Serialized Form
-
Package org.snpeff.binseq
-
Class org.snpeff.binseq.BinarySequence extends java.lang.Object implements Serializable
- serialVersionUID:
- 2349094116844619569L
-
Class org.snpeff.binseq.DnaAndQualitySequence extends BinarySequence implements Serializable
- serialVersionUID:
- 4523047567848438494L
-
Serialized Fields
-
codes
byte[] codes
-
-
Class org.snpeff.binseq.DnaAndQualitySequenceWithId extends DnaAndQualitySequence implements Serializable
- serialVersionUID:
- 4523294567844568494L
-
Serialized Fields
-
id
long id
-
-
Class org.snpeff.binseq.DnaNSequence extends DnaSequence implements Serializable
- serialVersionUID:
- 843945646419836582L
-
Serialized Fields
-
hasN
OpenBitSet hasN
-
-
Class org.snpeff.binseq.DnaSequence extends BinarySequence implements Serializable
- serialVersionUID:
- 4523047339848048494L
-
Serialized Fields
-
coder
DnaCoder coder
-
codes
long[] codes
-
length
int length
-
-
Class org.snpeff.binseq.DnaSequenceId extends DnaSequence implements Serializable
- serialVersionUID:
- 452657339854548494L
-
Serialized Fields
-
id
long id
-
-
Class org.snpeff.binseq.DnaSequencePe extends BinarySequence implements Serializable
- serialVersionUID:
- -7267466011654235050L
-
Serialized Fields
-
gap
int gap
-
seq1
DnaSequence seq1
-
seq2
DnaSequence seq2
-
-
Class org.snpeff.binseq.GenomicSequences extends java.lang.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 extends java.lang.Object implements Serializable
-
Class org.snpeff.binseq.coder.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 extends DnaCoder implements Serializable
-
-
Package org.snpeff.collections
-
Class org.snpeff.collections.AutoHashMap extends java.util.HashMap<K,V> implements Serializable
- serialVersionUID:
- 255818677257868365L
-
Serialized Fields
-
instance
V instance
-
-
Class org.snpeff.collections.MultivalueHashMap extends java.util.HashMap<K,java.util.LinkedList<V>> implements Serializable
- serialVersionUID:
- -8860279543165990227L
-
Class org.snpeff.collections.OpenBitSet extends java.lang.Object implements Serializable
-
Serialized Fields
-
bits
long[] bits
-
wlen
int wlen
-
-
-
-
Package org.snpeff.coverage
-
Class org.snpeff.coverage.CountFragments extends java.lang.Object implements Serializable
- serialVersionUID:
- 1150158182247576450L
-
Serialized Fields
-
coverageByName
java.util.HashMap<java.lang.String,CoverageChr> coverageByName
-
-
Class org.snpeff.coverage.Coverage extends java.lang.Object implements Serializable
- serialVersionUID:
- 1150158182247576450L
-
Serialized Fields
-
coverageByName
java.util.HashMap<java.lang.String,CoverageChr> coverageByName
-
-
Class org.snpeff.coverage.CoverageChr extends java.lang.Object implements Serializable
- serialVersionUID:
- -5620938926858131251L
-
Serialized Fields
-
count
short[] count
-
-
-
Package org.snpeff.fileIterator
-
Class org.snpeff.fileIterator.TableFile extends java.lang.Object implements Serializable
- serialVersionUID:
- 9180460090637138107L
-
Serialized Fields
-
fieldByName
java.util.HashMap<java.lang.String,java.lang.reflect.Field> fieldByName
-
fieldNames
java.lang.String[] fieldNames
-
fieldStr
java.lang.String fieldStr
-
fileName
java.lang.String fileName
-
hasTitle
boolean hasTitle
-
separator
java.lang.String separator
-
size
int size
-
verbose
boolean verbose
-
-
-
Package org.snpeff.geneOntology
-
Class org.snpeff.geneOntology.GoTerm extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
