Serialized Form
-
Package org.snpeff.binseq
-
Class org.snpeff.binseq.BinarySequence
class BinarySequence extends Object implements Serializable- serialVersionUID:
- 2349094116844619569L
-
Class org.snpeff.binseq.DnaAndQualitySequence
class DnaAndQualitySequence extends BinarySequence implements Serializable- serialVersionUID:
- 4523047567848438494L
-
Serialized Fields
-
codes
byte[] codes
-
-
Class org.snpeff.binseq.DnaAndQualitySequenceWithId
class DnaAndQualitySequenceWithId extends DnaAndQualitySequence implements Serializable- serialVersionUID:
- 4523294567844568494L
-
Serialized Fields
-
id
long id
-
-
Class org.snpeff.binseq.DnaNSequence
class DnaNSequence extends DnaSequence implements Serializable- serialVersionUID:
- 843945646419836582L
-
Serialized Fields
-
hasN
OpenBitSet hasN
-
-
Class org.snpeff.binseq.DnaSequence
class DnaSequence extends BinarySequence implements Serializable- serialVersionUID:
- 4523047339848048494L
-
Serialized Fields
-
coder
DnaCoder coder
-
codes
long[] codes
-
length
int length
-
-
Class org.snpeff.binseq.DnaSequenceId
class DnaSequenceId extends DnaSequence implements Serializable- serialVersionUID:
- 452657339854548494L
-
Serialized Fields
-
id
long id
-
-
Class org.snpeff.binseq.DnaSequencePe
class DnaSequencePe extends BinarySequence implements Serializable- serialVersionUID:
- -7267466011654235050L
-
Serialized Fields
-
gap
int gap
-
seq1
DnaSequence seq1
-
seq2
DnaSequence seq2
-
-
Class org.snpeff.binseq.GenomicSequences
class GenomicSequences extends Object implements Serializable- serialVersionUID:
- 2339867422366567569L
-
Serialized Fields
-
allSmallLoaded
boolean allSmallLoaded
-
debug
boolean debug
-
disableLoad
boolean disableLoad
-
genome
Genome genome
-
intervalForest
IntervalForest intervalForest
-
verbose
boolean verbose
-
-
-
Package org.snpeff.binseq.coder
-
Class org.snpeff.binseq.coder.Coder
class Coder extends Object implements Serializable -
Class org.snpeff.binseq.coder.DnaCoder
class DnaCoder extends Coder implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
COUNT_DIFFS
int[] COUNT_DIFFS
-
MASK_BASE
long[] MASK_BASE
-
MASK_HIGH
long[] MASK_HIGH
-
MASK_LOW
long[] MASK_LOW
-
-
Class org.snpeff.binseq.coder.DnaQualityCoder
class DnaQualityCoder extends DnaCoder implements Serializable
-
-
Package org.snpeff.collections
-
Class org.snpeff.collections.AutoHashMap
- serialVersionUID:
- 255818677257868365L
-
Serialized Fields
-
instance
V instance
-
-
Class org.snpeff.collections.MultivalueHashMap
- serialVersionUID:
- -8860279543165990227L
-
Class org.snpeff.collections.OpenBitSet
class OpenBitSet extends Object implements Serializable-
Serialized Fields
-
bits
long[] bits
-
wlen
int wlen
-
-
-
-
Package org.snpeff.coverage
-
Class org.snpeff.coverage.CountFragments
class CountFragments extends Object implements Serializable- serialVersionUID:
- 1150158182247576450L
-
Serialized Fields
-
coverageByName
HashMap<String,
CoverageChr> coverageByName
-
-
Class org.snpeff.coverage.Coverage
class Coverage extends Object implements Serializable- serialVersionUID:
- 1150158182247576450L
-
Serialized Fields
-
coverageByName
HashMap<String,
CoverageChr> coverageByName
-
-
Class org.snpeff.coverage.CoverageChr
class CoverageChr extends Object implements Serializable- serialVersionUID:
- -5620938926858131251L
-
Serialized Fields
-
count
short[] count
-
-
-
Package org.snpeff.fileIterator
-
Class org.snpeff.fileIterator.TableFile
class TableFile extends Object implements Serializable- serialVersionUID:
