- setQuiet(boolean, boolean) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setQuietMode() - Method in class org.snpeff.osCmd.StreamGobbler
- setRandom(Random) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- setRank(int) - Method in class org.snpeff.interval.Exon
- setRank(int) - Method in class org.snpeff.interval.Intron
- setRankedSymbols(int) - Method in class org.snpeff.geneOntology.GoTerm
- setRankSum(int) - Method in class org.snpeff.geneOntology.GoTerm
- setRankSum(long[][]) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
- setRareThreshold(double) - Method in class org.snpeff.codons.FindRareAaIntervals
- setReadLength(int) - Method in class org.snpeff.stats.ReadsOnMarkersModel
- setReadSequences(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Read sequences? Note: This is only used for debugging and testing
- setRedirectStderr(String) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setRedirectStdout(String) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setRedirectTo(String) - Method in class org.snpeff.osCmd.StreamGobbler
- setRedirectToOutput(boolean) - Method in class org.snpeff.osCmd.OsCmdQueue
- setRibosomalSlippage(boolean) - Method in class org.snpeff.interval.Transcript
- setSamples(int[][]) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
- setSaveLinesInMemory(boolean) - Method in class org.snpeff.osCmd.StreamGobbler
- setSaveStd(boolean) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setSaveStd(boolean) - Method in class org.snpeff.osCmd.OsCmdRunner
- setScore(double) - Method in class org.snpeff.interval.Custom
- setScore(double) - Method in class org.snpeff.interval.VariantWithScore
- setScore(String, double) - Method in class org.snpeff.stats.CountByType
- setSeparator(String) - Method in class org.snpeff.fileIterator.LineClassFileIterator
- setSequence(String) - Method in class org.snpeff.interval.Chromosome
-
Set sequence for this chromosome
- setSequence(String) - Method in class org.snpeff.interval.MarkerSeq
-
Set sequence WARNING: Sequence is always according to coding strand.
- setSequence(String) - Method in class org.snpeff.nextProt.NextProtXmlIsoform
-
Add an Isoform sequence
- setSequenceAlt(String) - Method in class org.snpeff.align.VariantRealign
- setSequenceRef(String) - Method in class org.snpeff.align.VariantRealign
- setSescription(String) - Method in class org.snpeff.geneOntology.GoTerm
- setShiftHgvs(boolean) - Method in class org.snpeff.SnpEff
- setShowExceptions(boolean) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setShowHeader(boolean) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setShowOnlyDifferentLines(boolean) - Method in class org.snpeff.util.Diff
- setSizeGrowthFactor(int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
- setSnpEffectPredictor(SnpEffectPredictor) - Method in class org.snpeff.snpEffect.Config
- setSnpEffectPredictor(SnpEffectPredictor) - Method in class org.snpeff.stats.ReadsOnMarkersModel
- setSpliceRegionExonSize(int) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- setSpliceRegionIntronMax(int) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- setSpliceRegionIntronMin(int) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- setSpliceSiteSize(int) - Method in class org.snpeff.SnpEff
- setSpliceSiteSize(int) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- setStacked(boolean) - Method in class org.snpeff.stats.plot.GoogleLineChart
- setStart(int) - Method in class org.snpeff.interval.Interval
- setStdoutAlert(String) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setStdoutAlertNotify(Object) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setStdOutFilter(LineFilter) - Method in class org.snpeff.osCmd.ExecuteOsCommand
- setStoreAlignments(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
- setStoreAlignments(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
- setStoreAlignments(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- setStoreSequences(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- setStrandMinus(boolean) - Method in class org.snpeff.interval.Interval
- setStrandMinus(boolean) - Method in class org.snpeff.interval.IntervalAndSubIntervals
- setString(String, String) - Method in class org.snpeff.snpEffect.Config
- setSubfieldSeparator(String) - Method in class org.snpeff.fileIterator.GuessTableTypes
- setSupressOutput(boolean) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setSupressOutput(boolean) - Method in class org.snpeff.SnpEff
- setSvgPlot(String) - Method in class org.snpeff.stats.TranslocationReport
- setSymbolIdSet(HashSet<String>) - Method in class org.snpeff.geneOntology.GoTerm
- setTags(String) - Method in class org.snpeff.interval.Transcript
- setTitle(String) - Method in class org.snpeff.stats.plot.GoogleLineChart
- setTitle(String) - Method in class org.snpeff.stats.plot.GooglePlotInt
- setTr1(Transcript) - Method in class org.snpeff.pdb.DistanceResult
- setTr2(Transcript) - Method in class org.snpeff.pdb.DistanceResult
- setTranscriptId(String) - Method in class org.snpeff.vcf.VcfEffect
- setTranscriptSet(TranscriptSet) - Method in class org.snpeff.spliceSites.SpliceTypes
- setTranscriptSupportLevel(TranscriptSupportLevel) - Method in class org.snpeff.interval.Transcript
- setTreatAllAsProteinCoding(boolean) - Method in class org.snpeff.snpEffect.Config
- setTrue() - Method in class org.snpeff.stats.BooleanMutable
- setUpdate(boolean) - Method in class org.snpeff.util.Download
- setUpDownStreamLength(int) - Method in class org.snpeff.SnpEff
- setUpDownStreamLength(int) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- setUseChromosomes(boolean) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- setUseFirstEffect(boolean) - Method in class org.snpeff.vcf.VcfEffect
- setUseGeneId(boolean) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setUseGeneId(boolean) - Method in class org.snpeff.vcf.VcfEffect
- setUseHgvs(boolean) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setUseHgvs(boolean) - Method in class org.snpeff.snpEffect.Config
- setUseHgvs(boolean) - Method in class org.snpeff.vcf.VcfEffect
- setUseMiliSecs(boolean) - Method in class org.snpeff.util.Timer
- setUseOicr(boolean) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setUseSequenceOntology(boolean) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setUseSequenceOntology(boolean) - Method in class org.snpeff.stats.VariantEffectStats
- setUseSpace(boolean) - Method in class org.snpeff.align.NeedlemanWunsch
- setValue(String, double) - Method in class org.snpeff.geneSets.GeneSets
-
Set experimental value for this gene
- setVariantEffectResutFilter(VariantEffectFilter) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setVariantRef(Variant) - Method in class org.snpeff.interval.VariantNonRef
- setVariantType(Variant.VariantType) - Method in class org.snpeff.align.VcfRefAltAlign
- setVariantType(Variant.VariantType) - Method in class org.snpeff.interval.Variant
- setvAxis(String) - Method in class org.snpeff.stats.plot.GoogleLineChart
- setVcfFileName(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
- setVcfHeader(VcfHeader) - Method in class org.snpeff.fileIterator.VcfFileIterator
-
Set header
- setVcfInfoNumber(VcfHeaderInfo.VcfInfoNumber) - Method in class org.snpeff.vcf.VcfHeaderInfo
- setVcfInfoType(VcfInfoType) - Method in class org.snpeff.vcf.VcfHeaderInfo
- setVerbose(boolean) - Method in class org.snpeff.binseq.GenomicSequences
- setVerbose(boolean) - Method in class org.snpeff.codons.FindRareAaIntervals
- setVerbose(boolean) - Method in class org.snpeff.coverage.CountReads
- setVerbose(boolean) - Method in class org.snpeff.coverage.CountReadsOnMarkers
- setVerbose(boolean) - Method in class org.snpeff.fastq.FastqSplit
- setVerbose(boolean) - Method in class org.snpeff.fileIterator.FileIterator
- setVerbose(boolean) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- setVerbose(boolean) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- setVerbose(boolean) - Method in class org.snpeff.geneSets.GeneSets
- setVerbose(boolean) - Method in class org.snpeff.gtex.Gtex
- setVerbose(boolean) - Method in class org.snpeff.interval.ExonSpliceCharacterizer
- setVerbose(boolean) - Method in class org.snpeff.interval.tree.IntervalTreeArray
- setVerbose(boolean) - Method in class org.snpeff.motif.Jaspar
- setVerbose(boolean) - Method in class org.snpeff.nextProt.NextProtDb
- setVerbose(boolean) - Method in class org.snpeff.osCmd.OsCmdQueue
- setVerbose(boolean) - Method in class org.snpeff.pdb.IdMapper
- setVerbose(boolean) - Method in class org.snpeff.pdb.ProteinInteractions
- setVerbose(boolean) - Method in class org.snpeff.ped.PedPedigree
- setVerbose(boolean) - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
- setVerbose(boolean) - Method in class org.snpeff.reactome.Reactome
- setVerbose(boolean) - Method in class org.snpeff.RegulationConsensusMultipleBed
- setVerbose(boolean) - Method in class org.snpeff.RegulationFileConsensus
- setVerbose(boolean) - Method in class org.snpeff.RegulationFileSplitBytType
- setVerbose(boolean) - Method in class org.snpeff.SnpEff
- setVerbose(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
- setVerbose(boolean) - Method in class org.snpeff.snpEffect.Config
- setVerbose(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- setVerbose(boolean) - Method in interface org.snpeff.snpEffect.VcfAnnotator
-
Set verbose mode
- setVerbose(boolean) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
- setVerbose(boolean) - Method in class org.snpeff.spliceSites.SpliceTypes
- setVerbose(boolean) - Method in class org.snpeff.spliceSites.TranscriptSet
- setVerbose(boolean) - Method in class org.snpeff.stats.ReadsOnMarkersModel
- setVerbose(boolean) - Method in class org.snpeff.util.Download
- setVerbose(boolean) - Method in class org.snpeff.vcf.FileIndexChrPos
- setVerbose(boolean) - Method in class org.snpeff.vcf.Pedigree
- setVersion(String) - Method in class org.snpeff.interval.Transcript
- setVersion(String) - Method in class org.snpeff.outputFormatter.OutputFormatter
- setWeight(double) - Method in class org.snpeff.reactome.Entity
- setWidth(int) - Method in class org.snpeff.stats.plot.GoogleLineChart
- setxAxisLabel(String) - Method in class org.snpeff.stats.plot.GooglePlotInt
- setxLables(ArrayList<String>) - Method in class org.snpeff.stats.plot.GoogleLineChart
- Sex - Enum Class in org.snpeff.ped
- shiftArgs - Variable in class org.snpeff.SnpEff
- shiftCoordinates(int) - Method in class org.snpeff.interval.Interval
- shiftCoordinates(int) - Method in class org.snpeff.interval.IntervalAndSubIntervals
- shouldApply(Variant) - Method in class org.snpeff.interval.Marker
-
True if the variant should be applied to the marker
- show() - Method in class org.snpeff.Zzz
- show(Object) - Static method in class org.snpeff.util.Timer
-
Show absolute timer value and a message
- SHOW_EVERY - Static variable in class org.snpeff.coverage.CountReads
- SHOW_EVERY - Static variable in class org.snpeff.coverage.CountReadsOnMarkers
- SHOW_EVERY - Static variable in class org.snpeff.Fastq2Fastq
- SHOW_EVERY - Static variable in class org.snpeff.interval.ExonSpliceCharacterizer
- SHOW_EVERY - Static variable in class org.snpeff.Qseq2Fastq
- SHOW_EVERY - Static variable in class org.snpeff.reactome.Reactome
- SHOW_EVERY - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- showChromoNamesDifferences() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
Shw differences in chromosome names
- showCodonChange - Static variable in class org.snpeff.interval.codonChange.CodonChange
- showGenes() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
-
Show genes in BED format
- showMark(int, int) - Static method in class org.snpeff.util.Gpr
-
Show a mark
- showMark(int, int, String) - Static method in class org.snpeff.util.Gpr
-
Show a mark
- showMarkStderr(int, int) - Static method in class org.snpeff.util.Gpr
-
Show a mark (on STDERR)
- showMismatch(String, String, String) - Static method in class org.snpeff.util.GprSeq
-
Show differences between two sequences
- showStackTrace(int) - Static method in class org.snpeff.util.Gpr
- showStackTrace(int, int) - Static method in class org.snpeff.util.Gpr
-
Prints a stack trace for a number of steps
- showStdErr(Object) - Static method in class org.snpeff.util.Timer
-
Show absolute timer value and a message on STDERR
- shrink(byte[], int) - Static method in class org.snpeff.collections.ArrayUtil
- shrink(int[], int) - Static method in class org.snpeff.collections.ArrayUtil
- shrink(long[], int) - Static method in class org.snpeff.collections.ArrayUtil
- SIGM - Enum constant in enum class org.snpeff.reactome.Entity.TransferFunction
- SIGM_PLUS_MINUS - Enum constant in enum class org.snpeff.reactome.Entity.TransferFunction
- sigma(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Wrapper to Sqrt(variance)
- sigma(int, int) - Static method in class org.snpeff.probablility.RankSumPdf
-
Wrapper to Sqrt(variance)
- SIGN_WIDTH - Static variable in class org.snpeff.svg.SvgIntron
- SIGNIFICANCE_LEVEL_95 - Static variable in class org.snpeff.gsa.ScoreList
- silenceWarning(ErrorWarningType) - Static method in class org.snpeff.util.Log
- SILENT - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.FunctionalClass
- SIMES - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
- simpleName(String) - Static method in class org.snpeff.interval.Chromosome
-
Simplify chromosome name
- simpleName(String) - Method in class org.snpeff.interval.ChromosomeSimpleName
-
Simplify chromosome name
- simpleNameCache(String) - Method in class org.snpeff.interval.ChromosomeSimpleName
-
Query cache before simplifying name
- size - Variable in class org.snpeff.fileIterator.TableFile
- size() - Method in class org.snpeff.binseq.indexer.SequenceIndexer
-
Number of sequences in this index
- size() - Method in class org.snpeff.collections.OpenBitSet
-
Returns the current capacity of this set.