acc
java.lang.String acc
-
childs
java.util.HashSet<GoTerm> childs
-
description
java.lang.String description
-
goTerms
GoTerms goTerms
-
interestingSymbolIdSet
java.util.HashSet<java.lang.String> interestingSymbolIdSet
-
level
int level
-
maxRank
int maxRank
-
nameSpace
java.lang.String nameSpace
-
parents
java.util.HashSet<GoTerm> parents
-
rankedSymbols
int rankedSymbols
-
rankSum
long rankSum
-
symbolIdSet
java.util.HashSet<java.lang.String> symbolIdSet
-
-
Class org.snpeff.geneOntology.GoTerms extends java.lang.Object implements Serializable
-
Serialized Fields
-
goTermsByGoTermAcc
java.util.HashMap<java.lang.String,GoTerm> goTermsByGoTermAcc
-
goTermsBySymbolId
java.util.HashMap<java.lang.String,java.util.Set<GoTerm>> goTermsBySymbolId
-
interestingSymbolIdsSet
java.util.HashSet<java.lang.String> interestingSymbolIdsSet
-
label
java.lang.String label
-
maxRank
int maxRank
-
nameSpace
java.lang.String nameSpace
-
rankSymbolId
java.util.HashMap<java.lang.String,java.lang.Integer> rankSymbolId
-
-
-
-
Package org.snpeff.geneSets
-
Class org.snpeff.geneSets.GeneSet extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
description
java.lang.String description
-
genes
java.util.HashSet<java.lang.String> genes
-
geneSets
GeneSets geneSets
-
interestingGenesCount
int interestingGenesCount
-
maxRank
int maxRank
-
name
java.lang.String name
-
rankedGenesCount
int rankedGenesCount
-
rankSum
long rankSum
-
-
Class org.snpeff.geneSets.GeneSets extends java.lang.Object implements Serializable
- serialVersionUID:
- -359594418467719013L
-
Serialized Fields
-
doNotAddIfNotInGeneSet
boolean doNotAddIfNotInGeneSet
-
genes
java.util.HashSet<java.lang.String> genes
-
geneSetsByGene
java.util.HashMap<java.lang.String,java.util.HashSet<GeneSet>> geneSetsByGene
-
geneSetsByName
java.util.HashMap<java.lang.String,GeneSet> geneSetsByName
-
interestingGenes
java.util.HashSet<java.lang.String> interestingGenes
-
label
java.lang.String label
-
valueByGene
java.util.HashMap<java.lang.String,java.lang.Double> valueByGene
-
verbose
boolean verbose
-
-
Class org.snpeff.geneSets.GeneSetsRanked extends GeneSets implements Serializable
- serialVersionUID:
- -7922357470081599803L
-
Serialized Fields
-
maxRank
int maxRank
-
rankByGene
java.util.HashMap<java.lang.String,java.lang.Integer> rankByGene
-
-
-
Package org.snpeff.genotypes
-
Class org.snpeff.genotypes.Genotypes extends java.lang.Object implements Serializable
- serialVersionUID:
- 5417498450863908076L
-
Serialized Fields
-
genotypeVectors
GenotypeVector[] genotypeVectors
-
vcfFileName
java.lang.String vcfFileName
-
-
Class org.snpeff.genotypes.GenotypeVector extends java.lang.Object implements Serializable
- serialVersionUID:
- 4734574592894281057L
-
Serialized Fields
-
genotype
byte[] genotype
-
size
int size
-
-
-
Package org.snpeff.interval
-
Class org.snpeff.interval.Cds extends Marker implements Serializable
- serialVersionUID:
- 1636197649250882952L
-
Serialized Fields
-
frame
byte frame
-
-
Class org.snpeff.interval.Chromosome extends Marker implements Serializable
- serialVersionUID:
- 1636197649250882952L
-
Serialized Fields
-
chromosomeNum
double chromosomeNum
-
circular
boolean circular
-
sequence
DnaSequence sequence
-
-
Class org.snpeff.interval.Custom extends Marker implements Serializable
- serialVersionUID:
- -6843535415295857726L
-
Serialized Fields
