Package org.snpsift.annotate
Class AnnotateVcfDbMem
- java.lang.Object
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- org.snpsift.annotate.AnnotateVcfDb
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- org.snpsift.annotate.AnnotateVcfDbMem
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public class AnnotateVcfDbMem extends AnnotateVcfDb
Annotate using a VCF "database" Note: Reads and loads the whole VCF file into memory- Author:
- pcingola
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Field Summary
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Fields inherited from class org.snpsift.annotate.AnnotateVcfDb
annotateEmpty, chrPrev, dbVcf, debug, errCount, existsInfoField, hasVcfInfoPerAlleleRef, infoFields, MAX_ERRORS, prependInfoFieldName, useAllInfoFields, useId, useInfoFields, useRefAlt, vcfDbFile, vcfInfoPerAllele, vcfInfoPerAlleleRef, verbose
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Constructor Summary
Constructors Constructor Description AnnotateVcfDbMem(java.lang.String dbFileName)
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Method Summary
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Methods inherited from class org.snpsift.annotate.AnnotateVcfDb
annotate, annotateExists, annotateIds, annotateInfo, close, discoverInfoFields, discoverInfoFields, find, find, findDbExists, findDbId, findDbInfo, findDbInfo, findDbInfoAlt, findDbInfoRef, match, open, prependInfoName, query, setAnnotateEmpty, setDebug, setExistsInfoField, setInfoFields, setPrependInfoFieldName, setUseId, setUseRefAlt, setVerbose, toString, uniqueIds, warn
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