- size() - Method in class org.snpeff.fileIterator.TableFile
-
Array size
- size() - Method in class org.snpeff.geneSets.GeneSet
- size() - Method in class org.snpeff.genotypes.GenotypeVector
- size() - Method in class org.snpeff.gsa.ChrPosScoreList
- size() - Method in class org.snpeff.gsa.ScoreList
- size() - Method in class org.snpeff.gtex.GtexExperiment
- size() - Method in class org.snpeff.interval.Genes
- size() - Method in class org.snpeff.interval.Interval
- size() - Method in class org.snpeff.interval.Markers
- size() - Method in class org.snpeff.interval.tree.IntervalForest
- size() - Method in class org.snpeff.interval.tree.IntervalTree
-
Size: number of entries in the interval list
- size() - Method in class org.snpeff.interval.tree.IntervalTreeArray
- size() - Method in class org.snpeff.interval.tree.IntervalTreeOri
-
Size: number of entries in the interval list
- size() - Method in interface org.snpeff.interval.tree.Itree
-
Size: number of entries in this tree
- size() - Method in class org.snpeff.nmer.NmerCount
- size() - Method in class org.snpeff.osCmd.OsCmdQueue
- size() - Method in class org.snpeff.ped.PedEntry
-
Number of phenotypes
- size() - Method in class org.snpeff.ped.PedGenotype
- size() - Method in class org.snpeff.ped.PedPedigree
- size() - Method in class org.snpeff.ped.PlinkMap
- size() - Method in class org.snpeff.reactome.events.Complex
- size() - Method in class org.snpeff.reactome.events.Pathway
- size() - Method in class org.snpeff.reactome.Monitor
- size() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- size() - Method in class org.snpeff.snpEffect.VariantEffects
- size() - Method in class org.snpeff.stats.ChrPosStats
- size() - Method in class org.snpeff.stats.CountByKey
- size() - Method in class org.snpeff.stats.PosStats
- size() - Method in class org.snpeff.vcf.FileIndexChrPos
-
File size
- SIZE_BRANCH - Static variable in class org.snpeff.spliceSites.SpliceTypes
- SIZE_CONSENSUS_ACCEPTOR - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- SIZE_CONSENSUS_DONOR - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- sizeEffective() - Method in class org.snpeff.geneSets.GeneSet
-
Number of genes that have a value
- sizeof(String) - Method in class org.snpeff.interval.Gene
-
Size of a genetic region for a given gene
- sizeResults() - Method in class org.snpeff.reactome.Monitor
- skip(long) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- SKIPPED - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
- SMALL - Static variable in class org.snpeff.probablility.RankSumPdf
-
A small number
- SMALL_VARIANT_SIZE_THRESHOLD - Static variable in class org.snpeff.snpEffect.SnpEffectPredictor
- SmithWaterman - Class in org.snpeff.align
-
Smith-Waterman (local sequence alignment) algorithm for sequence alignment (short strings, since it's not memory optimized)
- SmithWaterman(String, String) - Constructor for class org.snpeff.align.SmithWaterman
- snoRNA - Enum constant in enum class org.snpeff.interval.BioType
- SNP - Enum constant in enum class org.snpeff.interval.Variant.VariantType
- SnpEff - Class in org.snpeff
-
SnpEff's main command line program
- SnpEff() - Constructor for class org.snpeff.SnpEff
- SnpEff(String[]) - Constructor for class org.snpeff.SnpEff
- SnpEff.GeneDatabaseFormat - Enum Class in org.snpeff
-
Available gene database formats
- SnpEff.InputFormat - Enum Class in org.snpeff
-
Available input formats
- SnpEff.OutputFormat - Enum Class in org.snpeff
-
Available output formats
- snpEffCmd - Variable in class org.snpeff.SnpEff
- SnpEffCmdAcat - Class in org.snpeff.snpEffect.commandLine
-
ACAT: Create ACAT score for T2D project Note: This is just used to compile 'ACAT' score in T2D-GENES project, not useful at all for general audience.
- SnpEffCmdAcat() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
- SnpEffCmdBuild - Class in org.snpeff.snpEffect.commandLine
-
Command line program: Build database
- SnpEffCmdBuild() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
- SnpEffCmdBuildNextProt - Class in org.snpeff.snpEffect.commandLine
-
Parse NetxProt XML file and build a database http://www.nextprot.org/
- SnpEffCmdBuildNextProt() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdBuildNextProt
- SnpEffCmdCds - Class in org.snpeff.snpEffect.commandLine
-
Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structures
- SnpEffCmdCds() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
- SnpEffCmdCds(String, String, String) - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
- SnpEffCmdCds(Config) - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
- SnpEffCmdClosest - Class in org.snpeff.snpEffect.commandLine
-
Command line: Find closes marker to each variant
- SnpEffCmdClosest() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
- SnpEffCmdClosest(Config) - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
- SnpEffCmdCount - Class in org.snpeff.snpEffect.commandLine
-
Count reads from a BAM file given a list of intervals
- SnpEffCmdCount() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdCount
- SnpEffCmdDatabases - Class in org.snpeff.snpEffect.commandLine
-
Show all databases configures in snpEff.config Create an HTML 'download' table based on the config file Also creates a list of genome for Galaxy menu
- SnpEffCmdDatabases() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
- SnpEffCmdDownload - Class in org.snpeff.snpEffect.commandLine
-
Command line program: Download and install a (pre built) database
- SnpEffCmdDownload() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdDownload
- SnpEffCmdDump - Class in org.snpeff.snpEffect.commandLine
-
Command line program: Build database
- SnpEffCmdDump() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdDump
- SnpEffCmdDump.DumpFormat - Enum Class in org.snpeff.snpEffect.commandLine
- SnpEffCmdEff - Class in org.snpeff.snpEffect.commandLine
-
Command line program: Predict variant effects
- SnpEffCmdEff() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- SnpEffCmdGenes2Bed - Class in org.snpeff.snpEffect.commandLine
-
Simple test program
- SnpEffCmdGenes2Bed() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
- SnpEffCmdGsa - Class in org.snpeff.snpEffect.commandLine
-
Command line: Gene-Sets Analysis Perform gene set analysys
- SnpEffCmdGsa() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
- SnpEffCmdLen - Class in org.snpeff.snpEffect.commandLine
-
Calculate the maximum interval length by type, for all markers in a genome
- SnpEffCmdLen() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdLen
- SnpEffCmdPdb - Class in org.snpeff.snpEffect.commandLine
-
PDB distance analysis
- SnpEffCmdPdb() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
- SnpEffCmdProtein - Class in org.snpeff.snpEffect.commandLine
-
Command line: Read protein sequences from a file and compare them to the ones calculated from our data structures Note: This is done in order to see potential incompatibility errors between genome sequence and annotation.
- SnpEffCmdProtein() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- SnpEffCmdProtein(Config, String) - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- SnpEffCmdSeq - Class in org.snpeff.snpEffect.commandLine
-
Command line program: Show a transcript or a gene
- SnpEffCmdSeq() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdSeq
- SnpEffCmdShow - Class in org.snpeff.snpEffect.commandLine
-
Command line program: Show a transcript or a gene
- SnpEffCmdShow() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdShow
- SnpEffCmdSpliceAnalysis - Class in org.snpeff.spliceSites
-
Analyze sequences from splice sites
- SnpEffCmdSpliceAnalysis() - Constructor for class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- SnpEffCmdTranslocationsReport - Class in org.snpeff.snpEffect.commandLine
-
Create an SVG representation of a Marker
- SnpEffCmdTranslocationsReport() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
- SnpEffectPredictor - Class in org.snpeff.snpEffect
-
Predicts effects of SNPs
- SnpEffectPredictor(Genome) - Constructor for class org.snpeff.snpEffect.SnpEffectPredictor
- SnpEffPredictorFactory - Class in org.snpeff.snpEffect.factory
-
This class creates a SnpEffectPredictor from a file (or a set of files) and a configuration
- SnpEffPredictorFactory(Config, int) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- SnpEffPredictorFactoryEmbl - Class in org.snpeff.snpEffect.factory
-
This class creates a SnpEffectPredictor from an Embl file.
- SnpEffPredictorFactoryEmbl(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryEmbl
- SnpEffPredictorFactoryEmbl(Config, String) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryEmbl
- SnpEffPredictorFactoryFeatures - Class in org.snpeff.snpEffect.factory
-
This class creates a SnpEffectPredictor from a 'features' file.
- SnpEffPredictorFactoryFeatures(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
- SnpEffPredictorFactoryGenBank - Class in org.snpeff.snpEffect.factory
-
This class creates a SnpEffectPredictor from a GenBank file.
- SnpEffPredictorFactoryGenBank(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenBank
- SnpEffPredictorFactoryGenBank(Config, String) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenBank
- SnpEffPredictorFactoryGenesFile - Class in org.snpeff.snpEffect.factory
-
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)
- SnpEffPredictorFactoryGenesFile(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenesFile
- SnpEffPredictorFactoryGff - Class in org.snpeff.snpEffect.factory
-
This class creates a SnpEffectPredictor from a GFF file.
- SnpEffPredictorFactoryGff(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
- SnpEffPredictorFactoryGff2 - Class in org.snpeff.snpEffect.factory
-
This class creates a SnpEffectPredictor from a GFF2 file.
- SnpEffPredictorFactoryGff2(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff2
- SnpEffPredictorFactoryGff3 - Class in org.snpeff.snpEffect.factory
-
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
- SnpEffPredictorFactoryGff3(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff3
- SnpEffPredictorFactoryGtf22 - Class in org.snpeff.snpEffect.factory
-
This class creates a SnpEffectPredictor from a GTF 2.2 file References: http://mblab.wustl.edu/GTF22.html
- SnpEffPredictorFactoryGtf22(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22
- SnpEffPredictorFactoryKnownGene - Class in org.snpeff.snpEffect.factory
-
This class creates a SnpEffectPredictor from a TXT file dumped using UCSC table browser Fields in this table Field Example SQL type Info Description ----- ------- -------- ---- ----------- name uc001aaa.3 varchar(255) values Name of gene chrom chr1 varchar(255) values Reference sequence chromosome or scaffold strand + char(1) values + or - for strand txStart 11873 int(10) unsigned range Transcription start position txEnd 14409 int(10) unsigned range Transcription end position cdsStart 11873 int(10) unsigned range Coding region start cdsEnd 11873 int(10) unsigned range Coding region end exonCount 3 int(10) unsigned range Number of exons exonStarts 11873,12612,13220, longblob Exon start positions exonEnds 12227,12721,14409, longblob Exon end positions proteinID varchar(40) values UniProt display ID for Known Genes, UniProt accession or RefSeq protein ID for UCSC Genes alignID uc001aaa.3 varchar(255) values Unique identifier for each (known gene, alignment position) pair
- SnpEffPredictorFactoryKnownGene(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene
- SnpEffPredictorFactoryRand - Class in org.snpeff.snpEffect.factory
-
This class creates a random set of chromosomes, genes, transcripts and exons
- SnpEffPredictorFactoryRand(Config, Random, int, int, int) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
- SnpEffPredictorFactoryRefSeq - Class in org.snpeff.snpEffect.factory
-
This class creates a SnpEffectPredictor from a TXT file dumped using UCSC table browser RefSeq table schema: http://genome.ucsc.edu/cgi-bin/hgTables field example SQL type info description bin 585 smallint(5) range Indexing field to speed chromosome range queries.