- 9180460090637138107L
-
-
Package org.snpeff.geneOntology
-
Class org.snpeff.geneOntology.GoTerm
class GoTerm extends Object implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
acc
String acc
-
childs
HashSet<GoTerm> childs
-
description
String description
-
goTerms
GoTerms goTerms
-
interestingSymbolIdSet
HashSet<String> interestingSymbolIdSet
-
level
int level
-
maxRank
int maxRank
-
nameSpace
String nameSpace
-
parents
HashSet<GoTerm> parents
-
rankedSymbols
int rankedSymbols
-
rankSum
long rankSum
-
symbolIdSet
HashSet<String> symbolIdSet
-
-
Class org.snpeff.geneOntology.GoTerms
class GoTerms extends Object implements Serializable-
Serialized Fields
-
goTermsByGoTermAcc
HashMap<String,
GoTerm> goTermsByGoTermAcc -
goTermsBySymbolId
HashMap<String,
Set<GoTerm>> goTermsBySymbolId -
interestingSymbolIdsSet
HashSet<String> interestingSymbolIdsSet
-
label
String label
-
maxRank
int maxRank
-
nameSpace
String nameSpace
-
rankSymbolId
HashMap<String,
Integer> rankSymbolId
-
-
-
-
Package org.snpeff.geneSets
-
Class org.snpeff.geneSets.GeneSet
class GeneSet extends Object implements Serializable- serialVersionUID:
- 1L
-
Class org.snpeff.geneSets.GeneSets
class GeneSets extends Object implements Serializable- serialVersionUID:
- -359594418467719013L
-
Serialized Fields
-
doNotAddIfNotInGeneSet
boolean doNotAddIfNotInGeneSet
-
genes
HashSet<String> genes
-
geneSetsByGene
HashMap<String,
HashSet<GeneSet>> geneSetsByGene -
geneSetsByName
HashMap<String,
GeneSet> geneSetsByName -
interestingGenes
HashSet<String> interestingGenes
-
label
String label
-
valueByGene
HashMap<String,
Double> valueByGene -
verbose
boolean verbose
-
-
Class org.snpeff.geneSets.GeneSetsRanked
class GeneSetsRanked extends GeneSets implements Serializable- serialVersionUID:
- -7922357470081599803L
-
-
Package org.snpeff.genotypes
-
Class org.snpeff.genotypes.Genotypes
class Genotypes extends Object implements Serializable- serialVersionUID:
- 5417498450863908076L
-
Serialized Fields
-
genotypeVectors
GenotypeVector[] genotypeVectors
-
vcfFileName
String vcfFileName
-
-
Class org.snpeff.genotypes.GenotypeVector
class GenotypeVector extends Object implements Serializable- serialVersionUID:
- 4734574592894281057L
-
Serialized Fields
-
genotype
byte[] genotype
-
size
int size
-
-
-
Package org.snpeff.interval
-
Class org.snpeff.interval.Cds
class Cds extends Marker implements Serializable- serialVersionUID:
- 1636197649250882952L
-
Serialized Fields
-
frame
byte frame
-
-
Class org.snpeff.interval.Chromosome
class Chromosome extends Marker implements Serializable- serialVersionUID:
- 1636197649250882952L
-
Serialized Fields
-
chromosomeNum
double chromosomeNum
-
circular
boolean circular
-
sequence
DnaSequence sequence
-
-
Class org.snpeff.interval.Custom
class Custom extends Marker implements Serializable- serialVersionUID:
- -6843535415295857726L
-
Serialized Fields
-
label
String label
-
score
double score
-
-
Class org.snpeff.interval.Downstream
class Downstream extends Marker implements Serializable- serialVersionUID:
- 1636197649250882952L
-
Class org.snpeff.interval.Exon
class Exon extends MarkerSeq implements Serializable- serialVersionUID:
- 5324352193278472543L
-
Serialized Fields
-
aaIdxEnd
int aaIdxEnd
-
aaIdxStart
int aaIdxStart
-
frame
byte frame
-
rank
int rank
-
spliceSites
ArrayList<SpliceSite> spliceSites
-
spliceType
Exon.ExonSpliceType spliceType
-
-
Class org.snpeff.interval.Gene
- serialVersionUID:
- 8419206759034068147L
-
Class org.snpeff.interval.GenericMarker
class GenericMarker extends Marker implements Serializable- serialVersionUID:
- -1645062778820144533L
-
Serialized Fields
-
line
String line
-
-
Class org.snpeff.interval.Genes
class Genes extends Object implements Serializable- serialVersionUID:
- 9022385501946879197L
-
Class org.snpeff.interval.Genome
class Genome extends Marker implements Serializable- serialVersionUID:
- -330362012383572257L
-
Serialized Fields
-
chromoFastaFiles
String[] chromoFastaFiles
-
chromosomeNamesSorted
List<String> chromosomeNamesSorted
-
chromosomes
HashMap<String,
Chromosome> chromosomes -
codingInfo
Boolean codingInfo
-
cytoBands
CytoBands cytoBands
-
fastaDir
String fastaDir
-
genes
Genes genes
-
genomeId
int genomeId
-
genomicSequences
GenomicSequences genomicSequences
-
length
long length
-
species
String species
-
transcriptSupportLevelInfo
Boolean transcriptSupportLevelInfo
-
version
String version
-
-
Class org.snpeff.interval.GffMarker
class GffMarker extends Custom implements Serializable- serialVersionUID:
- -164502778854644537L
-
Class org.snpeff.interval.Gtf2Marker
class Gtf2Marker extends GffMarker implements Serializable- serialVersionUID:
- 5416962964309837838L
-
Class org.snpeff.interval.Intergenic
class Intergenic extends Marker implements Serializable- serialVersionUID:
- -2487664381262354896L
-
Serialized Fields
-
name
String name
-
-
Class org.snpeff.interval.IntergenicConserved
class IntergenicConserved extends Marker implements Serializable- serialVersionUID:
- -1816568396090993792L
-
Class org.snpeff.interval.Interval
class Interval extends Object implements Serializable- serialVersionUID:
- -3547434510230920403L
-
Class org.snpeff.interval.IntervalAndSubIntervals
class IntervalAndSubIntervals extends Marker implements Serializable- serialVersionUID:
- 1636197649250882952L
-
Class org.snpeff.interval.Intron
class Intron extends Marker implements Serializable- serialVersionUID:
- -8283322526157264389L
-
Serialized Fields
-
exonAfter
Exon exonAfter
-
exonBefore
Exon exonBefore
-
rank
int rank
-
spliceSites
ArrayList<SpliceSite> spliceSites
-
-
Class org.snpeff.interval.IntronConserved
class IntronConserved extends Marker implements Serializable- serialVersionUID:
- -3148108162409498012L
-
Class org.snpeff.interval.Marker
class Marker extends Interval implements Serializable- serialVersionUID:
- 7878886900660027549L
-
Serialized Fields
-
type
EffectType type
-
-
Class org.snpeff.interval.MarkerParentId
class MarkerParentId extends Marker implements Serializable-
Serialized Fields
-
parentId
int parentId
-
-
-
Class org.snpeff.interval.Markers
class Markers extends Object implements Serializable- serialVersionUID:
- 259791388087691277L
-
Class org.snpeff.interval.MarkerSeq
class MarkerSeq extends Marker implements Serializable- serialVersionUID:
- -8794533547221460207L
-
Serialized Fields
-
sequence
DnaSequence sequence
-
-
Class org.snpeff.interval.MicroRnaBindingSite
class MicroRnaBindingSite extends Marker implements Serializable- serialVersionUID:
- -9089500641817245554L
-
Serialized Fields
-
pValue
double pValue
-
-
Class org.snpeff.interval.Motif
class Motif extends Marker implements Serializable- serialVersionUID:
- 8464487883781181867L
-
Class org.snpeff.interval.NextProt
class NextProt extends Marker implements Serializable- serialVersionUID:
- 8939301304881007289L
-
Class org.snpeff.interval.ProteinInteractionLocus
