Uses of Class org.snpeff.interval.Marker (SnpEff 5.1 API)

Packages that use Marker

Package

Description

org.snpeff.binseq

org.snpeff.coverage

org.snpeff.fileIterator

org.snpeff.interval

org.snpeff.interval.codonChange

org.snpeff.interval.tree

org.snpeff.outputFormatter

org.snpeff.probablility

org.snpeff.serializer

org.snpeff.snpEffect

org.snpeff.snpEffect.factory

org.snpeff.snpEffect.testCases.unity

org.snpeff.stats

org.snpeff.svg

org.snpeff.vcf

Uses of Marker in org.snpeff.binseq

Methods in org.snpeff.binseq with parameters of type Marker

Modifier and Type

Method

Description

MarkerSeq

GenomicSequences.queryMarkerSequence(Marker marker)

Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form database

String

GenomicSequences.querySequence(Marker marker)

Get sequence for a marker
Uses of Marker in org.snpeff.coverage

Methods in org.snpeff.coverage that return types with arguments of type Marker

Modifier and Type

Method

Description

CountByKey<Marker>

CountReads.getCountBases()

CountByKey<Marker>

CountReads.getCountReads()

Methods in org.snpeff.coverage with parameters of type Marker

Modifier and Type

Method

Description

void

CountReads.addMarkerType(Marker marker, String type)

void

CountReadsOnMarkers.addMarkerType(Marker marker, String type)

void

MarkerTypes.addType(Marker marker, String type)

double

CountFragments.avgCoverage(Marker m)

Calculate Fragments Per Kilobase of exon per Million fragments mapped (FPKM)

double

Coverage.avgCoverage(Marker m)

Calculate average coverage per base

long

Coverage.coverage(Marker m)

Calculate total coverage per base

String

MarkerTypes.getSubType(Marker marker)

Some markers have sub-types

String

MarkerTypes.getType(Marker marker)

Get marker type

String

MarkerTypes.getTypeRank(Marker marker)

Get marker + rank (in case of exon or intron)

boolean

MarkerTypes.isType(Marker m, String mtype)
Uses of Marker in org.snpeff.fileIterator

Classes in org.snpeff.fileIterator with type parameters of type Marker

Modifier and Type

Class

Description

class

MarkerFileIterator<M extends Marker>

Opens a Marker file and iterates over all markers
Uses of Marker in org.snpeff.interval

Classes in org.snpeff.interval with type parameters of type Marker

Modifier and Type

Class

Description

class

IntervalAndSubIntervals<T extends Marker>

Interval that contains sub intervals.

Subclasses of Marker in org.snpeff.interval

Modifier and Type

Class

Description

class

Cds

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.

class

Chromosome

Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid

class

Custom

This is a custom interval (i.e.

class

Downstream

Interval for a gene, as well as some other information: exons, utrs, cds, etc.

class

Exon

Interval for an exon

class

Gene

Interval for a gene, as well as transcripts

class

GenericMarker

An interval intended as a mark

class

Genome

This is just used for the Interval class.

class

GffMarker

An interval intended as a mark

class

Gtf2Marker

An interval intended as a mark

class

Intergenic

Interval for in intergenic region

class

IntergenicConserved

Interval for a conserved intergenic region

class

IntervalAndSubIntervals<T extends Marker>

Interval that contains sub intervals.

class

Intron

Intron

class

IntronConserved

Interval for a conserved non-coding region in an intron

class

MarkerParentId

This is a marker used as a 'fake' parent during data serialization

class

MarkerSeq

Marker with a DNA sequence

class

MicroRnaBindingSite

miRna binding site (usually this was predicted by some algorithm)

class

Motif

Regulatory elements

class

NextProt

NextProt annotation marker

class

ProteinInteractionLocus

Protein interaction: An amino acid that is "in contact" with another amino acid.

class

ProteinProteinInteractionLocus

Protein interaction: An amino acid that is "in contact" with another amino acid within the same protein.

class

ProteinStructuralInteractionLocus

Protein interaction: An amino acid that is "in contact" with another amino acid.

class

RareAminoAcid

Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.

class

Regulation

Regulatory elements

class

SpliceSite

Interval for a splice site Reference: http://en.wikipedia.org/wiki/RNA_splicing Spliceosomal introns often reside in eukaryotic protein-coding genes.

class

SpliceSiteAcceptor

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

class

SpliceSiteBranch

A (putative) branch site.

class

SpliceSiteBranchU12

A (putative) U12 branch site.