-
label
java.lang.String label
-
score
double score
-
-
Class org.snpeff.interval.Downstream extends Marker implements Serializable
- serialVersionUID:
- 1636197649250882952L
-
Class org.snpeff.interval.Exon extends MarkerSeq implements Serializable
- serialVersionUID:
- 5324352193278472543L
-
Serialized Fields
-
aaIdxEnd
int aaIdxEnd
-
aaIdxStart
int aaIdxStart
-
frame
byte frame
-
rank
int rank
-
spliceSites
java.util.ArrayList<SpliceSite> spliceSites
-
spliceType
Exon.ExonSpliceType spliceType
-
-
Class org.snpeff.interval.Gene extends IntervalAndSubIntervals<Transcript> implements Serializable
- serialVersionUID:
- 8419206759034068147L
-
Class org.snpeff.interval.GenericMarker extends Marker implements Serializable
- serialVersionUID:
- -1645062778820144533L
-
Serialized Fields
-
line
java.lang.String line
-
-
Class org.snpeff.interval.Genes extends java.lang.Object implements Serializable
- serialVersionUID:
- 9022385501946879197L
-
Class org.snpeff.interval.Genome extends Marker implements Serializable
- serialVersionUID:
- -330362012383572257L
-
Serialized Fields
-
chromoFastaFiles
java.lang.String[] chromoFastaFiles
-
chromosomeNamesSorted
java.util.List<java.lang.String> chromosomeNamesSorted
-
chromosomes
java.util.HashMap<java.lang.String,Chromosome> chromosomes
-
codingInfo
java.lang.Boolean codingInfo
-
cytoBands
CytoBands cytoBands
-
fastaDir
java.lang.String fastaDir
-
genes
Genes genes
-
genomeId
int genomeId
-
genomicSequences
GenomicSequences genomicSequences
-
length
long length
-
species
java.lang.String species
-
transcriptSupportLevelInfo
java.lang.Boolean transcriptSupportLevelInfo
-
version
java.lang.String version
-
-
Class org.snpeff.interval.GffMarker extends Custom implements Serializable
- serialVersionUID:
- -164502778854644537L
-
Serialized Fields
-
frame
int frame
-
gffType
GffType gffType
-
gffTypeStr
java.lang.String gffTypeStr
-
keys
java.util.Set<java.lang.String> keys
-
keyValues
java.util.Map<java.lang.String,java.lang.String> keyValues
-
source
java.lang.String source
-
-
Class org.snpeff.interval.Gtf2Marker extends GffMarker implements Serializable
- serialVersionUID:
- 5416962964309837838L
-
Class org.snpeff.interval.Intergenic extends Marker implements Serializable
- serialVersionUID:
- -2487664381262354896L
-
Serialized Fields
-
name
java.lang.String name
-
-
Class org.snpeff.interval.IntergenicConserved extends Marker implements Serializable
- serialVersionUID:
- -1816568396090993792L
-
Class org.snpeff.interval.Interval extends java.lang.Object implements Serializable
- serialVersionUID:
- -3547434510230920403L
-
Serialized Fields
-
chromosomeNameOri
java.lang.String chromosomeNameOri
-
end
int end
-
id
java.lang.String id
-
parent
Interval parent
-
start
int start
-
strandMinus
boolean strandMinus
-
-
Class org.snpeff.interval.IntervalAndSubIntervals extends Marker implements Serializable
- serialVersionUID:
- 1636197649250882952L
-
Class org.snpeff.interval.Intron extends Marker implements Serializable
- serialVersionUID:
- -8283322526157264389L
-
Serialized Fields
-
exonAfter
Exon exonAfter
-
exonBefore
Exon exonBefore
-
rank
int rank
-
spliceSites
java.util.ArrayList<SpliceSite> spliceSites
-
-
Class org.snpeff.interval.IntronConserved extends Marker implements Serializable
- serialVersionUID:
- -3148108162409498012L
-
Class org.snpeff.interval.Marker extends Interval implements Serializable