- SnpEffPredictorFactoryRefSeq(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRefSeq
- snpOrMnp() - Method in class org.snpeff.snpEffect.HgvsProtein
-
SNP or MNP changes
- snRNA - Enum constant in enum class org.snpeff.interval.BioType
- SOFTWARE_NAME - Static variable in class org.snpeff.SnpEff
- sort() - Method in class org.snpeff.interval.Markers
-
Sort intervals
- sort() - Method in class org.snpeff.reactome.Monitor
- sort() - Method in class org.snpeff.snpEffect.VariantEffects
- sort(boolean, boolean) - Method in class org.snpeff.interval.Markers
-
Sort intervals
- sortCds() - Method in class org.snpeff.interval.Transcript
- sorted() - Method in class org.snpeff.interval.Genes
- sorted() - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Return a collection of sub intervals sorted by natural order
- sortedStrand() - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Return a collection of sub intervals sorted by start position (if strand is >= 0) or by reverse end position (if strand invalid input: '<' 0)
- SOURCE - Enum constant in enum class org.snpeff.genBank.Feature.Type
- SPLICE_REGION_EXON_SIZE - Static variable in class org.snpeff.interval.SpliceSite
- SPLICE_REGION_INTRON_MAX - Static variable in class org.snpeff.interval.SpliceSite
- SPLICE_REGION_INTRON_MIN - Static variable in class org.snpeff.interval.SpliceSite
- SPLICE_SITE_ACCEPTOR - Enum constant in enum class org.snpeff.snpEffect.EffectType
- SPLICE_SITE_BRANCH - Enum constant in enum class org.snpeff.snpEffect.EffectType
- SPLICE_SITE_BRANCH_U12 - Enum constant in enum class org.snpeff.snpEffect.EffectType
- SPLICE_SITE_DONOR - Enum constant in enum class org.snpeff.snpEffect.EffectType
- SPLICE_SITE_REGION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- spliceRegionExonSize - Variable in class org.snpeff.SnpEff
- spliceRegionIntronMax - Variable in class org.snpeff.SnpEff
- spliceRegionIntronMin - Variable in class org.snpeff.SnpEff
- SpliceSite - Class in org.snpeff.interval
-
Interval for a splice site Reference: http://en.wikipedia.org/wiki/RNA_splicing Spliceosomal introns often reside in eukaryotic protein-coding genes.
- SpliceSite() - Constructor for class org.snpeff.interval.SpliceSite
- SpliceSite(Exon, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSite
- SpliceSite(Intron, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSite
- SpliceSiteAcceptor - Class in org.snpeff.interval
-
Interval for a splice site acceptor Note: Splice sites donnor are defined as the last 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicing
- SpliceSiteAcceptor() - Constructor for class org.snpeff.interval.SpliceSiteAcceptor
- SpliceSiteAcceptor(Intron, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSiteAcceptor
- SpliceSiteBranch - Class in org.snpeff.interval
-
A (putative) branch site.
- SpliceSiteBranch() - Constructor for class org.snpeff.interval.SpliceSiteBranch
- SpliceSiteBranch(Intron, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSiteBranch
- SpliceSiteBranchU12 - Class in org.snpeff.interval
-
A (putative) U12 branch site.
- SpliceSiteBranchU12() - Constructor for class org.snpeff.interval.SpliceSiteBranchU12
- SpliceSiteBranchU12(Intron, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSiteBranchU12
- SpliceSiteDonor - Class in org.snpeff.interval
-
Interval for a splice site donnor Note: Splice sites donnor are defined as the first 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicing
- SpliceSiteDonor() - Constructor for class org.snpeff.interval.SpliceSiteDonor
- SpliceSiteDonor(Intron, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSiteDonor
- SpliceSiteRegion - Class in org.snpeff.interval
-
Interval for a splice site acceptor From Sequence Ontology: A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
- SpliceSiteRegion() - Constructor for class org.snpeff.interval.SpliceSiteRegion
- SpliceSiteRegion(Exon, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSiteRegion
- SpliceSiteRegion(Intron, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSiteRegion
- spliceSites() - Method in class org.snpeff.interval.Transcript
- spliceSiteSize - Variable in class org.snpeff.SnpEff
- SpliceTypes - Class in org.snpeff.spliceSites
-
Analyze sequences from splice sites
- SpliceTypes(Config) - Constructor for class org.snpeff.spliceSites.SpliceTypes
- split(String) - Method in class org.snpeff.vcf.VcfEffect
-
Split a 'effect' string to an array of strings
- split(String, char) - Static method in class org.snpeff.util.Gpr
-
Splits a separated string into an array of
String
tokens. - splitFile(RegulationFileIterator, String) - Method in class org.snpeff.RegulationFileSplitBytType
-
Read a regulation file and split into one file for each "regulation type"
- sRNA - Enum constant in enum class org.snpeff.interval.BioType
- sseqid - Variable in class org.snpeff.fileIterator.BlastResultEntry
- sstart - Variable in class org.snpeff.fileIterator.BlastResultEntry
- stab(int) - Method in class org.snpeff.interval.tree.IntervalTree
-
Perform a stabbing query, returning the interval objects
- stab(int) - Method in class org.snpeff.interval.tree.IntervalTreeArray
- stab(int) - Method in class org.snpeff.interval.tree.IntervalTreeOri
-
Perform a stabbing query, returning the interval objects
- stab(int) - Method in interface org.snpeff.interval.tree.Itree
-
Perform a stabbing query, returning the interval objects
- stab(int, int, Markers) - Method in class org.snpeff.interval.tree.IntervalTreeArray
- stab(Integer) - Method in class org.snpeff.interval.tree.IntervalNode
-
Perform a stabbing query on the node
- stab(Integer) - Method in class org.snpeff.interval.tree.IntervalNodeOri
-
Perform a stabbing query on the node
- stab(String, int) - Method in class org.snpeff.interval.tree.IntervalForest
-
Obtain all intervals that intersect with 'point'
- stab(Marker) - Method in class org.snpeff.interval.tree.IntervalForest
-
Obtain all intervals that intersect with 'marker.start'
- stabIntersects(int, int, Markers) - Method in class org.snpeff.interval.tree.IntervalTreeArray
-
Stab entries intersecting 'point' at node 'idx'
- STANDARD_TABLE - Static variable in class org.snpeff.codons.CodonTables
- STANDARD_TABLE_NAME - Static variable in class org.snpeff.codons.CodonTables
- start - Variable in class org.snpeff.binseq.indexer.OverlapRessult
- start - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- start - Variable in class org.snpeff.genBank.FeatureCoordinates
- start - Variable in class org.snpeff.interval.Interval
- start() - Method in class org.snpeff.util.Timer
- START_CODON - Enum constant in enum class org.snpeff.interval.GffType
- START_GAINED - Enum constant in enum class org.snpeff.snpEffect.EffectType
- START_LOST - Enum constant in enum class org.snpeff.snpEffect.EffectType
- startElement(String, String, String, Attributes) - Method in class org.snpeff.nextProt.NextProtHandler
-
Parse XML's element start
- startSection(Marker) - Method in class org.snpeff.outputFormatter.BedOutputFormatter
- startSection(Marker) - Method in class org.snpeff.outputFormatter.OutputFormatter
-
Starts a new section
- startSection(Marker) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
- stats() - Method in class org.snpeff.stats.MineMarkerIntervals
- stats() - Method in class org.snpeff.stats.MineTwoMarkerIntervals
- STOP_CODON - Enum constant in enum class org.snpeff.interval.GffType
- STOP_GAINED - Enum constant in enum class org.snpeff.snpEffect.EffectType
- STOP_LOST - Enum constant in enum class org.snpeff.snpEffect.EffectType
- stopCriteria(Result) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
-
Stop criteria
- stopCriteria(Result) - Method in class org.snpeff.geneSets.algorithm.RankSumPValueGreedyAlgorithm
-
Stop criteria
- strand - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- strandMinus - Variable in class org.snpeff.interval.Interval
- strandMinus - Variable in class org.snpeff.snpEffect.Hgvs
- strandPlus - Variable in class org.snpeff.snpEffect.Hgvs
- StreamGobbler - Class in org.snpeff.osCmd
-
Read the contents of a stream in a separate thread This class is used when executing OS commands in order to read STDOUT / STDERR and prevent process blocking It can alert an AlertListener when a given string is in the stream
- strict - Variable in class org.snpeff.SnpEff
- String - Enum constant in enum class org.snpeff.vcf.VcfInfoType
- string2fasta(String, String) - Static method in class org.snpeff.util.GprSeq
-
Transform into a FASTA formatted string
- StringDiff - Class in org.snpeff.align
- StringDiff(String, String) - Constructor for class org.snpeff.align.StringDiff
- StringDiff(String, String, String, String) - Constructor for class org.snpeff.align.StringDiff
- sub(double) - Method in class org.snpeff.stats.CounterDouble
- sub(long) - Method in class org.snpeff.stats.Counter
- sub(long) - Method in class org.snpeff.stats.CounterDouble
- SUB_FIELD_SEP - Static variable in class org.snpeff.vcf.VcfEntry
- subIntervals() - Method in class org.snpeff.interval.IntervalAndSubIntervals
-
Return a collection of sub intervals
- subsample(int, boolean) - Method in class org.snpeff.stats.plot.GooglePlotInt
-
Re sample data so it has at most 'numberOfPoints'
- SubsequenceComparator<T> - Class in org.snpeff.binseq.comparator
-
Compare two subsequences (actually it compares two sequences from different starting points)
- SubsequenceComparator() - Constructor for class org.snpeff.binseq.comparator.SubsequenceComparator
- SuffixIndexerNmer<T> - Class in org.snpeff.binseq.indexer
-
Index all suffixes of all the sequences (it indexes using Nmers).
- SuffixIndexerNmer(SubsequenceComparator<T>, int) - Constructor for class org.snpeff.binseq.indexer.SuffixIndexerNmer
- sum() - Method in class org.snpeff.gsa.ScoreList
-
Get sum of scores
- sum() - Method in class org.snpeff.stats.CountByType
-
Sum all counts.
