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mbaudis committed Feb 5, 2025
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174 changes: 87 additions & 87 deletions docs/generated/requestParameterComponents.md
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Expand Up @@ -7,32 +7,32 @@ Component definitions for `requestProfiles`. The definition of each parameter as

#### description
A GA4GH RefGet identifier for the __adjacent__ sequence in adjacency/fusion scenarios.
**$ref:** `#/$defs/RefgetAccession`
* `$ref`: `#/$defs/RefgetAccession`

### `AdjacencyStart`

#### description
Start position or range (_i.e._ in case of a fuzzy breakpoint) on an adjacent sequence in case of a sequence adjecency Status: PROPOSED FOR BEACON v2.n, based on VRS v2 with modification
**oneOf:**
* `integer `
* `{'$ref': '#/$defs/Range'}`
* `oneOf`:
- `integer`
- `{'$ref': '#/$defs/Range'}`

### `AdjacencyEnd`

#### description
End position or range (_i.e._ in case of a fuzzy breakpoint) on an adjacent sequence in case of a sequence adjecency Status: PROPOSED FOR BEACON v2.n, based on VRS v2 with modification
**oneOf:**
* `integer `
* `{'$ref': '#/$defs/Range'}`
* `oneOf`:
- `integer`
- `{'$ref': '#/$defs/Range'}`

### `AminoacidChange`

#### description
Aminoacid alteration of interest. Format 1 letter Origin: Beacon v2.0
**type:** `string`
**examples:**
* `V600E `
* `M734V`
* `type`: `string`
* `examples`:
- `V600E`
- `M734V`