- serialVersionUID:
- 7878886900660027549L
-
Serialized Fields
-
type
EffectType type
-
-
Class org.snpeff.interval.MarkerParentId extends Marker implements Serializable
-
Serialized Fields
-
parentId
int parentId
-
-
-
Class org.snpeff.interval.Markers extends java.lang.Object implements Serializable
- serialVersionUID:
- 259791388087691277L
-
Serialized Fields
-
markers
java.util.ArrayList<Marker> markers
-
name
java.lang.String name
-
-
Class org.snpeff.interval.MarkerSeq extends Marker implements Serializable
- serialVersionUID:
- -8794533547221460207L
-
Serialized Fields
-
sequence
DnaSequence sequence
-
-
Class org.snpeff.interval.MicroRnaBindingSite extends Marker implements Serializable
- serialVersionUID:
- -9089500641817245554L
-
Serialized Fields
-
pValue
double pValue
-
-
Class org.snpeff.interval.Motif extends Marker implements Serializable
- serialVersionUID:
- 8464487883781181867L
-
Serialized Fields
-
pwm
Pwm pwm
-
pwmId
java.lang.String pwmId
-
pwmName
java.lang.String pwmName
-
-
Class org.snpeff.interval.NextProt extends Marker implements Serializable
- serialVersionUID:
- 8939301304881007289L
-
Serialized Fields
-
highlyConservedAaSequence
boolean highlyConservedAaSequence
-
name
java.lang.String name
-
transcriptId
java.lang.String transcriptId
-
-
Class org.snpeff.interval.ProteinInteractionLocus extends Marker implements Serializable
- serialVersionUID:
- 1L
-
Class org.snpeff.interval.ProteinProteinInteractionLocus extends ProteinInteractionLocus implements Serializable
- serialVersionUID:
- -2111056845758378137L
-
Serialized Fields
-
trInteract
Transcript trInteract
-
-
Class org.snpeff.interval.ProteinStructuralInteractionLocus extends ProteinInteractionLocus implements Serializable
- serialVersionUID:
- 1416019843839053485L
-
Class org.snpeff.interval.RareAminoAcid extends Marker implements Serializable
- serialVersionUID:
- -1926572865764543849L
-
Class org.snpeff.interval.Regulation extends Marker implements Serializable
- serialVersionUID:
- -5607588295343642199L
-
Serialized Fields
-
name
java.lang.String name
-
regulationType
java.lang.String regulationType
-
-
Class org.snpeff.interval.SpliceSite extends Marker implements Serializable
- serialVersionUID:
- 1636197649250882952L
-
Class org.snpeff.interval.SpliceSiteAcceptor extends SpliceSite implements Serializable
- serialVersionUID:
- -7416687954435361328L
-
Class org.snpeff.interval.SpliceSiteBranch extends SpliceSite implements Serializable
- serialVersionUID:
- 7903892379174750342L
-
Class org.snpeff.interval.SpliceSiteBranchU12 extends SpliceSiteBranch implements Serializable
- serialVersionUID:
- 7903892379174750342L
-
Class org.snpeff.interval.SpliceSiteDonor extends SpliceSite implements Serializable
- serialVersionUID:
- -2117470153797320999L
-
Class org.snpeff.interval.SpliceSiteRegion extends SpliceSite implements Serializable
- serialVersionUID:
- -7416687954435361328L
-
Class org.snpeff.interval.Transcript extends IntervalAndSubIntervals<Exon> implements Serializable
- serialVersionUID:
- -2665025617916107311L
-
Serialized Fields
-
aa2pos
int[] aa2pos
-
aaCheck
boolean aaCheck
-
bioType
BioType bioType
-
canonical
boolean canonical
-
cds
java.lang.String cds
-
cds2pos
int[] cds2pos
-
cdsEnd
int cdsEnd
-
cdss
java.util.List<Cds> cdss
-
cdsStart
int cdsStart
-
corrected
boolean corrected
-
dnaCheck
boolean dnaCheck
-
downstream
Downstream downstream
