Package org.snpeff.interval
Class VariantNonRef
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Variant
org.snpeff.interval.VariantNonRef
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
A variant respect to non-reference (e.g. comparing cancer vs. somatic tissue).
- Author:
- pcingola
- See Also:
-
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.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
isNonRef()
Create a new variant realigning it towards the leftmost positionvoid
setVariantRef
(Variant variantRef) 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
-
Constructor Details
-
VariantNonRef
public VariantNonRef() -
VariantNonRef
-
-
Method Details
-
getGenotype
- Overrides:
getGenotype
in classVariant
-
getVariantRef
-
isNonRef
public boolean isNonRef() -
realignLeft
Description copied from class:Variant
Create a new variant realigning it towards the leftmost position- Overrides:
realignLeft
in classVariant
-
setVariantRef
-
toString
-