### `CopyChange`

Expand All @@ -56,16 +56,16 @@ MUST use a primaryCode representing one of:
\- EFO:0030072
```
Origin: Beacon v2.n, based on VRS v1.3+
**type:** `string`
**enum:**
* `EFO:0030069 `
* `EFO:0020073 `
* `EFO:0030068 `
* `EFO:0030067 `
* `EFO:0030064 `
* `EFO:0030070 `
* `EFO:0030071 `
* `EFO:0030072`
* `type`: `string`
* `enum`:
- `EFO:0030069`
- `EFO:0020073`
- `EFO:0030068`
- `EFO:0030067`
- `EFO:0030064`
- `EFO:0030070`
- `EFO:0030071`
- `EFO:0030072`

### `GeneId`

Expand All @@ -75,25 +75,25 @@ Origin: Beacon v2.n, based on VRS v1.3+
* It is strongly suggested to use a symbol following
the HGNC (https://www.genenames.org) nomenclature.
Origin: Beacon v2.0
**type:** `string`
**examples:**
* `BRAF `
* `SCN5A`
* `type`: `string`
* `examples`:
- `BRAF`
- `SCN5A`

### `GenomicAlleleShortForm`

#### description
HGVSId descriptor Origin: Beacon v2.0
**type:** `string`
**examples:**
* `NM_004006.2:c.4375C>T`
* `type`: `string`
* `examples`:
- `NM_004006.2:c.4375C>T`

### `Range`

#### description
An array of 2 integer values. If referring to sequence positions the "0-based, inclusive" format is used.
**type:** `array`
**items:**
* `type`: `array`
* `items`:
- `type`: `integer`
- `minimum`: `0`
- `minItems`: `2`
Expand All @@ -103,24 +103,24 @@ An array of 2 integer values. If referring to sequence positions the "0-based, i

#### description
A GA4GH RefGet identifier for the reference sequence, _i.e._ either a computed GA4GH checksum or other unique namespaced identifier supported by the server. It replaces the `referenceName` and `assemblyId` parameters according to the VRS v2 definition. Origin: VRS v2 Reference: [GA4GH RefGet](http://samtools.github.io/hts-specs/refget.html)
**type:** `string`
**examples:**
* `refseq:NC_000009.12 `
* `ga4gh:SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU`
* `type`: `string`
* `examples`:
- `refseq:NC_000009.12`
- `ga4gh:SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU`

### `RepeatSubunitLength`

#### description
The number of residues in a repeat subunit. In contrast to the VRS model we allow for range queries (e.g. all repeats with subunits of 1 or 2). Origin: VRS v2
**oneOf:**
* `integer `
* `{'$ref': '#/$defs/Range'}`
* `oneOf`:
- `integer`
- `{'$ref': '#/$defs/Range'}`

### `RequestProfileId`

#### description
The `requestProfileId` parameter here allows beacons to check the type of query being performed and to compare the provided request parameters for conformity with the expected query profile. The parameter definition here is a placeholder; the definitions of typed queries will use constant values for their `requestProfileId` parameter. Origin: Beacon v2+
**type:** `string`
* `type`: `string`

### `Sequence`

Expand All @@ -133,31 +133,31 @@ DNA bases.
sequence. As example, a query of `ANNT` the Ns can take take any form of [ACGT]
and will match `ANNT`, `ACNT`, `ACCT`, `ACGT` ... and so forth.
Origin: VRS v1.n TODO: Review use of base characters.
**type:** `string`
* `type`: `string`

### `SequenceLength`

#### description
The sequence length when querying the conceptual representation of a sequence according to a VRS `ReferenceLengthExpression` class. Origin: VRS v2
**oneOf:**
* `integer `
* `{'$ref': '#/$defs/Range'}`
* `oneOf`:
- `integer`
- `{'$ref': '#/$defs/Range'}`

### `SequenceStart`

#### description
Start position or range (_i.e._ in case of a fuzzy breakpoint) on a sequence. Status: PROPOSED FOR BEACON v2.n, based on VRS v2 with modification
**oneOf:**
* `integer `
* `{'$ref': '#/$defs/Range'}`
* `oneOf`:
- `integer`
- `{'$ref': '#/$defs/Range'}`

### `SequenceEnd`

#### description
End position or range (_i.e._ in case of a fuzzy breakpoint) on a sequence. Status: PROPOSED FOR BEACON v2.n, based on VRS v2 with modification
**oneOf:**
* `integer `
* `{'$ref': '#/$defs/Range'}`
* `oneOf`:
- `integer`
- `{'$ref': '#/$defs/Range'}`

### `VariantId`

Expand All @@ -170,10 +170,10 @@ End position or range (_i.e._ in case of a fuzzy breakpoint) on a sequence. Stat
`identifiers.variantAlternateIds` but potentially can map to other
identifiers as well.
Status: PROPOSED FOR BEACON v2.n
**type:** `string`
**examples:**
* `ClinGen:CA152954 `
* `dbSNP:rs587780345`
* `type`: `string`
* `examples`:
- `ClinGen:CA152954`
- `dbSNP:rs587780345`

### `VariantMinLength`

Expand All @@ -186,9 +186,9 @@ Status: PROPOSED FOR BEACON v2.n
variants with indicated referenceBases and alternateBases, to enable
length-specific wildcard queries.
Origin: Beacon v2.0
**type:** `integer`
**format:** `int64`
**minimum:** `0`
* `type`: `integer`
* `format`: `int64`
* `minimum`: `0`

### `VariantMaxLength`

Expand All @@ -201,41 +201,41 @@ Origin: Beacon v2.0
