Uses of Class
org.snpeff.interval.Markers
Packages that use Markers
Package
Description
-
Uses of Markers in org.snpeff
Methods in org.snpeff that return MarkersModifier and TypeMethodDescriptionprotected Markers
SnpEff.loadMarkers
(String fileName) Read markers file Supported formats: BED, TXT, BigBed, GFF -
Uses of Markers in org.snpeff.fileIterator
Methods in org.snpeff.fileIterator that return Markers -
Uses of Markers in org.snpeff.interval
Methods in org.snpeff.interval that return MarkersModifier and TypeMethodDescriptionAdd all intervalsMarkers.intersect()
Perform the intersection of all overlapping sub-intervalsIntersection between 'marker' and all sub-intervalsGene.markers()
IntervalAndSubIntervals.markers()
A list of all markers in this transcriptTranscript.markers()
A list of all markers in this transcriptMarkers.merge()
Merge overlapping intervals This is the same as 'union()' method, but the algorithm is more efficientReturn the difference between two markersCalculate 'set minus' using one intervalReturns the result of this set minus 'intervals'Query all genomic regions that intersect 'marker'Query all genomic regions that intersect 'marker'Query all genomic regions that intersect 'marker'Query all genomic regions that intersect 'marker' (this makes sense in Gene, Transcript, Exon, etc.)Marker.query
(IntervalForest intervalForest) Return a collection of intervals that intersect this markerQuery all genomic regions that intersect 'marker'VariantBnd.query
(IntervalForest intervalForest) Return a collection of intervals that intersect both ends of this variantstatic Markers
Markers.readMarkers
(String fileName) Read markers from a file Supported formats: BED, BigBed, VCF, TXTstatic Markers
Read intervals from a file using a simplt TXT format Format: chr \t start \t end \t id Note: Zero-based positionsMarkers.sort()
Sort intervalsMarkers.sort
(boolean byEnd, boolean reverse) Sort intervalsMarkers.union()
Perform the union of all overlapping intervalsMarkers.unique()
Remove duplicated markersMethods in org.snpeff.interval with parameters of type MarkersModifier and TypeMethodDescriptionAdd all intervalsvoid
Add all markersMarkerUtil.collapseZeroGap
(Markers markersOri) Collapse adjacent intervals (i.e.boolean
Are all intervals equal?Returns the result of this set minus 'intervals'Constructors in org.snpeff.interval with parameters of type Markers -
Uses of Markers in org.snpeff.interval.tree
Fields in org.snpeff.interval.tree declared as MarkersModifier and TypeFieldDescriptionprotected Markers
IntervalTree.intervals
protected Markers
IntervalTreeOri.intervals
protected Markers
IntervalTreeArray.markers
Methods in org.snpeff.interval.tree that return MarkersModifier and TypeMethodDescriptionIntervalTree.getIntervals()
IntervalTreeArray.getIntervals()
IntervalTreeOri.getIntervals()
Itree.getIntervals()
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.Query all intervals that intersect with 'interval'Query all intervals that intersect with any interval in 'intervals'Perform an interval intersection query on the nodePerform an interval intersection query on the nodePerform an interval query, returning the intervals that intersect with 'interval'Query index to find all VCF entries intersecting 'marker' Store VCF entries in 'results'Perform an interval query, returning the intervals that intersect with 'interval'Perform an interval query, returning the intervals that intersect with 'interval'IntervalForest.queryUnique
(Markers markers) 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'Obtain all intervals that intersect with 'point'Obtain all intervals that intersect with 'marker.start'Perform a stabbing query on the nodePerform a stabbing query on the nodeIntervalTree.stab
(int point) Perform a stabbing query, returning the interval objectsIntervalTreeArray.stab
(int point) IntervalTreeOri.stab
(int point) Perform a stabbing query, returning the interval objectsItree.stab
(int point) Perform a stabbing query, returning the interval objectsMethods in org.snpeff.interval.tree with parameters of type MarkersModifier and TypeMethodDescriptionvoid
Add all intervalsvoid
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 buildvoid
void