-
firstCodingExon
Exon firstCodingExon
-
introns
java.util.List<Intron> introns
-
mRna
java.lang.String mRna
-
protein
java.lang.String protein
-
proteinCoding
boolean proteinCoding
-
ribosomalSlippage
boolean ribosomalSlippage
-
spliceRegionExonSize
int spliceRegionExonSize
-
spliceRegionIntronMax
int spliceRegionIntronMax
-
spliceRegionIntronMin
int spliceRegionIntronMin
-
spliceSiteSize
int spliceSiteSize
-
transcriptSupportLevel
TranscriptSupportLevel transcriptSupportLevel
-
upDownLength
int upDownLength
-
upstream
Upstream upstream
-
utrs
java.util.List<Utr> utrs
-
version
java.lang.String version
-
-
Class org.snpeff.interval.Upstream extends Marker implements Serializable
- serialVersionUID:
- 1636197649250882952L
-
Class org.snpeff.interval.Utr extends Marker implements Serializable
- serialVersionUID:
- 1636197649250882952L
-
Class org.snpeff.interval.Utr3prime extends Utr implements Serializable
- serialVersionUID:
- 5688641008301281991L
-
Class org.snpeff.interval.Utr5prime extends Utr implements Serializable
- serialVersionUID:
- 3710420226746056364L
-
Serialized Fields
-
utrs
java.util.List<Utr5prime> utrs
-
-
Class org.snpeff.interval.Variant extends Marker implements Serializable
- serialVersionUID:
- -2928105165111400441L
-
Serialized Fields
-
alt
java.lang.String alt
-
genotype
java.lang.String genotype
-
imprecise
boolean imprecise
-
ref
java.lang.String ref
-
variantType
Variant.VariantType variantType
-
-
Class org.snpeff.interval.VariantBnd extends Variant implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
before
boolean before
-
endPoint
Marker endPoint
-
left
boolean left
-
-
Class org.snpeff.interval.VariantNonRef extends Variant implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
variantRef
Variant variantRef
-
-
Class org.snpeff.interval.VariantWithScore extends Variant implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
score
double score
-
-
-
Package org.snpeff.interval.tree
-
Class org.snpeff.interval.tree.IntervalForest extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
debug
boolean debug
-
forest
java.util.HashMap<java.lang.String,Itree> forest
-
name
java.lang.String name
-
-
Class org.snpeff.interval.tree.IntervalNode extends java.lang.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 extends java.lang.Object implements Serializable
- serialVersionUID:
- -444656480302906048L
-
Serialized Fields
-
center
java.lang.Integer center
-
intervals
java.util.SortedMap<Marker,java.util.List<Marker>> intervals
-
leftNode
IntervalNodeOri leftNode
-
rightNode
IntervalNodeOri rightNode
-
-
Class org.snpeff.interval.tree.IntervalTree extends java.lang.Object implements Serializable
- serialVersionUID:
- 1808077263026999072L
-
Serialized Fields
-
head
IntervalNode head
-
inSync
boolean inSync
-
intervals
Markers intervals
-
-
Class org.snpeff.interval.tree.IntervalTreeOri extends java.lang.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 extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
hash
gnu.trove.map.hash.TLongIntHashMap hash
-
nmerSize
int nmerSize
-
-
Class org.snpeff.nmer.NmerCountWc extends NmerCount implements Serializable
- serialVersionUID:
- 1L
-
-
Package org.snpeff.snpEffect
-
Class org.snpeff.snpEffect.Config extends java.lang.Object implements Serializable
- serialVersionUID:
- 877453207407217465L
-
Serialized Fields
-
bundleByGenomeId
