GC-AssemblySet

Defined in file genome_collection.asn
C++ class: CGC_AssemblySet


GC-AssemblySet ::= SEQUENCE {
    -- The identifier of this assembly
    -- examples: GC internal id, Assembly-accession.version
    -- Types of DbTags used:
    -- db "GenColl", tag id 
    -- db "GenColl", tag str 
    -- db "AGP", tag id 
    -- db "GenColl_Chain", tag id 

    -- db "UCSC_name", tag str 
    -- db "Ensembl_name",tag str 
    id SET OF Dbtag,

    -- set type: Assembly-Sets can be of 2 categories
    set-type INTEGER {
        full-assembly(0), -- full-assembly: set of asm-units
        assembly-set(100), --set of full-assemblies
        -- stopper
        other(255)
    },

    -- 'class' defines the semantics of how to interpret this item
    class INTEGER {
        -- general type of full-assembly (not expected to be used)
        full-assembly(0),
        -- this assembly represents a single haploid assembly in its entirety
        haploid(1),
        -- this assembly has exactly one unit and at least one alt-loci
        haploid-with-alt-loci(2),
        -- assembly represents a diploid assembly; we expect at least two
        -- haploid-unit assemblies contained herein
        diploid(3),
        -- unresolved-diploid: single unit which includes the diploid sequences
        unresolved-diploid(4),
        -- second part of diploid; linked to another haploid full-assembly
        -- this one is alt-loci or second full-haploid
        alternate-haplotype(5),
        alternate-pseudohaplotype(6),
        -- assembly is a collection for annotation
        annotation-target-set(101),
        -- analysis set used for sequencing by alignments
        analysis-set(102),
        -- stopper
        other(255)
    },

    -- descriptors live in a shared data block
    desc GC-AssemblyDesc,

    -- we contain hierarchically a set of assemblies
    primary-assembly GC-Assembly,
    more-assemblies SET OF GC-Assembly OPTIONAL,
    -- statistics
    -- "stats" field holds stats for all chromosomes combined:
    stats GC-SequenceStats OPTIONAL

}