class ProteinInteractionLocus extends Marker implements Serializable- serialVersionUID:
- 1L
-
Class org.snpeff.interval.ProteinProteinInteractionLocus
class ProteinProteinInteractionLocus extends ProteinInteractionLocus implements Serializable- serialVersionUID:
- -2111056845758378137L
-
Serialized Fields
-
trInteract
Transcript trInteract
-
-
Class org.snpeff.interval.ProteinStructuralInteractionLocus
class ProteinStructuralInteractionLocus extends ProteinInteractionLocus implements Serializable- serialVersionUID:
- 1416019843839053485L
-
Class org.snpeff.interval.RareAminoAcid
class RareAminoAcid extends Marker implements Serializable- serialVersionUID:
- -1926572865764543849L
-
Class org.snpeff.interval.Regulation
class Regulation extends Marker implements Serializable- serialVersionUID:
- -5607588295343642199L
-
Class org.snpeff.interval.SpliceSite
class SpliceSite extends Marker implements Serializable- serialVersionUID:
- 1636197649250882952L
-
Class org.snpeff.interval.SpliceSiteAcceptor
class SpliceSiteAcceptor extends SpliceSite implements Serializable- serialVersionUID:
- -7416687954435361328L
-
Class org.snpeff.interval.SpliceSiteBranch
class SpliceSiteBranch extends SpliceSite implements Serializable- serialVersionUID:
- 7903892379174750342L
-
Class org.snpeff.interval.SpliceSiteBranchU12
class SpliceSiteBranchU12 extends SpliceSiteBranch implements Serializable- serialVersionUID:
- 7903892379174750342L
-
Class org.snpeff.interval.SpliceSiteDonor
class SpliceSiteDonor extends SpliceSite implements Serializable- serialVersionUID:
- -2117470153797320999L
-
Class org.snpeff.interval.SpliceSiteRegion
class SpliceSiteRegion extends SpliceSite implements Serializable- serialVersionUID:
- -7416687954435361328L
-
Class org.snpeff.interval.Transcript
- serialVersionUID:
- -2665025617916107311L
-
Serialized Fields
-
aa2pos
int[] aa2pos
-
aaCheck
boolean aaCheck
-
bioType
BioType bioType
-
canonical
boolean canonical
-
cds
String cds
-
cds2pos
int[] cds2pos
-
cdsEnd
int cdsEnd
-
cdss
List<Cds> cdss
-
cdsStart
int cdsStart
-
corrected
boolean corrected
-
dnaCheck
boolean dnaCheck
-
downstream
Downstream downstream
-
firstCodingExon
Exon firstCodingExon
-
introns
List<Intron> introns
-
mRna
String mRna
-
protein
String protein
-
proteinCoding
boolean proteinCoding
-
proteinId
String proteinId
-
ribosomalSlippage
boolean ribosomalSlippage
-
spliceRegionExonSize
int spliceRegionExonSize
-
spliceRegionIntronMax
int spliceRegionIntronMax
-
spliceRegionIntronMin
int spliceRegionIntronMin
-
spliceSiteSize
int spliceSiteSize
-
tags
String tags
-
transcriptSupportLevel
TranscriptSupportLevel transcriptSupportLevel
-
upDownLength
int upDownLength
-
upstream
Upstream upstream
-
utrs
List<Utr> utrs
-
version
String version
-
-
Class org.snpeff.interval.Upstream
class Upstream extends Marker implements Serializable- serialVersionUID:
- 1636197649250882952L
-
Class org.snpeff.interval.Utr
class Utr extends Marker implements Serializable- serialVersionUID:
- 1636197649250882952L
-
Class org.snpeff.interval.Utr3prime
class Utr3prime extends Utr implements Serializable- serialVersionUID:
- 5688641008301281991L
-
Class org.snpeff.interval.Utr5prime
class Utr5prime extends Utr implements Serializable- serialVersionUID:
- 3710420226746056364L
-
Class org.snpeff.interval.Variant
class Variant extends Marker implements Serializable- serialVersionUID:
- -2928105165111400441L
-
Serialized Fields
-
alt
String alt
-
genotype
String genotype
-
imprecise
boolean imprecise
-
ref
String ref