- SUM - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
- SUMMARY_CSV_TEMPLATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- SUMMARY_GENES_TEMPLATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- SUMMARY_TEMPLATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- suppressOutput - Variable in class org.snpeff.SnpEff
- Svg - Class in org.snpeff.svg
-
Create an SVG representation of a Marker
- Svg() - Constructor for class org.snpeff.svg.Svg
- Svg(Marker, Svg) - Constructor for class org.snpeff.svg.Svg
- SvgBnd - Class in org.snpeff.svg
-
Create an SVG representation of a BND (translocation) variant In a VCF file, there are four possible translocations (BND) entries: REF ALT Meaning type 1: s t[p[ piece extending to the right of p is joined after t type 2: s t]p] reverse comp piece extending left of p is joined after t type 3: s ]p]t piece extending to the left of p is joined before t type 4: s [p[t reverse comp piece extending right of p is joined before t
- SvgBnd(VariantBnd, Svg, Svg) - Constructor for class org.snpeff.svg.SvgBnd
- SvgCds - Class in org.snpeff.svg
-
Create an SVG representation of a Marker
- SvgCds(Cds, Svg) - Constructor for class org.snpeff.svg.SvgCds
- SvgExon - Class in org.snpeff.svg
-
Create an SVG representation of a Marker
- SvgExon(Exon, Svg) - Constructor for class org.snpeff.svg.SvgExon
- SvgGene - Class in org.snpeff.svg
-
Create an SVG representation of a Marker
- SvgGene(Gene, Svg) - Constructor for class org.snpeff.svg.SvgGene
- SvgIntron - Class in org.snpeff.svg
-
Create an SVG representation of a Marker
- SvgIntron(Intron, Svg) - Constructor for class org.snpeff.svg.SvgIntron
- SvgNextProt - Class in org.snpeff.svg
-
Create an SVG representation of a NextProt annotation tracks
- SvgNextProt(Transcript, Svg, Markers) - Constructor for class org.snpeff.svg.SvgNextProt
- SvgScale - Class in org.snpeff.svg
-
Create an SVG representation of a "Scale and Chromsome labels
- SvgScale(Marker, Svg) - Constructor for class org.snpeff.svg.SvgScale
- SvgSpacer - Class in org.snpeff.svg
-
Leave an empty vertical space
- SvgSpacer(Marker, Svg) - Constructor for class org.snpeff.svg.SvgSpacer
- SvgTranscript - Class in org.snpeff.svg
-
Create an SVG representation of a transcript
- SvgTranscript(Transcript, Svg) - Constructor for class org.snpeff.svg.SvgTranscript
- SvgTranslocation - Class in org.snpeff.svg
-
Create an SVG representation of a BND (translocation) variant In a VCF file, there are four possible translocations (BND) entries: REF ALT Meaning type 1: s t[p[ piece extending to the right of p is joined after t type 2: s t]p] reverse comp piece extending left of p is joined after t type 3: s ]p]t piece extending to the left of p is joined before t type 4: s [p[t reverse comp piece extending right of p is joined before t
- SvgTranslocation(Transcript, Transcript, VariantBnd, SnpEffectPredictor) - Constructor for class org.snpeff.svg.SvgTranslocation
- SYNONYMOUS_CODING - Enum constant in enum class org.snpeff.snpEffect.EffectType
- SYNONYMOUS_START - Enum constant in enum class org.snpeff.snpEffect.EffectType
- SYNONYMOUS_STOP - Enum constant in enum class org.snpeff.snpEffect.EffectType
T
- T - Static variable in class org.snpeff.fastq.FastqSplit
- T2D_GENES - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
- TableFile - Class in org.snpeff.fileIterator
-
Load a table from a file.
- TableFile(int) - Constructor for class org.snpeff.fileIterator.TableFile
- TableFile(String) - Constructor for class org.snpeff.fileIterator.TableFile
- TableFile(String, String) - Constructor for class org.snpeff.fileIterator.TableFile
- tabs(int) - Static method in class org.snpeff.util.Gpr
- tags - Variable in class org.snpeff.SnpEff
- tagsNo - Variable in class org.snpeff.SnpEff
- tail(Object) - Static method in class org.snpeff.util.Gpr
- TANH - Enum constant in enum class org.snpeff.reactome.Entity.TransferFunction
- TB - Static variable in class org.snpeff.util.Gpr
- TEC - Enum constant in enum class org.snpeff.interval.BioType
- TEMPLATES_DIR - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- TERMINATION_CODON - Static variable in class org.snpeff.codons.CodonTable
- TERMINATION_CODON_1 - Static variable in class org.snpeff.codons.CodonTable
- terminology - Variable in class org.snpeff.nextProt.CvTerm
- test(int[], int[], double[]) - Method in class org.snpeff.probablility.CochranArmitageTest
-
Calculate CochranArmitageTest using the following contingency table B=1 B=2 ...
- text(double, double, String) - Method in class org.snpeff.svg.Svg
- TEXT_SIZE - Static variable in class org.snpeff.svg.Svg
- TEXT_STYLE - Static variable in class org.snpeff.svg.Svg
- TfamEntry - Class in org.snpeff.ped
-
An entry in a TFAM table.
- TfamEntry(String) - Constructor for class org.snpeff.ped.TfamEntry
- TfamEntry(String, String, String, String, Sex, double) - Constructor for class org.snpeff.ped.TfamEntry
- THRESHOLD_BRANCH_U12_PERCENTILE - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- THRESHOLD_COUNT - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- THRESHOLD_COUNT - Static variable in class org.snpeff.spliceSites.SpliceTypes
- THRESHOLD_ENTROPY - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- THRESHOLD_ENTROPY - Static variable in class org.snpeff.spliceSites.SpliceTypes
- THRESHOLD_P - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- THRESHOLD_P - Static variable in class org.snpeff.spliceSites.SpliceTypes
- THRESHOLD_U12_OBSERVED_EXPECTED - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- Timer - Class in org.snpeff.util
- Timer() - Constructor for class org.snpeff.util.Timer
- title() - Method in class org.snpeff.geneSets.GeneStats
- TO_BASE - Static variable in class org.snpeff.binseq.coder.DnaCoder
- toArray() - Method in class org.snpeff.interval.Markers
- toArray(T[]) - Method in class org.snpeff.interval.Markers
- toBase(int) - Method in class org.snpeff.binseq.coder.Coder
-
Decode a base using a binary representation
- toBase(int) - Method in class org.snpeff.binseq.coder.DnaCoder
-
Decode a base using 2 bits
- toBase(int) - Method in class org.snpeff.binseq.coder.DnaQualityCoder
-
Decode a base using 2 bits
- toBase(long, int) - Method in class org.snpeff.binseq.coder.Coder
-
Decode a base from a given position in a word
- toBase(long, int) - Method in class org.snpeff.binseq.coder.DnaCoder
- toByteSize(long) - Static method in class org.snpeff.util.Gpr
- toFile(String, Object) - Static method in class org.snpeff.util.Gpr
-
Write an object to a file
- toFile(String, Object, boolean) - Static method in class org.snpeff.util.Gpr
-
Write an object to a file
- toFileGz(String, Object) - Static method in class org.snpeff.util.Gpr
-
Write an object to a file (as a string) Note: The file is compressed using GZIP
- toFileSerialize(String, Object) - Static method in class org.snpeff.util.Gpr
-
Write an object to a file by invoking Serialization methods
- toFileSerializeGz(String, Object) - Static method in class org.snpeff.util.Gpr
-
Write an object to a file by invoking Serialization methods Note: The file is compressed using GZIP
- toggle() - Method in class org.snpeff.stats.BooleanMutable
- toQuality(int) - Method in class org.snpeff.binseq.coder.Coder
-
Decode a quality
- toQuality(int) - Method in class org.snpeff.binseq.coder.DnaQualityCoder
- toR(double, int, int) - Method in class org.snpeff.probablility.Binomial
-
Convert values to 'R' command
- toR(int, int, int, int) - Method in class org.snpeff.probablility.Hypergeometric
-
Convert values to 'R' command
- toR(int, int, int, int, boolean) - Method in class org.snpeff.probablility.FisherExactTest
-
Convert values to Fisher's 'R' command
- toSequenceOntology(EffFormatVersion, Variant) - Method in enum class org.snpeff.snpEffect.EffectType
- toStr() - Method in class org.snpeff.interval.Interval
-
To string as a simple "chr:start-end" format
- toStr() - Method in class org.snpeff.snpEffect.VariantEffect
- toStr() - Method in class org.snpeff.vcf.VcfEntry
-
To string as a simple "CHR:START_REF/ALTs" format
- toString() - Method in class org.snpeff.align.NeedlemanWunsch
- toString() - Method in class org.snpeff.align.NeedlemanWunschOverlap
- toString() - Method in class org.snpeff.align.StringDiff
- toString() - Method in class org.snpeff.align.VariantRealign
- toString() - Method in class org.snpeff.binseq.DnaAndQualitySequence
- toString() - Method in class org.snpeff.binseq.DnaNSequence
- toString() - Method in class org.snpeff.binseq.DnaSequence
- toString() - Method in class org.snpeff.binseq.DnaSequenceByte
- toString() - Method in class org.snpeff.binseq.DnaSequenceId
- toString() - Method in class org.snpeff.binseq.DnaSequencePe
- toString() - Method in class org.snpeff.binseq.GenomicSequences
- toString() - Method in class org.snpeff.binseq.indexer.OverlapRessult
- toString() - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
- toString() - Method in class org.snpeff.codons.CodonTable
- toString() - Method in class org.snpeff.codons.FindRareAaIntervals
- toString() - Method in class org.snpeff.collections.HashLongLongArray
- toString() - Method in class org.snpeff.coverage.CountFragments
- toString() - Method in class org.snpeff.coverage.CountReadsOnMarkers
-
Print table to STDOUT
- toString() - Method in class org.snpeff.coverage.Coverage
- toString() - Method in class org.snpeff.coverage.CoverageChr
- toString() - Method in class org.snpeff.fileIterator.BlastResultEntry
- toString() - Method in class org.snpeff.fileIterator.FileIterator
- toString() - Method in class org.snpeff.fileIterator.GuessTableTypes
- toString() - Method in class org.snpeff.fileIterator.MatrixEntry
- toString() - Method in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- toString() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
- toString() - Method in class org.snpeff.genBank.Feature
- toString() - Method in class org.snpeff.genBank.FeatureCoordinates
- toString() - Method in class org.snpeff.genBank.Features
- toString() - Method in class org.snpeff.geneOntology.GoTerm
- toString() - Method in class org.snpeff.geneOntology.GoTerms
- toString() - Method in class org.snpeff.geneSets.GeneSet
- toString() - Method in class org.snpeff.geneSets.GeneSets
- toString() - Method in class org.snpeff.geneSets.GeneStats
- toString() - Method in class org.snpeff.geneSets.Result
- toString() - Method in class org.snpeff.gsa.ChrPosScoreList
- toString() - Method in class org.snpeff.gsa.ScoreList
- toString() - Method in class org.snpeff.gtex.Gtex
- toString() - Method in class org.snpeff.gtex.GtexExperiment
- toString() - Method in class org.snpeff.interval.Cds
- toString() - Method in class org.snpeff.interval.Chromosome
- toString() - Method in class org.snpeff.interval.CircularCorrection
- toString() - Method in class org.snpeff.interval.codonChange.CodonChange
- toString() - Method in class org.snpeff.interval.Custom
- toString() - Method in class org.snpeff.interval.CytoBands
- toString() - Method in class org.snpeff.interval.Exon
