Uses of Class
org.snpeff.interval.Marker

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
java.lang.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, java.lang.String type)
void	CountReadsOnMarkers.addMarkerType(Marker marker, java.lang.String type)
void	MarkerTypes.addType(Marker marker, java.lang.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
java.lang.String	MarkerTypes.getSubType(Marker marker)	Some markers have sub-types
java.lang.String	MarkerTypes.getType(Marker marker)	Get marker type
java.lang.String	MarkerTypes.getTypeRank(Marker marker)	Get marker + rank (in case of exon or intron)
boolean	MarkerTypes.isType(Marker m, java.lang.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 java.util.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 java.util.Map<Marker,Marker>	MarkerUtil.collapseZeroGap(Markers markersOri)	Collapse adjacent intervals (i.e.
static java.util.Map<Marker,Marker>	MarkerUtil.collapseZeroGap(Markers markersOri)	Collapse adjacent intervals (i.e.
java.util.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
java.util.List<Marker>	Markers.getMarkers()
java.util.Iterator<java.util.Set<Marker>>	IntervalSetIterator.iterator()
java.util.Iterator<Marker>	Markers.iterator()
java.util.Set<Marker>	IntervalSetIterator.next()
static java.util.Map<Marker,Marker>	MarkerUtil.redundant(java.util.Collection<? extends Marker> markersOri)	Redundant markers in a list: Find intervals that are totally included in other intervals in the list
static java.util.Map<Marker,Marker>	MarkerUtil.redundant(java.util.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)
java.util.List<Utr>	Transcript.findUtrs(Marker marker)	Return the UTR that intersects 'marker' (null if not found)
java.lang.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
java.lang.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(java.util.Collection<? extends Marker> mm)	Add all markers in this collection
int	Marker.distanceBases(java.util.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 java.util.Map<Marker,Marker>	MarkerUtil.redundant(java.util.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

Constructor	Description
Custom(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String label)
Gene(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String geneName, BioType bioType)
GenericMarker(Marker parent, int start, int end, java.lang.String id)
GffMarker(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
Gtf2Marker(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
IntervalAndSubIntervals(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
Marker(Marker parent, int start, int end)
Marker(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
MarkerSeq(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
MarkerSeq(Marker parent, int start, int end, java.lang.String seq)
MicroRnaBindingSite(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, double pValue)
Motif(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String pwmName, java.lang.String pwmId)
RareAminoAcid(Marker parent, int start, int end, java.lang.String id)
Regulation(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String name, java.lang.String regulationType)
Variant(Marker parent, int start, int end, java.lang.String id)	This constructor is used when we only have interval data (e.g.
Variant(Marker parent, int position, java.lang.String referenceStr, java.lang.String altStr)
Variant(Marker parent, int position, java.lang.String referenceStr, java.lang.String altStr, java.lang.String id)
VariantBnd(Marker parent, int start, java.lang.String ref, java.lang.String alt, Chromosome chrTr, int startTr, boolean left, boolean before)
VariantWithScore(Marker parent, int start, int end, java.lang.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 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
java.util.Iterator<Marker>	IntervalNodeOri.iterator()
java.util.Iterator<Marker>	IntervalTree.iterator()
java.util.Iterator<Marker>	IntervalTreeArray.iterator()
java.util.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(java.util.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
java.lang.String	BedOutputFormatter.endSection(Marker marker)	Finish up section
java.lang.String	OutputFormatter.endSection(Marker marker)	Finish up section
java.lang.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
java.lang.String	MarkerSerializer.save(java.lang.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, java.lang.String message)	Add an effect
void	VariantEffects.add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.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
java.util.Set<java.lang.String>	SnpEffectPredictor.regions(Marker marker, boolean showGeneDetails, boolean compareTemplate)	Name of the regions hit by a marker
java.util.Set<java.lang.String>	SnpEffectPredictor.regions(Marker marker, boolean showGeneDetails, boolean compareTemplate, java.lang.String id)	Name of the regions hit by a marker
void	VariantEffect.set(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.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(java.util.List<Marker> features)

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

Constructor	Description
VariantEffect(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.String codonsOld, java.lang.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(java.lang.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

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

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