class

SpliceSiteDonor

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

class

SpliceSiteRegion

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.

class

Transcript

Interval for a transcript, as well as some other information: exons, utrs, cds, etc.

class

Upstream

Interval for a gene, as well as some other information: exons, utrs, cds, etc.

class

Utr

Interval for a UTR (5 prime UTR and 3 prime UTR

class

Utr3prime

Interval for a UTR (5 prime UTR and 3 prime UTR

class

Utr5prime

Interval for a UTR (5 prime UTR and 3 prime UTR

class

Variant

A variant represents a change in a reference sequence

class

VariantBnd

A 'BND' variant (i.e.

class

VariantNonRef

A variant respect to non-reference (e.g.

class

VariantWithScore

A variant that has a numeric score.

Fields in org.snpeff.interval with type parameters of type Marker

Modifier and Type

Field

Description

protected ArrayList<Marker>

Markers.markers

Methods in org.snpeff.interval that return Marker

Modifier and Type

Method

Description

Marker

Marker.apply(Variant variant)

Apply a variant to a marker.

protected Marker

Marker.applyDel(Variant variant)

Apply a Variant to a marker.

protected Marker

Marker.applyDup(Variant variant)

Apply a Variant to a marker.

protected Marker

Marker.applyIns(Variant variant)

Apply a Variant to a marker.

protected Marker

Marker.applyMixed(Variant variant)

Apply a mixed variant Note: MIXED variant is interpreted as "MNP + InDel"

Marker

Transcript.cdsMarker()

Create a marker of the coding region in this transcript

Marker

Marker.clone()

Marker

Marker.cloneShallow()

Perform a shallow clone

Marker

Markers.get(int i)

Marker

VariantBnd.getEndPoint()

Marker

Marker.getParent()

Marker

Transcript.getTss()

Create a TSS marker

Marker

Marker.intersect(Marker marker)

Intersect of two markers

Marker[]

Markers.toArray()

Marker

Marker.union(Marker m)

Union of two markers

Marker

MarkerSeq.union(Marker m)

Union of two markers

Methods in org.snpeff.interval that return types with arguments of type Marker

Modifier and Type

Method

Description

static Map<Marker,Marker>

MarkerUtil.collapseZeroGap(Markers markersOri)

Collapse adjacent intervals (i.e.

static Map<Marker,Marker>

MarkerUtil.collapseZeroGap(Markers markersOri)

Collapse adjacent intervals (i.e.

List<Marker>

Genes.createUpDownStream(int upDownLength)

Creates a list of UP/DOWN stream regions (for each transcript) Upstream (downstream) stream is defined as upDownLength before (after) transcript Note: If upDownLength <=0 no interval is created

List<Marker>

Markers.getMarkers()

Iterator<Set<Marker>>

IntervalSetIterator.iterator()

Iterator<Marker>

Markers.iterator()

Set<Marker>

IntervalSetIterator.next()

static Map<Marker,Marker>

MarkerUtil.redundant(Collection<? extends Marker> markersOri)

Redundant markers in a list: Find intervals that are totally included in other intervals in the list

static Map<Marker,Marker>

MarkerUtil.redundant(Collection<? extends Marker> markersOri)

Redundant markers in a list: Find intervals that are totally included in other intervals in the list

Methods in org.snpeff.interval with parameters of type Marker

Modifier and Type

Method

Description

void

CytoBands.add(Marker m)

boolean

Markers.add(Marker marker)

Add an interval to the collection

void

Gene.addPerGene(Marker marker)

Add a gene dependent marker

protected void

Marker.adjust(Marker child)

Adjust [start,end] to include child

int

IntervalComparatorByEnd.compare(Marker i1, Marker i2)

int

IntervalComparatorByStart.compare(Marker i1, Marker i2)

int

Marker.distance(Marker interval)

How far apart are these intervals?

Exon

Transcript.findExon(Marker marker)

Return an exon intersecting 'marker' (first exon found)

List<Utr>

Transcript.findUtrs(Marker marker)

Return the UTR that intersects 'marker' (null if not found)

String

MarkerSeq.getSequence(Marker marker)

Get sequence intersecting 'marker' WARNING: Sequence is always according to coding strand.

boolean

Marker.includes(Marker marker)

Is 'interval' completely included in 'this'?