variants with indicated referenceBases and alternateBases, to enable
length-specific wildcard queries.
Origin: Beacon v2.0
**type:** `integer`
**format:** `int64`
**minimum:** `1`
* `type`: `integer`
* `format`: `int64`
* `minimum`: `1`

### `Assembly`

#### description
Genomic assembly accession and version as RefSqeq assembly accession (e.g. "GCF_000001405.39") or a versioned assembly name or synonym such as UCSC Genome Browser assembly (e.g. "hg38") or Genome Reference Consortium Human (e.g. "GRCh38.p13") names. DEPRECATION NOTE: The use of a assembly specific sequence identifier obviates this parameter. Not part of VRS v2 aligned model versions.
**type:** `string`
**example:**
* `GCF_000001405.39 `
* `hg38 `
* `GRCh38.p13`
* `type`: `string`
* `example`:
- `GCF_000001405.39`
- `hg38`
- `GRCh38.p13`

### `RefSeqId`

#### description
Reference sequence id for genomic reference sequence in which variant coordinates are given, e.g. "refseq:NC_000009.12" for human chromosome 9 in the GRCh38 assembly. The use of the assembly specific RefSeqId is recommended although alternatively names, synonymous or aliases e.g. "chr9" could be used in conjunction with an `Assembly` parameter. DEPRECATION NOTE: To be replaced with the `RefgetAccession` from VRS v2.
**type:** `string`
**example:**
* `refseq:NC_000009.12 `
* `chr9 `
* `NC_012920.1`
* `type`: `string`
* `example`:
- `refseq:NC_000009.12`
- `chr9`
- `NC_012920.1`

### `ReferenceBases`

#### description
The reference bases for the variant at the indicated position. It is based on the VCF cocept of having (anchored) reference bases at an indicated genomic location in combination with `alternateBases` to define their replacement. In contrast, standards such as GA4GH VRS only indicate the `sequence` observed at a given base position, including the use of an empty sequence together with `start` + `end` positions with `end - start > 0` to indicate deletions. Origin: VCF derived (optional) use in Beacon v0.3 -> v2.1 Status: LEGACY
**$ref:** `#/$defs/Sequence`
* `$ref`: `#/$defs/Sequence`

### `AlternateBases`

#### description
The bases of a sequence variant at a given position differing from the reference sequence, as defined by the `referenceBases` parameter. Please see `refereenceBases` for further information. Origin: VCF derived use in Beacon v0.3 -> v2.1 Status: LEGACY
**$ref:** `./common/requestParameterComponents.yaml#/$defs/Sequence`
* `$ref`: `./common/requestParameterComponents.yaml#/$defs/Sequence`

### `VariantType`

Expand All @@ -251,12 +251,12 @@ The `variantType` is used to query variants which are not defined through a sequ
over `variantType` for copy number variations. However, additional
concepts so far have not been covered and might warrant use of an
additional parameter (`variantClass`?).
**type:** `string`
**examples:**
* `EFO:0030070 `
* `DUP `
* `DEL `
* `EFO:0030069`
* `type`: `string`
* `examples`:
- `EFO:0030070`
- `DUP`
- `DEL`
- `EFO:0030069`

### `Start`

Expand Down Expand Up @@ -289,13 +289,13 @@ Precise or fuzzy start coordinate position(s), allele locus (0-based, inclusive)
and ending between `end[0]` <-> `end[1]`
- single or double sided precise matches can be achieved by setting
`start[1]=start[0]+1` and `end[1]=end[0]+1`
**type:** `array`
**items:**
* `type`: `array`
* `items`:
- `type`: `integer`
- `format`: `int64`
- `minimum`: `0`
**minItems:** `1`
**maxItems:** `2`
* `minItems`: `1`
* `maxItems`: `2`

### `End`

Expand All @@ -305,13 +305,13 @@ NOTE: See the `start` parameter for information on the potential replacement
Precise or bracketing the end of the variants of interest:
* (0-based, exclusive) - see `start`
* for bracket queries, provide 2 values (e.g. [111,222])."
**type:** `array`
**items:**
* `type`: `array`
* `items`:
- `type`: `integer`
- `format`: `int64`
- `minimum`: `1`
**minItems:** `1`
**maxItems:** `2`
* `minItems`: `1`
* `maxItems`: `2`

### `MateName`

Expand All @@ -321,16 +321,16 @@ Status: DEPRECATED in v2.n Notes:
it was never properly documented and is not considered a part of the
supported Beacon v2.n specification. It is now fully implemented in the
VRS v2 based `adjacencyAccession` parameter.
**$ref:** `#/$defs/RefSeqId`
* `$ref`: `#/$defs/RefSeqId`

### `MateStart`
**type:** `integer`
* `type`: `integer`

#### description
genomic start position of fusion partner breakpoint region Status: DEPRECATED in v2.n (see `mateName`)

### `MateEnd`
**type:** `integer`
* `type`: `integer`

#### description
genomic end position of fusion partner breakpoint region Status: DEPRECATED in v2.n (see `mateName`)
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