Package org.snpeff.interval
Class VariantBnd
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Variant
org.snpeff.interval.VariantBnd
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
A 'BND' variant (i.e. translocation) consisting of two endpoints
- Author:
- pcingola
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from class org.snpeff.interval.Variant
Variant.VariantType
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Field Summary
Fields inherited from class org.snpeff.interval.Variant
alt, genotype, HUGE_DELETION_RATIO_THRESHOLD, HUGE_DELETION_SIZE_THRESHOLD, imprecise, NO_VARIANT, ref, variantType
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
ConstructorsConstructorDescriptionVariantBnd
(Marker parent, int start, String ref, String alt, Chromosome chrTr, int startTr, boolean left, boolean before) -
Method Summary
Methods inherited from class org.snpeff.interval.Variant
clone, cloneShallow, compareTo, decompose, factory, getAlt, getGenotype, getReference, getVariantType, hashCode, isDel, isDup, isElongation, isImprecise, isInDel, isIns, isInterval, isInv, isMixed, isMnp, isNonRef, isShowWarningIfParentDoesNotInclude, isSnp, isStructuralHuge, isTruncation, isVariant, lengthChange, netChange, netChange, reverse, setGenotype, setImprecise, setVariantType, toStringEnsembl, toStringOld
Methods inherited from class org.snpeff.interval.Marker
adjust, apply, applyDel, applyDup, applyIns, applyMixed, codonTable, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, minus, query, readTxt, serializeParse, serializeSave, shouldApply, union, variantEffect, variantEffectNonRef
Methods inherited from class org.snpeff.interval.Interval
equals, findParent, getChromosome, getChromosomeName, getChromosomeNameOri, getChromosomeNum, getEnd, getGenome, getGenomeName, getId, getStart, getStrand, intersects, intersects, intersects, intersects, intersectSize, isCircular, isSameChromo, isStrandMinus, isStrandPlus, isValid, setChromosomeNameOri, setEnd, setId, setParent, setStart, setStrandMinus, shiftCoordinates, size, toStr, toStringAsciiArt, toStrPos
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Constructor Details
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VariantBnd
public VariantBnd() -
VariantBnd
public VariantBnd(Marker parent, int start, String ref, String alt, Chromosome chrTr, int startTr, boolean left, boolean before)
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Method Details
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getEndPoint
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isBefore
public boolean isBefore() -
isBnd
public boolean isBnd() -
isLeft
public boolean isLeft() -
isStructural
public boolean isStructural()- Overrides:
isStructural
in classVariant
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query
Return a collection of intervals that intersect both ends of this variant -
realignLeft
Description copied from class:Variant
Create a new variant realigning it towards the leftmost position- Overrides:
realignLeft
in classVariant
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toString
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