Package org.snpeff.vcf
Class VariantVcfEntry
- 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.vcf.VariantVcfEntry
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class VariantVcfEntry extends Variant
Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants. IMPORTANT: The reason why we need this is because a VcfEntry may have multiple variants (e.g. multiallelic entry). These entries may need to be added multiple times to different nodes in an interval tree.- 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
Fields Modifier and Type Field Description protected VcfEntry
vcfEntry
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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 VariantVcfEntry(Variant variant, VcfEntry vcfEntry)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static java.util.Collection<VariantVcfEntry>
factory(VcfEntry vcfEntry)
Create a collection of allVcfEntry
getVcfEntry()
java.lang.String
toString()
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Methods inherited from class org.snpeff.interval.Variant
clone, cloneShallow, compareTo, decompose, factory, getAlt, getGenotype, getReference, getVariantType, hashCode, isBnd, isDel, isDup, isElongation, isImprecise, isInDel, isIns, isInterval, isInv, isMixed, isMnp, isNonRef, isShowWarningIfParentDoesNotInclude, isSnp, isStructural, isStructuralHuge, isTruncation, isVariant, lengthChange, netChange, netChange, realignLeft, 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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Field Detail
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vcfEntry
protected VcfEntry vcfEntry
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Method Detail
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factory
public static java.util.Collection<VariantVcfEntry> factory(VcfEntry vcfEntry)
Create a collection of all
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getVcfEntry
public VcfEntry getVcfEntry()
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