-
variantType
Variant.VariantType variantType
-
-
Class org.snpeff.interval.VariantBnd
class VariantBnd extends Variant implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
before
boolean before
-
endPoint
Marker endPoint
-
left
boolean left
-
-
Class org.snpeff.interval.VariantNonRef
class VariantNonRef extends Variant implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
variantRef
Variant variantRef
-
-
Class org.snpeff.interval.VariantWithScore
class VariantWithScore extends Variant implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
score
double score
-
-
-
Package org.snpeff.interval.tree
-
Class org.snpeff.interval.tree.IntervalForest
class IntervalForest extends Object implements Serializable- serialVersionUID:
- 1L
-
Class org.snpeff.interval.tree.IntervalNode
class IntervalNode extends Object implements Serializable- serialVersionUID:
- -444656480302906048L
-
Serialized Fields
-
center
int center
-
intervalsCenter
Marker[] intervalsCenter
-
leftNode
IntervalNode leftNode
-
rightNode
IntervalNode rightNode
-
-
Class org.snpeff.interval.tree.IntervalNodeOri
class IntervalNodeOri extends Object implements Serializable- serialVersionUID:
- -444656480302906048L
-
Serialized Fields
-
center
Integer center
-
intervals
SortedMap<Marker,
List<Marker>> intervals -
leftNode
IntervalNodeOri leftNode
-
rightNode
IntervalNodeOri rightNode
-
-
Class org.snpeff.interval.tree.IntervalTree
class IntervalTree extends Object implements Serializable- serialVersionUID:
- 1808077263026999072L
-
Serialized Fields
-
head
IntervalNode head
-
inSync
boolean inSync
-
intervals
Markers intervals
-
-
Class org.snpeff.interval.tree.IntervalTreeOri
class IntervalTreeOri extends Object implements Serializable- serialVersionUID:
- 1808077263026999072L
-
Serialized Fields
-
head
IntervalNodeOri head
-
inSync
boolean inSync
-
intervals
Markers intervals
-
-
-
Package org.snpeff.nmer
-
Class org.snpeff.nmer.NmerCount
class NmerCount extends Object implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
hash
gnu.trove.map.hash.TLongIntHashMap hash
-
nmerSize
int nmerSize
-
-
Class org.snpeff.nmer.NmerCountWc
class NmerCountWc extends NmerCount implements Serializable- serialVersionUID:
- 1L
-
-
Package org.snpeff.snpEffect
-
Class org.snpeff.snpEffect.Config
class Config extends Object implements Serializable- serialVersionUID:
- 877453207407217465L
-
Serialized Fields
-
bundleByGenomeId
HashMap<String,
String> bundleByGenomeId -
configDirPath
String configDirPath
-
configFileCanonicaPath
String configFileCanonicaPath
-
configFileName
String configFileName
-
databaseRepository
String databaseRepository
-
databaseRepositoryKey
String databaseRepositoryKey
-
dataDir
String dataDir
-
debug
boolean debug
-
errorChromoHit
boolean errorChromoHit
-
errorOnMissingChromo
boolean errorOnMissingChromo
-
expandIub
boolean expandIub
-
genome
Genome genome
-
genomeById
HashMap<String,
Genome> genomeById -
genomeVersion
String genomeVersion
-
hgvs
boolean hgvs
-
hgvsOld
boolean hgvsOld
-
hgvsOneLetterAa
boolean hgvsOneLetterAa
-
hgvsShift
boolean hgvsShift
-
hgvsTrId
boolean hgvsTrId
-
lofDeleteProteinCodingBases
double lofDeleteProteinCodingBases
-
lofIgnoreProteinCodingAfter
double lofIgnoreProteinCodingAfter
-
lofIgnoreProteinCodingBefore
double lofIgnoreProteinCodingBefore
-
nameById
HashMap<String,
String> nameById -
onlyRegulation
boolean onlyRegulation
-
properties
Properties properties
-
quiet
boolean quiet
-
referenceById
HashMap<String,
