Package org.snpsift.fileIterator
Class DbNsfpEntry
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Variant
org.snpsift.fileIterator.DbNsfpEntry
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<org.snpeff.interval.Interval>
,org.snpeff.serializer.TxtSerializable
public class DbNsfpEntry
extends org.snpeff.interval.Variant
DbNSFP database entry:
Reference https://sites.google.com/site/jpopgen/dbNSFP
Added lazy parsing of key/value pairs
- Author:
- lletourn
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from class org.snpeff.interval.Variant
org.snpeff.interval.Variant.VariantType
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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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Add a valuegetVcfInfo
(String key) Get data in a VCF INFO field compatible formatboolean
Do we have values for this alleleprotected void
Parse dbSNFP 'Chr, pos, ref, alt' values from a single lineprotected void
Parse dbSNFP ALL values from a single line and store them in 'values' hashint
parsePosition
(String posStr) Parse a string as a 'position'.static String[]
splitValuesField
(String value) toString()
Methods inherited from class org.snpeff.interval.Variant
clone, 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
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Constructor Details
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DbNsfpEntry
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Method Details
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splitValuesField
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add
Add a value -
cloneShallow
- Overrides:
cloneShallow
in classorg.snpeff.interval.Variant
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getVcfInfo
Get data in a VCF INFO field compatible format -
hasValues
Do we have values for this allele -
parseChrPosRefAlt
protected void parseChrPosRefAlt()Parse dbSNFP 'Chr, pos, ref, alt' values from a single line -
parseKeyValues
protected void parseKeyValues()Parse dbSNFP ALL values from a single line and store them in 'values' hashNote: This method is supposed to be a lazy parsing of the key/value pairs, so it DOES NOT store 'chr, pos, ref, alt'. You can use `parseChrPosRefAlt()` for that.
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parsePosition
Parse a string as a 'position'. -
toString
- Overrides:
toString
in classorg.snpeff.interval.Variant
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