Marker

Marker.intersect(Marker marker)

Intersect of two markers

Markers

Markers.intersect(Marker marker)

Intersection between 'marker' and all sub-intervals

boolean

Interval.intersects(Marker interval)

Do the intervals intersect?

abstract boolean

SpliceSite.intersectsCoreSpliceSite(Marker marker)

Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins.

boolean

SpliceSiteAcceptor.intersectsCoreSpliceSite(Marker marker)

boolean

SpliceSiteBranch.intersectsCoreSpliceSite(Marker marker)

These are NOT core splice sites

boolean

SpliceSiteDonor.intersectsCoreSpliceSite(Marker marker)

boolean

SpliceSiteRegion.intersectsCoreSpliceSite(Marker marker)

int

Interval.intersectSize(Marker interval)

How much do intervals intersect?

protected boolean

Exon.isAdjustIfParentDoesNotInclude(Marker parent)

protected boolean

Marker.isAdjustIfParentDoesNotInclude(Marker parent)

Adjust parent if it does not include child?

protected boolean

Transcript.isAdjustIfParentDoesNotInclude(Marker parent)

boolean

Interval.isSameChromo(Marker interval)

boolean

Transcript.isUtr(Marker marker)

Markers

Marker.minus(Marker interval)

Return the difference between two markers

Markers

Markers.minus(Marker interval)

Calculate 'set minus' using one interval

String

Variant.netChange(Marker marker)

Only the part of the change that overlaps with a marker Return the change (always in positive strand)

Markers

CytoBands.query(Marker marker)

Markers

Exon.query(Marker marker)

Query all genomic regions that intersect 'marker'

Markers

IntervalAndSubIntervals.query(Marker marker)

Query all genomic regions that intersect 'marker'

Markers

Intron.query(Marker marker)

Query all genomic regions that intersect 'marker'

Markers

Marker.query(Marker marker)

Query all genomic regions that intersect 'marker' (this makes sense in Gene, Transcript, Exon, etc.)

Markers

Transcript.query(Marker marker)

Query all genomic regions that intersect 'marker'

Exon

Transcript.queryExon(Marker interval)

Return the first exon that intersects 'interval' (null if not found)

Marker

Marker.union(Marker m)

Union of two markers

Marker

MarkerSeq.union(Marker m)

Union of two markers

Method parameters in org.snpeff.interval with type arguments of type Marker

Modifier and Type

Method

Description

boolean

Markers.addAll(Collection<? extends Marker> mm)

Add all markers in this collection

int

Marker.distanceBases(List<? extends Marker> markers, boolean fromEnd)

Distance from the beginning/end of a list of intervals, until this SNP It count the number of bases in 'markers'

static Map<Marker,Marker>

MarkerUtil.redundant(Collection<? extends Marker> markersOri)

Redundant markers in a list: Find intervals that are totally included in other intervals in the list

Constructors in org.snpeff.interval with parameters of type Marker

Modifier

Constructor

Description

Custom(Marker parent, int start, int end, boolean strandMinus, String id, String label)

Gene(Marker parent, int start, int end, boolean strandMinus, String id, String geneName, BioType bioType)

GenericMarker(Marker parent, int start, int end, String id)

GffMarker(Marker parent, int start, int end, boolean strandMinus, String id)

Gtf2Marker(Marker parent, int start, int end, boolean strandMinus, String id)

IntervalAndSubIntervals(Marker parent, int start, int end, boolean strandMinus, String id)

Marker(Marker parent, int start, int end)

Marker(Marker parent, int start, int end, boolean strandMinus, String id)

MarkerSeq(Marker parent, int start, int end, boolean strandMinus, String id)

MarkerSeq(Marker parent, int start, int end, String seq)

MicroRnaBindingSite(Marker parent, int start, int end, boolean strandMinus, String id, double pValue)

Motif(Marker parent, int start, int end, boolean strandMinus, String id, String pwmName, String pwmId)

RareAminoAcid(Marker parent, int start, int end, String id)

Regulation(Marker parent, int start, int end, boolean strandMinus, String id, String name, String regulationType)

Variant(Marker parent, int start, int end, String id)

This constructor is used when we only have interval data (e.g.

