# Package org.snpsift.annotate

package org.snpsift.annotate

Related Packages
Package
Description
org.snpsift
org.snpsift.annotate.mem
Class
Description
AnnotateVcfDb
Annotate using a VCF "database"
AnnotateVcfDbMem
Annotate using a VCF "database" Note: Reads and loads the whole VCF file into memory
AnnotateVcfDbSorted
Annotate using a VCF "database" Note: Assumes that the VCF database file is sorted.
AnnotateVcfDbTabix
Annotate using a tabix indexed VCF "database"
DbMarker<Q extends org.snpeff.interval.Marker,R extends org.snpeff.interval.Marker>
Use a file as a 'marker' database.
DbVcf
Use a VCF file as a database for annotations A VCF database consists of a VCF file and an index.
DbVcfMem
Loads a VCF file into memory.
DbVcfSorted
Use an uncompressed sorted VCF file as a database for annotations Note: Assumes that the VCF database file is sorted and uncompressed.
DbVcfTabix
Use a bgzip-compressed, tabix indexed VCF file as a database for annotations
MarkerFile
Represents a marker in a file (located at 'fileIdx' bytes since the beginning of the file)
QueryResult
A database query and a result.
VcfIndex
An index for a VCF file
VcfIndexDataChromo
Represents a set of VCF entries stored in an (uncompressed) file All entries belong to the same chromosome
VcfIndexTree
Interval tree structure for an 'VcfIndexChromo' The whole tree is stored in a single class as a set of arrays.