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63 lines
No EOL
2.3 KiB
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<h3>GC-AssemblyUnit</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__AssemblyUnit.html">CGC_AssemblyUnit</a>
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GC-AssemblyUnit ::= SEQUENCE
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{
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-- The identifier of this assembly
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-- Contains: GenColl internal id, GenColl accession.version,
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-- AGP id, UCSC name, Ensembl name
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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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-- "Ensembl_name" and "UCSC_name" will not appear in the Unit level since
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-- these organizations do not define assembly-units.
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id SET OF <a href="Dbtag.html">Dbtag</a>,
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-- 'class' defines the semantics of how to interpret this item
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class INTEGER {
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-- units for haploid/diploid assemblies
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haploid-unit(1),
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-- this unit represents one or more alternate loci for a haploid
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-- assembly
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alt-loci(2),
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-- assembly-patch
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assembly-patch(3),
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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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-- collections of molecules for this assembly
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mols SET OF <a href="GC-Replicon.html">GC-Replicon</a> OPTIONAL,
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-- On primary assembly-unit: here will be the unplaced sequences
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-- On alt-loci: list of sequences aligned/unaligned to primary unit
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other-sequences SET OF <a href="GC-TaggedSequences.html">GC-TaggedSequences</a> OPTIONAL,
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-- statistics
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-- "stats" field holds stats for all chromosomes combined:
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-- ordered/unordered scaffolds
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-- "unplaced-stats" holds stats for ChrUn which is omitted from "stats"
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stats <a href="GC-SequenceStats.html">GC-SequenceStats</a> OPTIONAL,
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unplaced-stats SET OF <a href="GC-Scaf-stats.html">GC-Scaf-stats</a> OPTIONAL,
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unplaced-unlocalized-stats SET OF <a href="GC-Scaf-stats.html">GC-Scaf-stats</a> OPTIONAL
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}</pre>
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