Package org.snpsift.annotate
package org.snpsift.annotate
-
ClassDescriptionAnnotate using a VCF "database"Annotate using a VCF "database" Note: Reads and loads the whole VCF file into memoryAnnotate using a VCF "database" Note: Assumes that the VCF database file is sorted.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.Use a VCF file as a database for annotations A VCF database consists of a VCF file and an index.Loads a VCF file into memory.Use an uncompressed sorted VCF file as a database for annotations Note: Assumes that the VCF database file is sorted and uncompressed.Use a bgzip-compressed, tabix indexed VCF file as a database for annotationsRepresents a marker in a file (located at 'fileIdx' bytes since the beginning of the file)A database query and a result.An index for a VCF fileRepresents a set of VCF entries stored in an (uncompressed) file All entries belong to the same chromosomeInterval tree structure for an 'VcfIndexChromo' The whole tree is stored in a single class as a set of arrays.