Package org.snpeff.interval
Class VariantNonRef
- java.lang.Object
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- org.snpeff.interval.Interval
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- org.snpeff.interval.Marker
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- org.snpeff.interval.Variant
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- org.snpeff.interval.VariantNonRef
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class VariantNonRef extends Variant
A variant respect to non-reference (e.g. comparing cancer vs. somatic tissue).- Author:
- pcingola
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from class org.snpeff.interval.Variant
Variant.VariantType
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Field Summary
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Fields inherited from class org.snpeff.interval.Variant
alt, genotype, HUGE_DELETION_RATIO_THRESHOLD, HUGE_DELETION_SIZE_THRESHOLD, imprecise, NO_VARIANT, ref, variantType
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Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
Constructors Constructor Description VariantNonRef()
VariantNonRef(Variant variant, Variant variantRef)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getGenotype()
Variant
getVariantRef()
boolean
isNonRef()
Variant
realignLeft()
Create a new variant realigning it towards the leftmost positionvoid
setVariantRef(Variant variantRef)
java.lang.String
toString()
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Methods inherited from class org.snpeff.interval.Variant
clone, cloneShallow, compareTo, decompose, factory, getAlt, getReference, getVariantType, hashCode, isBnd, isDel, isDup, isElongation, isImprecise, isInDel, isIns, isInterval, isInv, isMixed, isMnp, isShowWarningIfParentDoesNotInclude, isSnp, isStructural, isStructuralHuge, isTruncation, isVariant, lengthChange, netChange, netChange, reverse, setGenotype, setImprecise, setVariantType, toStringEnsembl, toStringOld
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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, query, readTxt, serializeParse, serializeSave, shouldApply, union, variantEffect, variantEffectNonRef
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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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Method Detail
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getGenotype
public java.lang.String getGenotype()
- Overrides:
getGenotype
in classVariant
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getVariantRef
public Variant getVariantRef()
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realignLeft
public 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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setVariantRef
public void setVariantRef(Variant variantRef)
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