Variant(Marker parent, int position, String referenceStr, String altStr)

Variant(Marker parent, int position, String referenceStr, String altStr, String id)

VariantBnd(Marker parent, int start, String ref, String alt, Chromosome chrTr, int startTr, boolean left, boolean before)

VariantWithScore(Marker parent, int start, int end, String id, double score)
Uses of Marker in org.snpeff.interval.codonChange

Methods in org.snpeff.interval.codonChange with parameters of type Marker

Modifier and Type

Method

Description

protected VariantEffect

CodonChange.effect(Marker marker, EffectType effectType, boolean allowReplace)

Calculate variant effect

protected VariantEffect

CodonChange.effectNoCodon(Marker marker, EffectType effectType)

protected VariantEffect

CodonChange.effectNoCodon(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact)
Uses of Marker in org.snpeff.interval.tree

Fields in org.snpeff.interval.tree declared as Marker

Modifier and Type

Field

Description

protected static final Marker[]

IntervalTreeArray.EMPTY_MARKER_ARRAY

protected Marker[][]

IntervalTreeArray.intersectMarkers

protected Marker[]

IntervalNode.intervalsCenter

Methods in org.snpeff.interval.tree that return types with arguments of type Marker

Modifier and Type

Method

Description

Iterator<Marker>

IntervalNodeOri.iterator()

Iterator<Marker>

IntervalTree.iterator()

Iterator<Marker>

IntervalTreeArray.iterator()

Iterator<Marker>

IntervalTreeOri.iterator()

Methods in org.snpeff.interval.tree with parameters of type Marker

Modifier and Type

Method

Description

void

IntervalForest.add(Marker interval)

Add an interval

void

IntervalTree.add(Marker interval)

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

void

IntervalTreeArray.add(Marker interval)

void

IntervalTreeOri.add(Marker interval)

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

void

Itree.add(Marker interval)

Add an interval object to the interval tree's list

Markers

IntervalForest.query(Marker marker)

Query all intervals that intersect with 'interval'

Markers

IntervalForest.stab(Marker marker)

Obtain all intervals that intersect with 'marker.start'

Method parameters in org.snpeff.interval.tree with type arguments of type Marker

Modifier and Type

Method

Description

void

IntervalForest.add(Collection<? extends Marker> intervals)

Add all intervals
Uses of Marker in org.snpeff.outputFormatter

Methods in org.snpeff.outputFormatter with parameters of type Marker

Modifier and Type

Method

Description

String

BedOutputFormatter.endSection(Marker marker)

Finish up section

String

OutputFormatter.endSection(Marker marker)

Finish up section

String

VcfOutputFormatter.endSection(Marker marker)

Finish up section

void

OutputFormatter.printSection(Marker marker)

End this section and print results

void

BedOutputFormatter.startSection(Marker marker)

void

OutputFormatter.startSection(Marker marker)

Starts a new section

void

VcfOutputFormatter.startSection(Marker marker)
Uses of Marker in org.snpeff.probablility

Methods in org.snpeff.probablility that return Marker

Modifier and Type

Method

Description

Marker

RandMarker.rand(int readLen)

Create a random marker of size readLen
Uses of Marker in org.snpeff.serializer

Methods in org.snpeff.serializer that return Marker

Modifier and Type

Method

Description

protected Marker

MarkerSerializer.getMarkerById(int id)

Marker

MarkerSerializer.getNextFieldMarker()

Methods in org.snpeff.serializer with parameters of type Marker

Modifier and Type

Method

Description

void

MarkerSerializer.doNotSave(Marker m)

int

MarkerSerializer.getIdByMarker(Marker m)

int

MarkerSerializer.save(Marker m)

Save a marker

Method parameters in org.snpeff.serializer with type arguments of type Marker

Modifier and Type

Method

Description

String

MarkerSerializer.save(Iterable<Marker> markersCollection)

Save all markers
Uses of Marker in org.snpeff.snpEffect

Fields in org.snpeff.snpEffect declared as Marker

Modifier and Type

Field

Description

protected Marker

Hgvs.marker

protected Marker

VariantEffect.marker

Methods in org.snpeff.snpEffect that return Marker

Modifier and Type

Method

Description

Marker

VariantEffect.getMarker()

Marker

VariantEffectFusion.getMarker()

Marker

VariantEffectStructural.getMarker()

Methods in org.snpeff.snpEffect with parameters of type Marker

Modifier and Type

Method

Description

void

SnpEffectPredictor.add(Marker marker)

Add a marker

void

VariantEffects.add(Variant variant, Marker marker, EffectType effectType, String message)

Add an effect

void

VariantEffects.add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message)

Add an effect

void

VariantEffects.addEffectType(Variant variant, Marker marker, EffectType effectType)

Add: If possible, only add an effect type (otherwise add the full effect)

protected boolean

VariantEffectStructural.isGene(Marker m)

protected boolean

VariantEffectStructural.isTranscript(Marker m)

Markers

SnpEffectPredictor.query(Marker marker)

