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
}