- toString() - Method in class org.snpeff.interval.Gene
- toString() - Method in class org.snpeff.interval.Genes
- toString() - Method in class org.snpeff.interval.Genome
-
Show number of genes, transcripts invalid input: '&' exons
- toString() - Method in class org.snpeff.interval.GffMarker
- toString() - Method in class org.snpeff.interval.Interval
- toString() - Method in class org.snpeff.interval.IntervalSetIterator
- toString() - Method in class org.snpeff.interval.Marker
- toString() - Method in class org.snpeff.interval.Markers
- toString() - Method in class org.snpeff.interval.MarkerSeq
- toString() - Method in class org.snpeff.interval.Regulation
- toString() - Method in class org.snpeff.interval.Transcript
- toString() - Method in class org.snpeff.interval.tree.IntervalForest
- toString() - Method in class org.snpeff.interval.tree.IntervalNode
- toString() - Method in class org.snpeff.interval.tree.IntervalNodeOri
- toString() - Method in class org.snpeff.interval.tree.IntervalTree
- toString() - Method in class org.snpeff.interval.tree.IntervalTreeArray
- toString() - Method in class org.snpeff.interval.tree.IntervalTreeOri
- toString() - Method in class org.snpeff.interval.Variant
- toString() - Method in class org.snpeff.interval.VariantBnd
- toString() - Method in class org.snpeff.interval.VariantNonRef
- toString() - Method in class org.snpeff.motif.Pwm
- toString() - Method in class org.snpeff.motif.PwmAndSeqs
- toString() - Method in class org.snpeff.nextProt.CvTerm
- toString() - Method in class org.snpeff.nextProt.Location
- toString() - Method in class org.snpeff.nextProt.LocationTargetIsoform
- toString() - Method in class org.snpeff.nextProt.LocationTargetIsoformInteraction
- toString() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- toString() - Method in class org.snpeff.nextProt.NextProtXmlEntry
- toString() - Method in class org.snpeff.nextProt.NextProtXmlIsoform
- toString() - Method in class org.snpeff.nmer.Nmer
- toString() - Method in class org.snpeff.nmer.NmerCount
- toString() - Method in class org.snpeff.osCmd.ExecuteOsCommand
- toString() - Method in class org.snpeff.osCmd.OsCmdQueue
- toString() - Method in class org.snpeff.osCmd.OsCmdRunner
- toString() - Method in class org.snpeff.outputFormatter.BedAnnotationOutputFormatter
-
Show all effects
- toString() - Method in class org.snpeff.outputFormatter.BedOutputFormatter
-
Show all effects
- toString() - Method in class org.snpeff.outputFormatter.OutputFormatter
- toString() - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
- toString() - Method in class org.snpeff.pdb.DistanceResult
- toString() - Method in class org.snpeff.pdb.IdMapper
- toString() - Method in class org.snpeff.pdb.IdMapperEntry
- toString() - Method in class org.snpeff.ped.PedEntry
- toString() - Method in class org.snpeff.ped.PedGenotype
- toString() - Method in class org.snpeff.ped.PedPedigree
- toString() - Method in class org.snpeff.ped.TfamEntry
- toString() - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
- toString() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
- toString() - Method in class org.snpeff.reactome.Entity
- toString() - Method in class org.snpeff.reactome.events.Pathway
- toString() - Method in class org.snpeff.reactome.events.Reaction
- toString() - Method in class org.snpeff.reactome.Monitor
- toString() - Method in class org.snpeff.reactome.Reactome
- toString() - Method in class org.snpeff.sam.SamEntry
- toString() - Method in class org.snpeff.sam.SamHeaderRecordSq
- toString() - Method in class org.snpeff.snpEffect.Config
- toString() - Method in class org.snpeff.snpEffect.HgvsDna
- toString() - Method in class org.snpeff.snpEffect.HgvsProtein
- toString() - Method in class org.snpeff.snpEffect.LossOfFunction
- toString() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
- toString() - Method in class org.snpeff.snpEffect.VariantEffect
- toString() - Method in class org.snpeff.snpEffect.VariantEffectFusion
- toString() - Method in class org.snpeff.snpEffect.VariantEffects
- toString() - Method in class org.snpeff.snpEffect.VariantEffectStructural
- toString() - Method in class org.snpeff.spliceSites.AcgtTree
- toString() - Method in class org.snpeff.stats.AlleleCountStats
-
Show results to stdout
- toString() - Method in class org.snpeff.stats.Average
- toString() - Method in class org.snpeff.stats.AverageInt
- toString() - Method in class org.snpeff.stats.ChrPosStats
- toString() - Method in class org.snpeff.stats.CountByKey
- toString() - Method in class org.snpeff.stats.CountByType
- toString() - Method in class org.snpeff.stats.Counter
- toString() - Method in class org.snpeff.stats.CounterDouble
- toString() - Method in class org.snpeff.stats.FloatStats
- toString() - Method in class org.snpeff.stats.GenotypeStats
-
Show results to stdout
- toString() - Method in class org.snpeff.stats.HomHetStats
-
Show results to stdout
- toString() - Method in class org.snpeff.stats.IntStats
- toString() - Method in class org.snpeff.stats.ReadsOnMarkersModel
- toString() - Method in class org.snpeff.stats.TsTvStats
-
Show results to stdout
- toString() - Method in class org.snpeff.stats.VariantTypeStats
-
Show results to stdout
- toString() - Method in class org.snpeff.svg.Svg
- toString() - Method in class org.snpeff.svg.SvgBnd
- toString() - Method in class org.snpeff.svg.SvgCds
- toString() - Method in class org.snpeff.svg.SvgExon
- toString() - Method in class org.snpeff.svg.SvgGene
- toString() - Method in class org.snpeff.svg.SvgIntron
- toString() - Method in class org.snpeff.svg.SvgNextProt
- toString() - Method in class org.snpeff.svg.SvgScale
- toString() - Method in class org.snpeff.svg.SvgSpacer
- toString() - Method in class org.snpeff.svg.SvgTranscript
- toString() - Method in class org.snpeff.svg.SvgTranslocation
-
Create transcript and variant Svgs
- toString() - Method in class org.snpeff.util.CombinatorialIterator
- toString() - Method in class org.snpeff.util.Diff
- toString() - Method in class org.snpeff.util.KeyValue
- toString() - Method in class org.snpeff.util.Timer
- toString() - Method in class org.snpeff.util.Tuple
- toString() - Method in class org.snpeff.vcf.FileIndexChrPos.FileRegion
- toString() - Method in class org.snpeff.vcf.FileIndexChrPos.LineAndPos
- toString() - Method in class org.snpeff.vcf.FileIndexChrPos
- toString() - Method in class org.snpeff.vcf.LineChrPos
- toString() - Method in class org.snpeff.vcf.PedigreeEntry
- toString() - Method in class org.snpeff.vcf.VariantVcfEntry
- toString() - Method in class org.snpeff.vcf.VcfConsequence
- toString() - Method in class org.snpeff.vcf.VcfConsequenceHeader
- toString() - Method in class org.snpeff.vcf.VcfEffect
- toString() - Method in class org.snpeff.vcf.VcfEntry
- toString() - Method in class org.snpeff.vcf.VcfGenotype
- toString() - Method in class org.snpeff.vcf.VcfHeader
-
Get header information
- toString() - Method in class org.snpeff.vcf.VcfHeaderEntry
- toString() - Method in class org.snpeff.vcf.VcfHeaderFormat
- toString() - Method in class org.snpeff.vcf.VcfHeaderInfo
- toString() - Method in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
- toString() - Method in class org.snpeff.vcf.VcfLof
- toString(boolean) - Method in class org.snpeff.interval.Gene
- toString(boolean) - Method in class org.snpeff.interval.Transcript
- toString(boolean) - Method in class org.snpeff.ped.PedGenotype
- toString(boolean) - Method in class org.snpeff.stats.CountByType
- toString(boolean) - Method in class org.snpeff.stats.FloatStats
- toString(boolean[]) - Static method in class org.snpeff.util.Gpr
- toString(boolean, boolean) - Method in class org.snpeff.snpEffect.VariantEffect
- toString(double) - Static method in class org.snpeff.util.Gpr
- toString(double[]) - Static method in class org.snpeff.util.Gpr
- toString(double[][]) - Static method in class org.snpeff.util.Gpr
- toString(int) - Method in class org.snpeff.fileIterator.TableFile
-
Return line number 'index' as a string
- toString(int) - Method in class org.snpeff.interval.tree.IntervalTreeArray
- toString(int[]) - Static method in class org.snpeff.util.Gpr
- toString(int, HashSet<Entity>) - Method in class org.snpeff.reactome.Entity
- toString(int, HashSet<Entity>) - Method in class org.snpeff.reactome.events.Complex
- toString(int, HashSet<Entity>) - Method in class org.snpeff.reactome.events.Pathway
- toString(int, HashSet<Entity>) - Method in class org.snpeff.reactome.events.Reaction
- toString(long, boolean) - Static method in class org.snpeff.util.Timer
- toString(String) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
- toString(String) - Method in class org.snpeff.stats.CountByType
- toString(StringBuilder) - Method in class org.snpeff.interval.Genome
-
Show number of genes, transcripts invalid input: '&' exons Arr all errors to buffer
- toString(String, double, double, int) - Method in class org.snpeff.spliceSites.AcgtTree
- toStringAll() - Method in class org.snpeff.geneOntology.GoTerm
- toStringAll() - Method in class org.snpeff.geneSets.GeneSet
- toStringAll() - Method in class org.snpeff.gtex.GtexExperiment
- toStringAll() - Method in class org.snpeff.interval.tree.IntervalTreeArray
- toStringAll() - Method in class org.snpeff.nmer.NmerCount
- toStringAll(boolean) - Method in class org.snpeff.geneOntology.GoTerm
- toStringAll(int) - Method in class org.snpeff.nmer.NmerCount
- toStringAsciiArt(boolean) - Method in class org.snpeff.interval.Transcript
-
Show a transcript as an ASCII Art
- toStringAsciiArt(int) - Method in class org.snpeff.interval.Interval
-
Show it as an ASCII art
- toStringAsciiArt(int) - Method in class org.snpeff.interval.Markers
-
Show all intervals as an ASCII art
- toStringCache() - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Some cache statistics
- toStringCounts() - Method in class org.snpeff.stats.IntStats
-
Show a histogram as a list of numbers
- toStringDetails() - Method in class org.snpeff.reactome.Reactome
-
Show details
- toStringEnsembl() - Method in class org.snpeff.interval.Variant
-
Show variant in ENSEMBL's VEP format
- toStringHead(double[]) - Static method in class org.snpeff.util.Gpr
- toStringHeader() - Method in class org.snpeff.outputFormatter.BedAnnotationOutputFormatter
-
Show header
- toStringHeader() - Method in class org.snpeff.outputFormatter.BedOutputFormatter
-
Show header
- toStringHeader() - Method in class org.snpeff.outputFormatter.OutputFormatter
-
Show header
- toStringHeader() - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
-
Show header
- toStringHex() - Method in class org.snpeff.binseq.DnaSequenceByte
- toStringHisto() - Method in class org.snpeff.stats.IntStats
-
Show a histogram as a list of numbers
- toStringHistoPlot(String, String, String) - Method in class org.snpeff.stats.ChrPosStats
-
Create a histogram plot using Google charts
- toStringHtml(int, int, EffectType) - Method in class org.snpeff.motif.MotifLogo
-
Return an HTML string that represents the motif.