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 buildvoid
Add all intervals to interval tree's listprotected void
Build interval treeprotected int
Index intervals from 'start' to 'end' (index in 'markers')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.protected IntervalNode
Create a new nodeQuery all intervals that intersect with any interval in 'intervals'protected void
Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF entries in 'results'protected void
IntervalTreeArray.queryIntersects
(Interval marker, int idx, Markers results) Query entries intersecting 'marker' at node 'idx'IntervalForest.queryUnique
(Markers markers) 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'protected void
protected void
IntervalTreeArray.stabIntersects
(int point, int idx, Markers results) Stab entries intersecting 'point' at node 'idx'Constructors in org.snpeff.interval.tree with parameters of type MarkersModifierConstructorDescriptionIntervalForest
(Markers markers) IntervalNode
(Markers markers) IntervalNodeOri
(Markers markers) IntervalTree
(Markers intervals) Instantiate an interval tree with a list of intervalsIntervalTreeArray
(Markers markers) Instantiate an interval tree with a list of intervalsIntervalTreeOri
(Markers intervals) Instantiate an interval tree with a list of intervals -
Uses of Markers in org.snpeff.nextProt
Methods in org.snpeff.nextProt that return MarkersModifier and TypeMethodDescriptionNextProtMarkerFactory.addMarkers
(NextProtXmlEntry entry, NextProtXmlIsoform isoform, NextProtXmlAnnotation annotation, Location location, String trId) Create markers and add themNextProtMarkerFactory.getMarkers()
NextProtMarkerFactory.nextProt
(Transcript tr, String accession, String name, int aaStart, int aaEnd) Create a single NextProt markerNextProtMarkerFactory.nextProt
(Transcript tr, NextProtXmlAnnotation annotation, Location location) Create a list of NextProt markers according to this annotation -
Uses of Markers in org.snpeff.serializer
Methods in org.snpeff.serializer that return MarkersMethods in org.snpeff.serializer with parameters of type Markers -
Uses of Markers in org.snpeff.snpEffect
Methods in org.snpeff.snpEffect that return MarkersModifier and TypeMethodDescriptionSnpEffectPredictor.createGenomicRegions()
Create (and add) up-down stream, splice sites, intergenic, etcSnpEffectPredictor.getMarkers()
Return a collection of intervals that intersect 'marker'Return a collection of intervals that intersect 'marker' Query resulting genes, transcripts and exons to get ALL types of intervals possibleMethods in org.snpeff.snpEffect with parameters of type MarkersModifier and TypeMethodDescriptionvoid
Add a set of markersprotected void
SnpEffectPredictor.variantEffect
(Variant variant, VariantEffects variantEffects, Markers intersects) Calculate variant effect for each marker in 'intersect'Constructors in org.snpeff.snpEffect with parameters of type Markers -
Uses of Markers in org.snpeff.snpEffect.testCases.unity
Fields in org.snpeff.snpEffect.testCases.unity declared as MarkersModifier and TypeFieldDescriptionprotected Markers
TestCasesIntervalTree.markers
TestGenome.markers
Methods in org.snpeff.snpEffect.testCases.unity that return MarkersModifier and TypeMethodDescriptionprotected Markers
TestCasesIntervalTree.createRandomLargeMarkers
(Chromosome chr, int num) protected Markers
TestCasesIntervalTree.createRandomMarkers()
protected Markers
TestCasesIntervalTree.createRandomSmallMarkers
(Chromosome chr, int num) TestCasesIntervals.intersects
(Markers interval1, Marker intervals) protected Markers
TestCasesIntervalTree.queryNaive
(Marker query) Naively find all intervals intersecting 'marker'TestCasesIntervals.randomIntervals
(int numIntervals, int maxStart, int maxLength, int numChromo) Create a random set of intervalsMethods in org.snpeff.snpEffect.testCases.unity with parameters of type Markers -
Uses of Markers in org.snpeff.stats
Constructors in org.snpeff.stats with parameters of type MarkersModifierConstructorDescriptionMineMarkerIntervals
(Markers markers) MineTwoMarkerIntervals
(Markers markersA, Markers markersB) -
Uses of Markers in org.snpeff.svg
Constructors in org.snpeff.svg with parameters of type Markers