java.util.HashMap<java.lang.String,java.lang.String> bundleByGenomeId
-
configDirPath
java.lang.String configDirPath
-
configFileName
java.lang.String configFileName
-
databaseRepository
java.lang.String databaseRepository
-
databaseRepositoryKey
java.lang.String databaseRepositoryKey
-
dataDir
java.lang.String dataDir
-
debug
boolean debug
-
errorChromoHit
boolean errorChromoHit
-
errorOnMissingChromo
boolean errorOnMissingChromo
-
expandIub
boolean expandIub
-
genome
Genome genome
-
genomeById
java.util.HashMap<java.lang.String,Genome> genomeById
-
genomeVersion
java.lang.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
java.util.HashMap<java.lang.String,java.lang.String> nameById
-
onlyRegulation
boolean onlyRegulation
-
properties
java.util.Properties properties
-
quiet
boolean quiet
-
referenceById
java.util.HashMap<java.lang.String,java.lang.String> referenceById
-
snpEffectPredictor
SnpEffectPredictor snpEffectPredictor
-
treatAllAsProteinCoding
boolean treatAllAsProteinCoding
-
verbose
boolean verbose
-
versionsUrl
java.lang.String versionsUrl
-
-
Class org.snpeff.snpEffect.SnpEffectPredictor extends java.lang.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 extends java.lang.Object implements Serializable
-
Serialized Fields
-
countByKey
java.util.HashMap<T,java.lang.Long> countByKey
-
-
-
Class org.snpeff.stats.CountByType extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
countByType
java.util.HashMap<java.lang.String,java.lang.Long> countByType
-
scoreByType
java.util.HashMap<java.lang.String,java.lang.Double> scoreByType
-
-
Class org.snpeff.stats.CoverageByType extends AutoHashMap<java.lang.String,PosStats> implements Serializable
- serialVersionUID:
- 6365021779756255154L
-
Class org.snpeff.stats.GeneCountByTypeTable extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
bioType
java.util.HashMap<java.lang.String,java.lang.String> bioType
-
countersByType
java.util.HashMap<java.lang.String,CountByType> countersByType
-
counterSizeByType
java.util.HashMap<java.lang.String,CountByType> counterSizeByType
-
keys
java.util.HashSet<java.lang.String> keys
-
sizeByType
java.util.HashMap<java.lang.String,java.lang.Integer> sizeByType
-
types
java.util.HashSet<java.lang.String> types
-
-
Class org.snpeff.stats.IntStats extends java.lang.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 extends Variant implements Serializable
- serialVersionUID:
- 2589022632388179932L
-
Serialized Fields
-
vcfEntry
VcfEntry vcfEntry
-
-
Class org.snpeff.vcf.VcfEntry extends Marker implements Serializable
- serialVersionUID:
- 4226374412681243433L
-
Serialized Fields
-
alts
java.lang.String[] alts
-
altStr
java.lang.String altStr
-
chromosomeName
java.lang.String chromosomeName
-
filter
java.lang.String filter
-
format
java.lang.String format
-
formatFields
java.lang.String[] formatFields
-
genotypeFields
java.lang.String[] genotypeFields
-
genotypeFieldsStr
java.lang.String genotypeFieldsStr
-
genotypeScores
byte[] genotypeScores
-
info
java.util.HashMap<java.lang.String,java.lang.String> info
-
infoStr
java.lang.String infoStr
-
line
java.lang.String line
-
lineNum
int lineNum
-
quality
java.lang.Double quality
-
ref
java.lang.String ref
-
variants
java.util.LinkedList<Variant> variants
-
vcfEffects
java.util.List<VcfEffect> vcfEffects
-
vcfFileIterator
VcfFileIterator vcfFileIterator
-
vcfGenotypes
java.util.ArrayList<VcfGenotype> vcfGenotypes
-
-