- toStringHtmlBody() - Method in class org.snpeff.stats.plot.GoogleGeneRegionChart
- toStringHtmlBody() - Method in class org.snpeff.stats.plot.GoogleLineChart
- toStringHtmlHeader() - Method in class org.snpeff.stats.plot.GoogleBarChart
- toStringHtmlHeader() - Method in class org.snpeff.stats.plot.GoogleGeneRegionChart
- toStringHtmlHeader() - Method in class org.snpeff.stats.plot.GoogleLineChart
- toStringLine() - Method in class org.snpeff.stats.CountByType
- toStringNoGt() - Method in class org.snpeff.vcf.VcfEntry
-
Show only first eight fields (no genotype entries)
- toStringOld() - Method in class org.snpeff.interval.Variant
-
Old format, used for some test cases
- toStringPlot(String, String, boolean) - Method in class org.snpeff.stats.IntStats
-
Create a histogram plot using Google charts
- toStringPos() - Method in class org.snpeff.pdb.DistanceResult
-
Show genomic positions only
- toStringSequences() - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
- toStringSimple() - Method in class org.snpeff.reactome.Entity
- toStringSimple(boolean) - Method in class org.snpeff.snpEffect.VariantEffect
-
Get the simplest string describing the effect (this is mostly used for testcases)
- toStringSort() - Method in class org.snpeff.stats.CountByType
- toStringTab() - Method in class org.snpeff.stats.IntStats
- toStringTabTitle() - Static method in class org.snpeff.stats.IntStats
- toStringTop(int) - Method in class org.snpeff.stats.CountByType
- toStringTxt() - Method in class org.snpeff.interval.Markers
- toStringValues() - Method in class org.snpeff.stats.IntStats
-
Histogram values
- toStringVcfLof() - Method in class org.snpeff.snpEffect.LossOfFunction
-
Get LOF value for VCF info field
- toStringVcfNmd() - Method in class org.snpeff.snpEffect.LossOfFunction
-
Get NMD value for VCF info field
- ToStringVersion - Static variable in class org.snpeff.interval.Exon
- toStrPos() - Method in class org.snpeff.interval.Interval
-
To string as a simple "chr:start-end" format
- total() - Method in class org.snpeff.nmer.NmerCount
-
Total number of nmers
- TOTAL_TYPE - Static variable in class org.snpeff.stats.CountByType
- toURLString() - Method in class org.snpeff.stats.plot.GoogleChartVenn
-
Create a histogram plot using Google charts
- toURLString() - Method in class org.snpeff.stats.plot.GoogleGenePercentBar
-
Create a histogram plot using Google charts
- toURLString() - Method in class org.snpeff.stats.plot.GoogleHistogram
-
Create a histogram plot using Google charts
- toURLString() - Method in class org.snpeff.stats.plot.GooglePlot
-
Create a histogram plot using Google charts
- toURLString() - Method in class org.snpeff.stats.plot.GooglePlotInt
-
Create a histogram plot using Google charts
- tr - Variable in class org.snpeff.snpEffect.Hgvs
- TR_C_gene - Enum constant in enum class org.snpeff.interval.BioType
- TR_D_gene - Enum constant in enum class org.snpeff.interval.BioType
- TR_J_gene - Enum constant in enum class org.snpeff.interval.BioType
- TR_J_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- TR_V_gene - Enum constant in enum class org.snpeff.interval.BioType
- TR_V_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- trAaLen - Variable in class org.snpeff.pdb.IdMapperEntry
- transcribed_processed_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- transcribed_unitary_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- transcribed_unprocessed_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- Transcript - Class in org.snpeff.interval
-
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
- Transcript() - Constructor for class org.snpeff.interval.Transcript
- Transcript(Gene, int, int, boolean, String) - Constructor for class org.snpeff.interval.Transcript
- TRANSCRIPT - Enum constant in enum class org.snpeff.interval.GffType
- TRANSCRIPT - Enum constant in enum class org.snpeff.snpEffect.EffectType
- TRANSCRIPT_DELETED - Enum constant in enum class org.snpeff.snpEffect.EffectType
- TRANSCRIPT_DUPLICATION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- TRANSCRIPT_ID_SEPARATORS - Static variable in class org.snpeff.fileIterator.FastaFileIterator
- TRANSCRIPT_ID_SEPARATORS_REGEX - Static variable in class org.snpeff.fileIterator.FastaFileIterator
- TRANSCRIPT_INVERSION - Enum constant in enum class org.snpeff.snpEffect.EffectType
- transcriptId - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
- transcriptIdNoVersion(String) - Static method in class org.snpeff.pdb.IdMapper
-
Remove version form transcript ID
- transcriptIds(List<IdMapperEntry>) - Static method in class org.snpeff.pdb.IdMapper
- TranscriptSet - Class in org.snpeff.spliceSites
-
A set of transcripts
- TranscriptSet(Genome) - Constructor for class org.snpeff.spliceSites.TranscriptSet
- TranscriptSupportLevel - Enum Class in org.snpeff.interval
-
Transcript level support Reference: http://useast.ensembl.org/Help/Glossary?id=492;redirect=no
- TRANSFER_FUNCTION - Static variable in class org.snpeff.reactome.Entity
- transferFunction(double) - Method in class org.snpeff.reactome.Entity
-
Transfer function
- transferFunction(double, double, double, double, double) - Method in class org.snpeff.reactome.events.Reaction
-
Transfer function
- translated_unprocessed_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- translocation() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Translocation nomenclature.
- TranslocationReport - Class in org.snpeff.stats
-
Pojo for translocation reports
- TranslocationReport(VariantBnd, VcfEffect, Transcript, Transcript) - Constructor for class org.snpeff.stats.TranslocationReport
- treatAllAsProteinCoding - Variable in class org.snpeff.SnpEff
- trId - Variable in class org.snpeff.pdb.IdMapperEntry
- trId1 - Variable in class org.snpeff.pdb.DistanceResult
- trId2 - Variable in class org.snpeff.pdb.DistanceResult
- trim(Fastq) - Method in class org.snpeff.fastq.FastqTrimmer
-
Create a new fastq sequence by trimming the given sequence
- trimTrailingZeros() - Method in class org.snpeff.collections.OpenBitSet
-
Lowers numWords, the number of words in use, by checking for trailing zero words.
- TRNA - Enum constant in enum class org.snpeff.genBank.Feature.Type
- tsl(TranscriptSupportLevel) - Static method in enum class org.snpeff.interval.TranscriptSupportLevel
-
Return TSL level (-1 if not available / invalid)
- TSL_1 - Enum constant in enum class org.snpeff.interval.TranscriptSupportLevel
- TSL_2 - Enum constant in enum class org.snpeff.interval.TranscriptSupportLevel
- TSL_3 - Enum constant in enum class org.snpeff.interval.TranscriptSupportLevel
- TSL_4 - Enum constant in enum class org.snpeff.interval.TranscriptSupportLevel
- TSL_5 - Enum constant in enum class org.snpeff.interval.TranscriptSupportLevel
- TSL_NA - Enum constant in enum class org.snpeff.interval.TranscriptSupportLevel
-
The transcript was not analyzed for one of the following reasons: pseudo-gene annotation, including transcribed pseudo-genes human leukocyte antigen (HLA) transcript immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version)
- TSL_NULL_VALUE - Static variable in enum class org.snpeff.interval.TranscriptSupportLevel
- TsTvStats - Class in org.snpeff.stats
-
Calculate Ts/Tv rations per sample (transitions vs transversions)
- TsTvStats() - Constructor for class org.snpeff.stats.TsTvStats
- Tuple<A,
B> - Class in org.snpeff.util -
Tuple: A pair of objects
- Tuple(A, B) - Constructor for class org.snpeff.util.Tuple
- TXT - Enum constant in enum class org.snpeff.snpEffect.commandLine.SnpEffCmdDump.DumpFormat
- TxtSerializable - Interface in org.snpeff.serializer
- type - Variable in class org.snpeff.interval.Marker
- type - Variable in class org.snpeff.nextProt.Location
- typeOfReference() - Method in class org.snpeff.snpEffect.HgvsDna
-
Prefix for coding or non-coding sequences
- typeOfReference() - Method in class org.snpeff.snpEffect.HgvsProtein
-
Return "p." string with/without transcript ID, according to user command line options.
- types - Variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
U
- UCSC - Enum constant in enum class org.snpeff.interval.FrameType
- uncompressGenotypes() - Method in class org.snpeff.vcf.VcfEntry
-
Uncompress VCF entry having genotypes in "HO,HE,NA" fields
- union() - Method in class org.snpeff.interval.Markers
-
Perform the union of all overlapping intervals
- union(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
-
this = this OR other
- union(GoTerm) - Method in class org.snpeff.geneOntology.GoTerm
-
Union this term with 'goTerm' (union for 'symbolIdSet' and 'interestingSymbolIdSet').
- union(GeneSet) - Method in class org.snpeff.geneSets.GeneSet
-
Union this term with 'geneSet' (union for 'geneSet' and 'interestingGeneSet').
- union(Marker) - Method in class org.snpeff.interval.Marker
-
Union of two markers
- union(Marker) - Method in class org.snpeff.interval.MarkerSeq
-
Union of two markers
- unionCount(OpenBitSet, OpenBitSet) - Static method in class org.snpeff.collections.OpenBitSet
-
Returns the popcount or cardinality of the union of the two sets.
- UNIPROT_DATABASE - Static variable in class org.snpeff.pdb.PdbFile
- unique() - Method in class org.snpeff.interval.Markers
-
Remove duplicated markers
- unitary_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- Unknown - Enum constant in enum class org.snpeff.ped.Sex
- UNKNOWN - Enum constant in enum class org.snpeff.interval.FrameType
- UNKNOWN - Enum constant in enum class org.snpeff.interval.Gene.GeneType
- UNKNOWN - Enum constant in enum class org.snpeff.interval.GffType
- UNKNOWN - Enum constant in enum class org.snpeff.vcf.VcfInfoType
- UNLIMITED - Enum constant in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
- unprocessed_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
- unzip(String, String, String) - Method in class org.snpeff.util.Download
-
UnZIP all files
- updateCounts(String) - Method in class org.snpeff.motif.Pwm
- updateCounts(String, int) - Method in class org.snpeff.motif.Pwm
-
Update counts matrix.
- updateCounts(String, int, long) - Method in class org.snpeff.motif.PwmAndSeqs
-
Update counts matrix.
- upDownStreamLength - Variable in class org.snpeff.SnpEff
- Upstream - Class in org.snpeff.interval
-
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
- Upstream() - Constructor for class org.snpeff.interval.Upstream
- Upstream(Transcript, int, int, boolean, String) - Constructor for class org.snpeff.interval.Upstream
- UPSTREAM - Enum constant in enum class org.snpeff.snpEffect.EffectType
- urlBaseName(String) - Static method in class org.snpeff.util.Download
-
File name from URL (i.e.
- usage(String) - Method in class org.snpeff.fastq.FastqSplit
-
Usage message
- usage(String) - Method in class org.snpeff.SnpEff
-
Show 'usage' message and exit with an error code '-1'
- usage(String) - Method in interface org.snpeff.snpEffect.commandLine.CommandLine
-
Show 'usage' message and exit with an error code '-1'
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
-
Show usage and exit
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
-
Show 'usage;' message and exit with an error code '-1'
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuildNextProt
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
-
Show usage and exit
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
-
Show usage and exit
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCount
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDownload
-
Show 'usage;' message and exit with an error code '-1'
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDump
-
Show 'usage;' message and exit with an error code '-1'
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
-
Show 'usage;' message and exit with an error code '-1'
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
-
Show usage and exit
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdLen
-
Show usage and exit
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
-
Show 'usage;' message and exit with an error code '-1'
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
-
Show usage and exit
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdSeq
-
Show 'usage' message and exit with an error code '-1'
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdShow
-
Show 'usage;' message and exit with an error code '-1'
- usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
-
Show 'usage;' message and exit with an error code '-1'
- usage(String) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
- usage(String) - Method in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- usageDb() - Method in class org.snpeff.SnpEff
-
Show database load and build options
- usageGeneric() - Method in class org.snpeff.SnpEff
-
Show generic options
- usageGenericAndDb() - Method in class org.snpeff.SnpEff
- Utr - Class in org.snpeff.interval
-
Interval for a UTR (5 prime UTR and 3 prime UTR
- Utr() - Constructor for class org.snpeff.interval.Utr
- Utr(Exon, int, int, boolean, String) - Constructor for class org.snpeff.interval.Utr
- UTR_3 - Enum constant in enum class org.snpeff.genBank.Feature.Type
- UTR_3_DELETED - Enum constant in enum class org.snpeff.snpEffect.EffectType
- UTR_3_PRIME - Enum constant in enum class org.snpeff.snpEffect.EffectType
- UTR_5 - Enum constant in enum class org.snpeff.genBank.Feature.Type
- UTR_5_DELETED - Enum constant in enum class org.snpeff.snpEffect.EffectType
- UTR_5_PRIME - Enum constant in enum class org.snpeff.snpEffect.EffectType
- UTR3 - Enum constant in enum class org.snpeff.interval.GffType
- Utr3prime - Class in org.snpeff.interval
-
Interval for a UTR (5 prime UTR and 3 prime UTR
- Utr3prime() - Constructor for class org.snpeff.interval.Utr3prime
- Utr3prime(Exon, int, int, boolean, String) - Constructor for class org.snpeff.interval.Utr3prime
- UTR5 - Enum constant in enum class org.snpeff.interval.GffType
- Utr5prime - Class in org.snpeff.interval
-
Interval for a UTR (5 prime UTR and 3 prime UTR
- Utr5prime() - Constructor for class org.snpeff.interval.Utr5prime
- Utr5prime(Exon, int, int, boolean, String) - Constructor for class org.snpeff.interval.Utr5prime
- utrFromCds(boolean) - Method in class org.snpeff.interval.Transcript
-
Calculate UTR regions from CDSs
V
- value - Variable in class org.snpeff.stats.BooleanMutable
- value - Variable in class org.snpeff.util.KeyValue
- valueOf(String) - Static method in enum class org.snpeff.genBank.Feature.Type
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.gsa.ScoreList.ScoreSummary
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.interval.BioType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.interval.Exon.ExonSpliceType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.interval.FrameType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.interval.Gene.GeneType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.interval.GffType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.interval.TranscriptSupportLevel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.interval.Variant.VariantType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.logStatsServer.LogStats.RequestResult
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.ped.Sex
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.reactome.Entity.TransferFunction
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.reactome.events.Reaction.RegulationType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.SnpEff.GeneDatabaseFormat
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.SnpEff.InputFormat
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.SnpEff.OutputFormat
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.snpEffect.commandLine.SnpEffCmdDump.DumpFormat
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.snpEffect.EffectType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.snpEffect.ErrorWarningType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.snpEffect.VariantEffect.Coding
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.snpEffect.VariantEffect.EffectImpact
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.snpEffect.VariantEffect.FunctionalClass
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.util.Log.FatalErrorBehabiour
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.vcf.EffFormatVersion
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.vcf.VcfEntry.AlleleFrequencyType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpeff.vcf.VcfInfoType
-
Returns the enum constant of this class with the specified name.
