Package org.snpsift.annotate
Class AnnotateVcfDbSorted
java.lang.Object
org.snpsift.annotate.AnnotateVcfDb
org.snpsift.annotate.AnnotateVcfDbSorted
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
-
Field Summary
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
-
Constructor Summary
Constructors -
Method Summary
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
-
Constructor Details
-
AnnotateVcfDbSorted
-