Package org.snpsift.annotate


package org.snpsift.annotate
  • Class
    Description
    Annotate using a VCF "database"
    Annotate using a VCF "database" Note: Reads and loads the whole VCF file into memory
    Annotate 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 annotations
    Represents 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 file
    Represents a set of VCF entries stored in an (uncompressed) file All entries belong to the same chromosome
    Interval tree structure for an 'VcfIndexChromo' The whole tree is stored in a single class as a set of arrays.