- values() - Static method in enum class org.snpeff.genBank.Feature.Type
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Method in class org.snpeff.geneOntology.GoTerms
- values() - Static method in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Method in class org.snpeff.geneSets.GeneSets
- values() - Static method in enum class org.snpeff.gsa.ScoreList.ScoreSummary
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.interval.BioType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.interval.Exon.ExonSpliceType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.interval.FrameType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.interval.Gene.GeneType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Method in class org.snpeff.interval.Genes
- values() - Static method in enum class org.snpeff.interval.GffType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.interval.TranscriptSupportLevel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.interval.Variant.VariantType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.logStatsServer.LogStats.RequestResult
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Method in class org.snpeff.ped.PedPedigree
- values() - Static method in enum class org.snpeff.ped.Sex
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.reactome.Entity.TransferFunction
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.reactome.events.Reaction.RegulationType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.SnpEff.GeneDatabaseFormat
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.SnpEff.InputFormat
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.SnpEff.OutputFormat
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.snpEffect.commandLine.SnpEffCmdDump.DumpFormat
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.snpEffect.EffectType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.snpEffect.ErrorWarningType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.snpEffect.VariantEffect.Coding
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.snpEffect.VariantEffect.EffectImpact
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.snpEffect.VariantEffect.FunctionalClass
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.util.Log.FatalErrorBehabiour
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.vcf.EffFormatVersion
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.vcf.VcfEntry.AlleleFrequencyType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpeff.vcf.VcfInfoType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- variance(int) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
- variance(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Variance for a given N and N_T
- variance(int, int) - Static method in class org.snpeff.probablility.RankSumPdf
-
Variance for a given N and N_T
- variance(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
-
Calculate the variance References: http://en.wikipedia.org/wiki/Hypergeometric_distribution
- varianceSlow(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
-
Variance for a given N and N_T (slow method, only used for debugging)
- variant - Variable in class org.snpeff.snpEffect.Hgvs
- variant - Variable in class org.snpeff.snpEffect.VariantEffect
- Variant - Class in org.snpeff.interval
-
A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
- Variant() - Constructor for class org.snpeff.interval.Variant
- Variant(Marker, int, int, String) - Constructor for class org.snpeff.interval.Variant
-
This constructor is used when we only have interval data (e.g.
- Variant(Marker, int, String, String) - Constructor for class org.snpeff.interval.Variant
- Variant(Marker, int, String, String, String) - Constructor for class org.snpeff.interval.Variant
- Variant.VariantType - Enum Class in org.snpeff.interval
- VariantBnd - Class in org.snpeff.interval
-
A 'BND' variant (i.e.
- VariantBnd() - Constructor for class org.snpeff.interval.VariantBnd
- VariantBnd(Marker, int, String, String, Chromosome, int, boolean, boolean) - Constructor for class org.snpeff.interval.VariantBnd
- variantEffect - Variable in class org.snpeff.snpEffect.Hgvs
- variantEffect(Variant) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Predict the effect of a variant
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Custom
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Downstream
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Exon
-
Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' class
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Gene
-
Get some details about the effect on this gene
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Intron
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Marker
-
Calculate the effect of this variant
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.MicroRnaBindingSite
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Motif
-
Calculate the effect of this variant
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.NextProt
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.ProteinInteractionLocus
-
Calculate the effect of this variant
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.ProteinProteinInteractionLocus
-
Calculate the effect of this variant
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Regulation
-
Calculate the effect of this variant
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.SpliceSite
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Transcript
-
Get some details about the effect on this transcript
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Upstream
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Utr3prime
- variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Utr5prime
- variantEffect(Variant, VariantEffects, Markers) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
-
Calculate variant effect for each marker in 'intersect'
- VariantEffect - Class in org.snpeff.snpEffect
-
Effect of a variant.
- VariantEffect(Variant) - Constructor for class org.snpeff.snpEffect.VariantEffect
- VariantEffect(Variant, Marker, EffectType, VariantEffect.EffectImpact, String, String, int, int, int) - Constructor for class org.snpeff.snpEffect.VariantEffect
- VariantEffect.Coding - Enum Class in org.snpeff.snpEffect
- VariantEffect.EffectImpact - Enum Class in org.snpeff.snpEffect
- VariantEffect.FunctionalClass - Enum Class in org.snpeff.snpEffect
-
This class is only getFused for SNPs
- VariantEffectFilter - Class in org.snpeff.filter
-
A Generic ChangeEffect filter
- VariantEffectFilter() - Constructor for class org.snpeff.filter.VariantEffectFilter
- VariantEffectFusion - Class in org.snpeff.snpEffect
-
Effect of a structural variant (fusion) affecting two genes
- VariantEffectFusion(Variant, Marker, Marker) - Constructor for class org.snpeff.snpEffect.VariantEffectFusion
- variantEffectGene(Variant, VariantEffects) - Method in class org.snpeff.interval.Gene
-
Add gene-specific annotations
- variantEffectNonRef(Variant, VariantEffects) - Method in class org.snpeff.interval.Marker
-
Calculate the effect of this variant
- VariantEffects - Class in org.snpeff.snpEffect
-
A sorted collection of variant effects
- VariantEffects() - Constructor for class org.snpeff.snpEffect.VariantEffects
- VariantEffectStats - Class in org.snpeff.stats
-
Variants annotation statistics.
- VariantEffectStats(Genome) - Constructor for class org.snpeff.stats.VariantEffectStats
- VariantEffectStructural - Class in org.snpeff.snpEffect
-
Effect of a structural variant affecting multiple genes
- VariantEffectStructural(Variant) - Constructor for class org.snpeff.snpEffect.VariantEffectStructural
- VariantEffectStructural(Variant, Markers) - Constructor for class org.snpeff.snpEffect.VariantEffectStructural
- VariantFileIterator - Class in org.snpeff.fileIterator
-
Opens a sequence change file and iterates over all sequence changes
- VariantFileIterator(String) - Constructor for class org.snpeff.fileIterator.VariantFileIterator
- VariantFileIterator(String, Genome) - Constructor for class org.snpeff.fileIterator.VariantFileIterator
- VariantNonRef - Class in org.snpeff.interval
-
A variant respect to non-reference (e.g.
- VariantNonRef() - Constructor for class org.snpeff.interval.VariantNonRef
- VariantNonRef(Variant, Variant) - Constructor for class org.snpeff.interval.VariantNonRef
- VariantRealign - Class in org.snpeff.align
-
Re-align a variant towards the leftmost (rightmost) position Note: We perform a 'progressive' realignment, asking for more reference sequence as we need it
- VariantRealign() - Constructor for class org.snpeff.align.VariantRealign
- VariantRealign(Variant) - Constructor for class org.snpeff.align.VariantRealign
- variants - Variable in class org.snpeff.vcf.VcfEntry
- variants() - Method in class org.snpeff.vcf.VcfEntry
-
Create a list of variants from this VcfEntry
- VariantStats - Class in org.snpeff.stats
-
Variants statistics: These are statisticas at Variant level.
- VariantStats(Genome) - Constructor for class org.snpeff.stats.VariantStats
- VariantTxtFileIterator - Class in org.snpeff.fileIterator
-
Opens a sequence change file and iterates over all sequence changes TXT Format: Tab-separated format, containing five columns that correspond to: chr \t position \t refSeq \t newSeq \t strand \t quality \t coverage \t id \n Fields strand, quality, coverage and id are optional E.g.
- VariantTxtFileIterator(String) - Constructor for class org.snpeff.fileIterator.VariantTxtFileIterator
- VariantTxtFileIterator(String, Genome) - Constructor for class org.snpeff.fileIterator.VariantTxtFileIterator
- variantType - Variable in class org.snpeff.interval.Variant
- VariantTypeStats - Class in org.snpeff.stats
-
Count variant types (SNP, MNP, INS, DEL)
- VariantTypeStats() - Constructor for class org.snpeff.stats.VariantTypeStats
- VariantVcfEntry - Class in org.snpeff.vcf
-
Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants.
- VariantVcfEntry(Variant, VcfEntry) - Constructor for class org.snpeff.vcf.VariantVcfEntry
- VariantWithScore - Class in org.snpeff.interval
-
A variant that has a numeric score.
- VariantWithScore() - Constructor for class org.snpeff.interval.VariantWithScore
- VariantWithScore(Marker, int, int, String, double) - Constructor for class org.snpeff.interval.VariantWithScore
- vaultRNA - Enum constant in enum class org.snpeff.interval.BioType
- VCF - Enum constant in enum class org.snpeff.SnpEff.InputFormat
- VCF - Enum constant in enum class org.snpeff.SnpEff.OutputFormat
- VCF_ALT_MISSING_REF - Static variable in class org.snpeff.vcf.VcfEntry
- VCF_ALT_MISSING_REF_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
- VCF_ALT_NON_REF - Static variable in class org.snpeff.vcf.VcfEntry
- VCF_ALT_NON_REF_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
- VCF_ALT_NON_REF_gVCF - Static variable in class org.snpeff.vcf.VcfEntry
- VCF_ALT_NON_REF_gVCF_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
- VCF_INFO_ANN_NAME - Static variable in enum class org.snpeff.vcf.EffFormatVersion
- VCF_INFO_ANN_NAMES - Static variable in enum class org.snpeff.vcf.EffFormatVersion
- VCF_INFO_CSQ_NAME - Static variable in class org.snpeff.vcf.VcfConsequence
- VCF_INFO_EFF_NAME - Static variable in enum class org.snpeff.vcf.EffFormatVersion
- VCF_INFO_END - Static variable in class org.snpeff.vcf.VcfEntry
- VCF_INFO_HETS - Static variable in class org.snpeff.vcf.VcfEntry
- VCF_INFO_HOMS - Static variable in class org.snpeff.vcf.VcfEntry
- VCF_INFO_LOF_NAME - Static variable in class org.snpeff.snpEffect.LossOfFunction
- VCF_INFO_NAS - Static variable in class org.snpeff.vcf.VcfEntry
- VCF_INFO_NMD_NAME - Static variable in class org.snpeff.snpEffect.LossOfFunction
- VCF_INFO_OICR_NAME - Static variable in class org.snpeff.outputFormatter.VcfOutputFormatter
- VCF_INFO_PRIVATE - Static variable in class org.snpeff.vcf.VcfEntry
- VcfAnnotator - Interface in org.snpeff.snpEffect
-
Annotate a VCF file: E.g.
- VcfAnnotatorChain - Class in org.snpeff.snpEffect
-
Maintains a list of VcfAnnotators and applies them one by one in the specified order
- VcfAnnotatorChain() - Constructor for class org.snpeff.snpEffect.VcfAnnotatorChain
- VcfConsequence - Class in org.snpeff.vcf
-
An 'CSQ' entry in a vcf line ('Consequence' from ENSEMBL's VEP) Format: ##INFO=invalid input: '<'ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP.
