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 Variant
Variant.VariantType -
Field Summary
FieldsFields inherited from class Variant
alt, genotype, HUGE_DELETION_RATIO_THRESHOLD, HUGE_DELETION_SIZE_THRESHOLD, imprecise, NO_VARIANT, ref, variantTypeFields inherited from class Interval
chromosomeNameOri, end, id, parent, start, strandMinus -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic Collection<VariantVcfEntry> Create a collection of all invalid input: '<'Variant, VcfEntry>toString()Methods inherited from class 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, toStringOldMethods inherited from class 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, variantEffectNonRefMethods inherited from class 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
-
Field Details
-
vcfEntry
-
-
Constructor Details
-
VariantVcfEntry
-
-
Method Details
-
factory
Create a collection of all invalid input: '<'Variant, VcfEntry> -
getVcfEntry
-
toString
-