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2.7 KiB
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74 lines
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2.7 KiB
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<title>GC-AssemblySet</title>
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<h3>GC-AssemblySet</h3><pre>Defined in file <a href="genome_collection.asn.html">genome_collection.asn</a>
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C++ class: <a href="../doxyhtml/classCGC__AssemblySet.html">CGC_AssemblySet</a>
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GC-AssemblySet ::= SEQUENCE {
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-- The identifier of this assembly
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-- examples: GC internal id, Assembly-accession.version
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-- Types of DbTags used:
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-- db "GenColl", tag id <assembly-release-id>
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-- db "GenColl", tag str <assembly-accession.version>
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-- db "AGP", tag id <agp-sumbission-id>
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-- db "GenColl_Chain", tag id <assembly-chain-id>
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-- db "UCSC_name", tag str <UCSC identifier for assembly>
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-- db "Ensembl_name",tag str <Ensembl identifier for assembly>
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id SET OF <a href="Dbtag.html">Dbtag</a>,
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-- set type: Assembly-Sets can be of 2 categories
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set-type INTEGER {
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full-assembly(0), -- full-assembly: set of asm-units
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assembly-set(100), --set of full-assemblies
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-- stopper
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other(255)
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},
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-- 'class' defines the semantics of how to interpret this item
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class INTEGER {
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-- general type of full-assembly (not expected to be used)
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full-assembly(0),
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-- this assembly represents a single haploid assembly in its entirety
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haploid(1),
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-- this assembly has exactly one unit and at least one alt-loci
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haploid-with-alt-loci(2),
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-- assembly represents a diploid assembly; we expect at least two
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-- haploid-unit assemblies contained herein
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diploid(3),
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-- unresolved-diploid: single unit which includes the diploid sequences
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unresolved-diploid(4),
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-- second part of diploid; linked to another haploid full-assembly
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-- this one is alt-loci or second full-haploid
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alternate-haplotype(5),
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alternate-pseudohaplotype(6),
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-- assembly is a collection for annotation
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annotation-target-set(101),
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-- analysis set used for sequencing by alignments
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analysis-set(102),
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-- stopper
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other(255)
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},
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-- descriptors live in a shared data block
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desc <a href="GC-AssemblyDesc.html">GC-AssemblyDesc</a>,
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-- we contain hierarchically a set of assemblies
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primary-assembly <a href="GC-Assembly.html">GC-Assembly</a>,
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more-assemblies SET OF <a href="GC-Assembly.html">GC-Assembly</a> OPTIONAL,
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-- statistics
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-- "stats" field holds stats for all chromosomes combined:
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stats <a href="GC-SequenceStats.html">GC-SequenceStats</a> OPTIONAL
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}</pre>
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