- VcfConsequence(VcfConsequenceHeader, String) - Constructor for class org.snpeff.vcf.VcfConsequence
- VcfConsequenceHeader - Class in org.snpeff.vcf
-
An 'CSQ' entry in a vcf header line
- VcfConsequenceHeader(VcfFileIterator) - Constructor for class org.snpeff.vcf.VcfConsequenceHeader
- VcfEffect - Class in org.snpeff.vcf
-
An 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *
- VcfEffect(String) - Constructor for class org.snpeff.vcf.VcfEffect
-
Constructor: Guess format version
- VcfEffect(String, EffFormatVersion) - Constructor for class org.snpeff.vcf.VcfEffect
-
Constructor: Force format version
- VcfEffect(VariantEffect, EffFormatVersion) - Constructor for class org.snpeff.vcf.VcfEffect
- VcfEffect(VariantEffect, EffFormatVersion, boolean, boolean) - Constructor for class org.snpeff.vcf.VcfEffect
- vcfEffects - Variable in class org.snpeff.vcf.VcfEntry
- vcfEntry - Variable in class org.snpeff.vcf.VariantVcfEntry
- VcfEntry - Class in org.snpeff.vcf
-
A VCF entry is a line in a VCF file A VCF line can have multiple variants, and multiple genotypes
- VcfEntry(VcfFileIterator, String, int, boolean) - Constructor for class org.snpeff.vcf.VcfEntry
-
Create a line form a file iterator
- VcfEntry(VcfFileIterator, Marker, String, int, String, String, String, double, String, String, String) - Constructor for class org.snpeff.vcf.VcfEntry
- VcfEntry.AlleleFrequencyType - Enum Class in org.snpeff.vcf
- vcfFileIterator - Variable in class org.snpeff.vcf.VcfEntry
- VcfFileIterator - Class in org.snpeff.fileIterator
-
Opens a VCF file and iterates over all entries (i.e.
- VcfFileIterator() - Constructor for class org.snpeff.fileIterator.VcfFileIterator
- VcfFileIterator(BufferedReader) - Constructor for class org.snpeff.fileIterator.VcfFileIterator
- VcfFileIterator(String) - Constructor for class org.snpeff.fileIterator.VcfFileIterator
- VcfFileIterator(String, Genome) - Constructor for class org.snpeff.fileIterator.VcfFileIterator
- VcfGenotype - Class in org.snpeff.vcf
-
A VCF genotype field There is one genotype per sample in each VCF entry
- VcfGenotype(VcfEntry, String, String) - Constructor for class org.snpeff.vcf.VcfGenotype
- vcfGenotypes - Variable in class org.snpeff.vcf.VcfEntry
- VcfHapMapFileIterator - Class in org.snpeff.fileIterator
-
Opens a Hapmap phased file and iterates over all entries, returning VcfEntries for each line Note: Each HapMap file has one chromosome.
- VcfHapMapFileIterator(String, String, Genome) - Constructor for class org.snpeff.fileIterator.VcfHapMapFileIterator
- vcfHeader() - Method in enum class org.snpeff.vcf.EffFormatVersion
-
VCF header for each format type
- VcfHeader - Class in org.snpeff.vcf
-
Represents the header of a vcf file.
- VcfHeader() - Constructor for class org.snpeff.vcf.VcfHeader
- VcfHeaderEntry - Class in org.snpeff.vcf
-
Represents a info elements in a VCF file's header References: https://samtools.github.io/hts-specs/VCFv4.3.pdf http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
- VcfHeaderEntry(String) - Constructor for class org.snpeff.vcf.VcfHeaderEntry
-
Constructor
- VcfHeaderFormat - Class in org.snpeff.vcf
- VcfHeaderFormat(String) - Constructor for class org.snpeff.vcf.VcfHeaderFormat
-
Constructor using a "##FORMAT" line from a VCF file
- VcfHeaderFormat(String, VcfInfoType, String, String) - Constructor for class org.snpeff.vcf.VcfHeaderFormat
- VcfHeaderInfo - Class in org.snpeff.vcf
-
Represents a info elements in a VCF file References: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 INFO fields should be described as follows (all keys are required): ##INFO=invalid input: '<'ID=ID,Number=number,Type=type,Description=description> Possible Types for INFO fields are: Integer, Float, Flag, Character, and String.
- VcfHeaderInfo(String) - Constructor for class org.snpeff.vcf.VcfHeaderInfo
-
Constructor using a "##INFO" line from a VCF file
- VcfHeaderInfo(String, VcfInfoType, String, String) - Constructor for class org.snpeff.vcf.VcfHeaderInfo
- VcfHeaderInfo(VcfHeaderInfo) - Constructor for class org.snpeff.vcf.VcfHeaderInfo
- VcfHeaderInfo.VcfInfoNumber - Enum Class in org.snpeff.vcf
-
Number of values in an INFO field.
- vcfInfoDecode(String) - Static method in class org.snpeff.vcf.VcfEntry
-
Decode INFO value
- vcfInfoEncode(String) - Static method in class org.snpeff.vcf.VcfEntry
-
Encode a string to be used in an 'INFO' field value From the VCF 4.3 specification Characters with special meaning (such as field delimiters ';' in INFO or ':' FORMAT fields) must be represented using the capitalized percent encoding: %3A : (colon) %3B ; (semicolon) %3D = (equal sign) %25 % (percent sign) %2C , (comma) %0D CR %0A LF %09 TAB
- vcfInfoKeySafe(String) - Static method in class org.snpeff.vcf.VcfEntry
-
Return a string safe to be used in an 'INFO' field key
- vcfInfoNames - Static variable in enum class org.snpeff.vcf.EffFormatVersion
- vcfInfoNumber - Variable in class org.snpeff.vcf.VcfHeaderInfo
- vcfInfoType - Variable in class org.snpeff.vcf.VcfHeaderInfo
- VcfInfoType - Enum Class in org.snpeff.vcf
- vcfInfoValueSafe(String) - Static method in class org.snpeff.vcf.VcfEntry
-
Return a string safe to be used in an 'INFO' field value
- VcfLof - Class in org.snpeff.vcf
-
An 'LOF' entry in a vcf line
- VcfLof(String) - Constructor for class org.snpeff.vcf.VcfLof
- VcfLof(String, String, int, double) - Constructor for class org.snpeff.vcf.VcfLof
- VcfLof(Gene, double) - Constructor for class org.snpeff.vcf.VcfLof
- VcfLof(VcfEntry, String) - Constructor for class org.snpeff.vcf.VcfLof
- VcfNmd - Class in org.snpeff.vcf
-
An 'NMD' entry in a vcf line
- VcfNmd(String) - Constructor for class org.snpeff.vcf.VcfNmd
- VcfNmd(String, String, int, double) - Constructor for class org.snpeff.vcf.VcfNmd
- VcfNmd(Gene, double) - Constructor for class org.snpeff.vcf.VcfNmd
- VcfNmd(VcfEntry, String) - Constructor for class org.snpeff.vcf.VcfNmd
- VcfOutputFormatter - Class in org.snpeff.outputFormatter
-
Formats output as VCF
- VcfOutputFormatter() - Constructor for class org.snpeff.outputFormatter.VcfOutputFormatter
- VcfOutputFormatter(List<VcfEntry>) - Constructor for class org.snpeff.outputFormatter.VcfOutputFormatter
-
Add all vcf entries to a list (used only for debugging and test-cases)
- VcfRefAltAlign - Class in org.snpeff.align
-
Needleman-Wunsch (global sequence alignment) algorithm for sequence alignment Only used for short strings (algorithm is not optimized)
- VcfRefAltAlign(String, String) - Constructor for class org.snpeff.align.VcfRefAltAlign
- VcfStats - Class in org.snpeff.stats
-
VCF statistics: These are statisticas at VCF line (i.e.
- VcfStats() - Constructor for class org.snpeff.stats.VcfStats
- verbose - Variable in class org.snpeff.fileIterator.FileIterator
- verbose - Variable in class org.snpeff.fileIterator.TableFile
- verbose - Static variable in class org.snpeff.geneOntology.GoTerms
- verbose - Variable in class org.snpeff.interval.tree.IntervalTreeArray
- verbose - Variable in class org.snpeff.logStatsServer.LogStats
- verbose - Variable in class org.snpeff.SnpEff
- version(String, String, String, boolean) - Static method in class org.snpeff.logStatsServer.VersionCheck
-
Get version data
- VERSION - Static variable in class org.snpeff.SnpEff
- VERSION_AUTHOR - Static variable in class org.snpeff.SnpEff
- VERSION_BUILD - Static variable in class org.snpeff.SnpEff
- VERSION_MAJOR - Static variable in class org.snpeff.SnpEff
- VERSION_SHORT - Static variable in class org.snpeff.SnpEff
- VersionCheck - Class in org.snpeff.logStatsServer
-
Check is a new version is available
- VersionCheck(String, String, String) - Constructor for class org.snpeff.logStatsServer.VersionCheck
W
- warnCDF - Static variable in class org.snpeff.probablility.RankSumNoReplacementPdf
- warnCount - Static variable in class org.snpeff.util.Log
- warning - Variable in class org.snpeff.snpEffect.VariantEffect
- warning(String) - Static method in class org.snpeff.util.Log
- warning(ErrorWarningType, String) - Static method in class org.snpeff.util.Log
-
Show a warning message (up to MAX_ERRORS times)
- WARNING_CANNOT_ADD_UTR - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_CDS_TOO_SHORT - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_CHROMOSOME_CIRCULAR - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_CHROMOSOME_LENGTH - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_CHROMOSOME_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_DUPLICATE_PRIMARY_KEY - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_EXON_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_EXON_SEQUENCE_LENGTH - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_EXON_TOO_SHORT - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_FILE_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_FRAMES_ZERO - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_GENE_COORDINATES - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_GENE_ID_DUPLICATE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_GENE_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_INVALID_INFO_KEY - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_INVALID_INFO_VALUE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_RARE_AA_POSSITION_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_REF_DOES_NOT_MATCH_GENOME - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_SEQUENCE_NOT_AVAILABLE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_TRANSCRIPT_ID_DUPLICATE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_TRANSCRIPT_INCOMPLETE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_TRANSCRIPT_NO_START_CODON - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_TRANSCRIPT_NO_STOP_CODON - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- WARNING_TRANSCRIPT_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
- warningln(String) - Static method in class org.snpeff.util.Log
- wc() - Method in class org.snpeff.nmer.Nmer
-
Watson-Cricks complement of this nmer Since {A, C, G, T} is translated into binary {00, 01, 10, 11}.
- wc(char) - Static method in class org.snpeff.util.GprSeq
-
Watson-Cricks complement
- wc(String) - Static method in class org.snpeff.util.GprSeq
-
Watson-Cricks complement
- weight - Variable in class org.snpeff.reactome.Entity
- WEIGHT_DOMINANT - Static variable in class org.snpeff.probablility.CochranArmitageTest
- WEIGHT_RECESSIVE - Static variable in class org.snpeff.probablility.CochranArmitageTest
- WEIGHT_TREND - Static variable in class org.snpeff.probablility.CochranArmitageTest
- WITHIN_FIELD_SEP - Static variable in class org.snpeff.vcf.VcfEntry
- wlen - Variable in class org.snpeff.collections.OpenBitSet
- write(DataOutputStream) - Method in class org.snpeff.binseq.BinarySequence
-
Write to a binary stream
- write(DataOutputStream) - Method in class org.snpeff.binseq.DnaAndQualitySequence
-
Write data in binary format
- write(DataOutputStream) - Method in class org.snpeff.binseq.DnaAndQualitySequenceWithId
-
Write data in binary format
- write(DataOutputStream) - Method in class org.snpeff.binseq.DnaNSequence
-
Write data in binary format
- write(DataOutputStream) - Method in class org.snpeff.binseq.DnaSequence
-
Write data in binary format
- write(DataOutputStream) - Method in class org.snpeff.binseq.DnaSequenceId
-
Write data in binary format
- write(DataOutputStream) - Method in class org.snpeff.binseq.DnaSequencePe
-
Write data in binary format
- write(OutputStream) - Method in class org.snpeff.nmer.Nmer
X
- xor(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
-
this = this XOR other
- xorCount(OpenBitSet, OpenBitSet) - Static method in class org.snpeff.collections.OpenBitSet
-
Returns the popcount or cardinality of the exclusive-or of the two sets.
Z
- Z_SCORES - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
- Zzz - Class in org.snpeff
-
How to calculate hydrogen bonds: - https://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(or%20H,hydrogen%20bond%20acceptor%20(Ac).
- Zzz(String) - Constructor for class org.snpeff.Zzz
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