73 lines
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2.6 KiB
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73 lines
No EOL
2.6 KiB
HTML
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<title>VariantPlacement</title>
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<h3>VariantPlacement</h3><pre>Defined in file <a href="variation.asn.html">variation.asn</a>
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C++ class: <a href="../doxyhtml/classCVariantPlacement.html">CVariantPlacement</a>
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VariantPlacement ::= SEQUENCE
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{
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-- actual concrete placement we are considering
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loc <a href="Seq-loc.html">Seq-loc</a>,
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mol INTEGER {
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unknown(0),
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genomic(1), --"g." coordinates in HGVS
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cdna(2), --"c." coordinates in HGVS
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rna(3), --"n." coordinates in HGVS
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protein(4), --"p." coordinates in HGVS
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mitochondrion(5) --"mt." coordinates in HGVS
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},
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-- location flags
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placement-method INTEGER {
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projected(1),
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asserted(2),
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aligned(3)
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} OPTIONAL,
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-- location refinements, describing offsets into introns from product coordinates.
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-- Biological semantics: start-offset/stop-offset apply to bio-start/bio-stop respectively.
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-- positive = downstream; negative = upstream.
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start-offset INTEGER OPTIONAL,
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start-offset-fuzz <a href="Int-fuzz.html">Int-fuzz</a> OPTIONAL,
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stop-offset INTEGER OPTIONAL,
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stop-offset-fuzz <a href="Int-fuzz.html">Int-fuzz</a> OPTIONAL,
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-- 0-based position of bio-start relative to containing codon
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frame INTEGER OPTIONAL,
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-- for situations in which a raw location isn't sufficient
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seq <a href="Seq-literal.html">Seq-literal</a> OPTIONAL,
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-- reference to the assembly (GenColl ID) for this location
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assembly <a href="Dbtag.html">Dbtag</a> OPTIONAL,
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hgvs-name VisibleString OPTIONAL,
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-- the reference location for this variant
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comment VisibleString OPTIONAL,
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exceptions SET OF <a href="VariationException.html">VariationException</a> OPTIONAL,
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dbxrefs SET OF <a href="Dbtag.html">Dbtag</a> OPTIONAL, --e.g. rs#, that are placement-specific
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ext SET OF <a href="User-object.html">User-object</a> OPTIONAL, --for process-specific placement tags/labels
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gene-location INTEGER OPTIONAL, --Same semantics as <a href="VariantProperties.html">VariantProperties</a>.gene-location, except placement-specific
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id <a href="Object-id.html">Object-id</a> OPTIONAL,
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parent-id <a href="Object-id.html">Object-id</a> OPTIONAL, --id of the placement from which this one was derived
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so-terms SEQUENCE OF INTEGER OPTIONAL --Sequence Ontology terms for this placement
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}</pre>
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