Package org.snpeff.vcf
Class VariantVcfEntry
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Variant
org.snpeff.vcf.VariantVcfEntry
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
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:
-
Nested Class Summary
Nested classes/interfaces inherited from class org.snpeff.interval.Variant
Variant.VariantType
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Field Summary
FieldsFields 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
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic Collection<VariantVcfEntry>
Create a collection of all <Variant, VcfEntry>toString()
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
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