Return a collection of intervals that intersect 'marker'

Gene

SnpEffectPredictor.queryClosestGene(Marker inputInterval)

Find closest gene to this marker

Markers

SnpEffectPredictor.queryDeep(Marker marker)

Return a collection of intervals that intersect 'marker' Query resulting genes, transcripts and exons to get ALL types of intervals possible

Set<String>

SnpEffectPredictor.regions(Marker marker, boolean showGeneDetails, boolean compareTemplate)

Name of the regions hit by a marker

Set<String>

SnpEffectPredictor.regions(Marker marker, boolean showGeneDetails, boolean compareTemplate, String id)

Name of the regions hit by a marker

void

VariantEffect.set(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message)

void

VariantEffect.setMarker(Marker marker)

Set marker.

void

VariantEffects.setMarker(Marker marker)

Method parameters in org.snpeff.snpEffect with type arguments of type Marker

Modifier and Type

Method

Description

protected int

VariantEffectStructural.countGenes(List<Marker> features)

Constructors in org.snpeff.snpEffect with parameters of type Marker

Modifier

Constructor

Description

VariantEffect(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String codonsOld, String codonsNew, int codonNum, int codonIndex, int cDnaPos)

VariantEffectFusion(Variant variant, Marker mLeft, Marker mRight)
Uses of Marker in org.snpeff.snpEffect.factory

Methods in org.snpeff.snpEffect.factory that return Marker

Modifier and Type

Method

Description

protected Marker

SnpEffPredictorFactory.findMarker(String id)

Methods in org.snpeff.snpEffect.factory with parameters of type Marker

Modifier and Type

Method

Description

protected void

SnpEffPredictorFactory.add(Marker marker)

Add a generic Marker

protected void

SnpEffPredictorFactory.addMarker(Marker marker, boolean unique)

Add a marker to the collection
Uses of Marker in org.snpeff.snpEffect.testCases.unity

Methods in org.snpeff.snpEffect.testCases.unity with parameters of type Marker

Modifier and Type

Method

Description

void

TestGenome.add(Marker marker)

Add markers to SnpEffPredictor

protected int

TestCasesIntervalTree.compareQuery(Marker m, Itree intTree)

Perform a query using 'naive' lookup and interval forest.

Markers

TestCasesIntervals.intersects(Markers interval1, Marker intervals)

protected Markers

TestCasesIntervalTree.queryNaive(Marker query)

Naively find all intervals intersecting 'marker'
Uses of Marker in org.snpeff.stats

Methods in org.snpeff.stats with parameters of type Marker

Modifier and Type

Method

Description

void

PosStats.sample(Marker marker, Marker markerReference)

Use 'num' as a sample
Uses of Marker in org.snpeff.svg

Methods in org.snpeff.svg with parameters of type Marker

Modifier and Type

Method

Description

static Svg

Svg.factory(Marker m, Svg svg)

Constructors in org.snpeff.svg with parameters of type Marker

Modifier

Constructor

Description

Svg(Marker m, Svg svg)

SvgScale(Marker m, Svg svg)

SvgSpacer(Marker m, Svg svg)
Uses of Marker in org.snpeff.vcf

Subclasses of Marker in org.snpeff.vcf

Modifier and Type

Class

Description

class

VariantVcfEntry

Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants.

class

VcfEntry

A VCF entry (a line) in a VCF file

Constructors in org.snpeff.vcf with parameters of type Marker

Modifier

Constructor

Description

VcfEntry(VcfFileIterator vcfFileIterator, Marker parent, String chromosomeName, int start, String id, String ref, String altsStr, double quality, String filterPass, String infoStr, String format)

Uses of Classorg.snpeff.interval.Marker

Uses of Marker in org.snpeff.binseq

Uses of Marker in org.snpeff.coverage

Uses of Marker in org.snpeff.fileIterator

Uses of Marker in org.snpeff.interval

Uses of Marker in org.snpeff.interval.codonChange

Uses of Marker in org.snpeff.interval.tree

Uses of Marker in org.snpeff.outputFormatter

Uses of Marker in org.snpeff.probablility

Uses of Marker in org.snpeff.serializer

Uses of Marker in org.snpeff.snpEffect

Uses of Marker in org.snpeff.snpEffect.factory

Uses of Marker in org.snpeff.snpEffect.testCases.unity

Uses of Marker in org.snpeff.stats

Uses of Marker in org.snpeff.svg

Uses of Marker in org.snpeff.vcf

Uses of Class
org.snpeff.interval.Marker