VariantNonRef (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.interval.Interval
- - org.snpeff.interval.Marker
  - - org.snpeff.interval.Variant
    - - org.snpeff.interval.VariantNonRef

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

Nested Class Summary
- Nested classes/interfaces inherited from class org.snpeff.interval.Variant
  Variant.VariantType

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.Marker
  type
- Fields inherited from class org.snpeff.interval.Interval
  chromosomeNameOri, end, id, parent, start, strandMinus

Constructor Summary

Constructors
Constructor Description

VariantNonRef()

VariantNonRef(Variant variant, Variant variantRef)

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 position
`void`	`setVariantRef(Variant variantRef)`
`java.lang.String`	`toString()`

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

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

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

Methods inherited from class java.lang.Object
equals, finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - VariantNonRef
```
public VariantNonRef()
```
  - VariantNonRef
```
public VariantNonRef(Variant variant,
                     Variant variantRef)
```
- Method Detail
  - getGenotype
```
public java.lang.String getGenotype()
```
    Overrides:
    
    getGenotype in class Variant
  - getVariantRef
```
public Variant getVariantRef()
```
  - isNonRef
```
public boolean isNonRef()
```
    Overrides:
    
    isNonRef in class Variant
  - realignLeft
```
public Variant realignLeft()
```
    Description copied from class: Variant
    
    Create a new variant realigning it towards the leftmost position
    
    Overrides:
    
    realignLeft in class Variant
  - setVariantRef
```
public void setVariantRef(Variant variantRef)
```
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class Variant