String> referenceById -
snpEffectPredictor
SnpEffectPredictor snpEffectPredictor
-
treatAllAsProteinCoding
boolean treatAllAsProteinCoding
-
verbose
boolean verbose
-
versionsUrl
String versionsUrl
-
-
Class org.snpeff.snpEffect.SnpEffectPredictor
class SnpEffectPredictor extends Object implements Serializable- serialVersionUID:
- 4519418862303325081L
-
Serialized Fields
-
debug
boolean debug
-
genome
Genome genome
-
intervalForest
IntervalForest intervalForest
-
markers
Markers markers
-
spliceRegionExonSize
int spliceRegionExonSize
-
spliceRegionIntronMax
int spliceRegionIntronMax
-
spliceRegionIntronMin
int spliceRegionIntronMin
-
spliceSiteSize
int spliceSiteSize
-
upDownStreamLength
int upDownStreamLength
-
useChromosomes
boolean useChromosomes
-
-
-
Package org.snpeff.stats
-
Class org.snpeff.stats.CountByKey
class CountByKey extends Object implements Serializable -
Class org.snpeff.stats.CountByType
class CountByType extends Object implements Serializable- serialVersionUID:
- 1L
-
Class org.snpeff.stats.CoverageByType
- serialVersionUID:
- 6365021779756255154L
-
Class org.snpeff.stats.GeneCountByTypeTable
class GeneCountByTypeTable extends Object implements Serializable- serialVersionUID:
- 1L
-
Class org.snpeff.stats.IntStats
class IntStats extends Object implements Serializable-
Serialized Fields
-
counters
gnu.trove.map.hash.TIntIntHashMap counters
-
maxBins
int maxBins
-
needUpdate
boolean needUpdate
-
statsProcedure
org.snpeff.stats.StatsProcedure statsProcedure
-
-
-
-
Package org.snpeff.vcf
-
Class org.snpeff.vcf.VariantVcfEntry
class VariantVcfEntry extends Variant implements Serializable- serialVersionUID:
- 2589022632388179932L
-
Serialized Fields
-
vcfEntry
VcfEntry vcfEntry
-
-
Class org.snpeff.vcf.VcfEntry
class VcfEntry extends Marker implements Serializable- serialVersionUID:
- 4226374412681243433L
-
Serialized Fields
-
alts
String[] alts
-
altStr
String altStr
-
chromosomeName
String chromosomeName
-
filter
String filter
-
format
String format
-
formatFields
String[] formatFields
-
genotypeFields
String[] genotypeFields
-
genotypeFieldsStr
String genotypeFieldsStr
-
genotypeScores
byte[] genotypeScores
-
info
HashMap<String,
String> info -
infoStr
String infoStr
-
line
String line
-
lineNum
int lineNum
-
quality
Double quality
-
ref
String ref
-
variants
LinkedList<Variant> variants
-
vcfEffects
List<VcfEffect> vcfEffects
-
vcfFileIterator
VcfFileIterator vcfFileIterator
-
vcfGenotypes
ArrayList<VcfGenotype> vcfGenotypes
-
-
Class org.snpeff.vcf.VcfHeader
class VcfHeader extends Object implements Serializable-
Serialized Fields
-
chromLine
boolean chromLine
-
header
StringBuffer header
-
numberOfSamples
int numberOfSamples
-
sampleName2Num
Map<String,
Integer> sampleName2Num -
sampleNames
ArrayList<String> sampleNames
-
vcfFormatById
Map<String,
VcfHeaderFormat> vcfFormatById -
vcfInfoById
Map<String,
VcfHeaderInfo> vcfInfoById
-
-
-
Class org.snpeff.vcf.VcfHeaderEntry
class VcfHeaderEntry extends Object implements Serializable- serialVersionUID:
- 2024092601L
-
Class org.snpeff.vcf.VcfHeaderFormat
class VcfHeaderFormat extends VcfHeaderInfo implements Serializable -
Class org.snpeff.vcf.VcfHeaderInfo
class VcfHeaderInfo extends VcfHeaderEntry implements Serializable- serialVersionUID:
- 2024092501L
-
Serialized Fields
-
description
String description
-
implicit
boolean implicit
-
number
int number
-
vcfInfoNumber
VcfHeaderInfo.VcfInfoNumber vcfInfoNumber
-
vcfInfoType
VcfInfoType vcfInfoType
-
-