Package org.snpsift.annotate
Class AnnotateVcfDbSorted
- java.lang.Object
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- org.snpsift.annotate.AnnotateVcfDb
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- org.snpsift.annotate.AnnotateVcfDbSorted
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public class AnnotateVcfDbSorted extends AnnotateVcfDb
Annotate using a VCF "database" Note: Assumes that the VCF database file is sorted. Each VCF entry should be sorted according to position. Chromosome order does not matter (e.g. all entries for chr10 can be before entries for chr2). But entries for the same chromosome should be together.- 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 AnnotateVcfDbSorted(java.lang.String dbFileName, int maxBlockSize)
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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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