# Index

A B C D E F G H I J K L M N O P Q R S T U V W X Z
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) - Method in class org.snpeff.interval.tree.IntervalForest
  Add all intervals
add(Collection) - Method in class org.snpeff.binseq.indexer.SequenceIndexer
  Add a collection of sequences
add(K, Collection) - 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) - Method in class org.snpeff.interval.IntervalAndSubIntervals
  Add all intervals
addAll(Collection) - Method in class org.snpeff.interval.Markers
  Add all markers in this collection
addAll(Collection) - 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) - 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) - 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) - Method in class org.snpeff.reactome.Entity
  Calculate entities.
calc(HashSet) - 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) - Method in class org.snpeff.geneSets.GeneSets
  Checks that every symboolID is in the set (as 'interesting' genes)
checkInterestingGenes(Set) - Method in class org.snpeff.geneSets.GeneSetsRanked
  Checks that every symboolID is in the set (as 'interesting' genes)
checkInterestingSymbolIds(Set) - 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.snpEffect.ProteinFastaWriter
  Close file
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
CNV - Enum constant in enum class org.snpeff.interval.Variant.VariantType
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) - 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
COMPATIBLE_WITH_5_3 - Static variable in class org.snpeff.snpEffect.Config
COMPATIBLE_WITH_5_4 - 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) - Constructor for class org.snpeff.snpEffect.Config
  Create a configuration from 'configFileName'
Config(String, String, String, Map, 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) - 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, int) - Method in class org.snpeff.geneOntology.GoTerms
  Produce a GOTerm based on a list of GOTerms and a 'mask'
disjointSet(List, 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, 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 <T> 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, Set) - Method in class org.snpeff.interval.Gene
  Filter transcripts by tags
filterTags(Set, Set) - 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.
fromString(String) - Static method in class org.snpeff.fileIterator.VcfFileIterator
  Create a VcfFileIterator from a string containig VCF lines
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, 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
getNumberString() - Method in class org.snpeff.vcf.VcfHeaderInfo
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, 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?
hasAltNonRef() - Method in class org.snpeff.vcf.VcfEntry
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<Long> > (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
isAltNonRef(String) - Method in class org.snpeff.vcf.VcfEntry
  Is this ALT string a NON_REF? (gVCF)
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
isStopAaSymbol(char) - Method in class org.snpeff.codons.CodonTable
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) - 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) - 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) - 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) - 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_PADN - Static variable in class org.snpeff.vcf.VcfEntry
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) - 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) - Method in class org.snpeff.stats.plot.GoogleBarChart
  Scale column to total sum
Performance Results - Section in class org.snpeff.collections.OpenBitSet
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) - 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
ProteinFastaWriter - Class in org.snpeff.snpEffect
  Writes protein sequences to a FASTA file
ProteinFastaWriter(String, boolean, boolean) - Constructor for class org.snpeff.snpEffect.ProteinFastaWriter
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) - 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) - 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, 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, 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, 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) - 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) - 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) - 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) - 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) - Method in class org.snpeff.probablility.bootstrap.ReSampleMap
score(Collection) - 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) - 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, 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) - 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) - 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) - Method in class org.snpeff.geneSets.GeneSets
setGeneSetCount(List) - Method in class org.snpeff.geneSets.Result
setGeneSetCountLast(int) - Method in class org.snpeff.geneSets.Result
setGeneSets(List) - Method in class org.snpeff.geneSets.Result
  Assign geneSets
setGeneSets(GeneSets) - Method in class org.snpeff.geneSets.GeneSet
setGenesSet(HashSet) - 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) - Method in class org.snpeff.geneSets.GeneSets
setInterestingSymbolIdSet(HashSet) - 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) - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
setParent(Interval) - Method in class org.snpeff.interval.Interval
setParents(HashSet) - 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) - 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) - Method in class org.snpeff.geneOntology.GoTerm
setTags(String) - Method in class org.snpeff.interval.Transcript
setTesting(boolean) - Method in class org.snpeff.SnpEff
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) - 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, 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 ...
testing - Variable in class org.snpeff.SnpEff
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) - Method in class org.snpeff.reactome.Entity
toString(int, HashSet) - Method in class org.snpeff.reactome.events.Complex
toString(int, HashSet) - Method in class org.snpeff.reactome.events.Pathway
toString(int, HashSet) - 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) - 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_A_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_ASTERISK_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_B_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_C_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_D_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_G_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_H_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_INV - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_INV_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_K_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_M_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_MISSING_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_MISSING_REF - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_N_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_OLD - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_NON_REF_OLD_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_R_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_S_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_T_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_V_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_W_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
VCF_ALT_Y_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_IMPRECISE - 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
VCF_INFO_SVLEN - 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 The VcfEntry represents the VCF line, NOT the variant itself.
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) - 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
write(Variant, VariantEffects) - Method in class org.snpeff.snpEffect.ProteinFastaWriter
  Append ALT protein sequence to fasta protein file

## 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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