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ga4gh-beacon · Feb 5, 2025 · f306b85 · f306b85
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diff --git a/docs/generated/requestParameterComponents.md b/docs/generated/requestParameterComponents.md
@@ -13,25 +13,25 @@ A GA4GH RefGet identifier for the __adjacent__ sequence in adjacency/fusion scen
 
 #### 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`
+**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`
+**oneOf:**     
+* `integer    `
 * `{'$ref': '#/$defs/Range'}`        
 
 ### `AminoacidChange` 
 
 #### description
 Aminoacid alteration of interest. Format 1 letter Origin: Beacon v2.0    
 **type:** `string`    
-**examples:** 
-* `V600E`
+**examples:**     
+* `V600E    `
 * `M734V`        
 
 ### `CopyChange` 
@@ -57,14 +57,14 @@ MUST use a primaryCode representing one of:
 ```
 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`
+**enum:**     
+* `EFO:0030069    `
+* `EFO:0020073    `
+* `EFO:0030068    `
+* `EFO:0030067    `
+* `EFO:0030064    `
+* `EFO:0030070    `
+* `EFO:0030071    `
 * `EFO:0030072`        
 
 ### `GeneId` 
@@ -76,16 +76,16 @@ Origin: Beacon v2.n, based on VRS v1.3+
   the HGNC (https://www.genenames.org) nomenclature.
 Origin: Beacon v2.0    
 **type:** `string`    
-**examples:** 
-* `BRAF`
+**examples:**     
+* `BRAF    `
 * `SCN5A`        
 
 ### `GenomicAlleleShortForm` 
 
 #### description
 HGVSId descriptor Origin: Beacon v2.0    
 **type:** `string`    
-**examples:** 
+**examples:**     
 * `NM_004006.2:c.4375C>T`        
 
 ### `Range` 
@@ -104,16 +104,16 @@ 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`
+**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`
+**oneOf:**     
+* `integer    `
 * `{'$ref': '#/$defs/Range'}`        
 
 ### `RequestProfileId` 
@@ -139,24 +139,24 @@ Origin: VRS v1.n TODO: Review use of base characters.
 
 #### description
 The sequence length when querying the conceptual representation of a sequence according to a VRS `ReferenceLengthExpression` class. Origin: VRS v2    
-**oneOf:** 
-* `integer`
+**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`
+**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`
+**oneOf:**     
+* `integer    `
 * `{'$ref': '#/$defs/Range'}`        
 
 ### `VariantId` 
@@ -171,8 +171,8 @@ End position or range (_i.e._ in case of a fuzzy breakpoint) on a sequence. Stat
   identifiers as well.
 Status: PROPOSED FOR BEACON v2.n    
 **type:** `string`    
-**examples:** 
-* `ClinGen:CA152954`
+**examples:**     
+* `ClinGen:CA152954    `
 * `dbSNP:rs587780345`        
 
 ### `VariantMinLength` 
@@ -210,19 +210,19 @@ Origin: Beacon v2.0
 #### 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`
+**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`
+**example:**     
+* `refseq:NC_000009.12    `
+* `chr9    `
 * `NC_012920.1`        
 
 ### `ReferenceBases` 
@@ -252,10 +252,10 @@ The `variantType` is used to query variants which are not defined through a sequ
       concepts so far have not been covered and might warrant use of an
       additional parameter (`variantClass`?).    
 **type:** `string`    
-**examples:** 
-* `EFO:0030070`
-* `DUP`
-* `DEL`
+**examples:**     
+* `EFO:0030070    `
+* `DUP    `
+* `DEL    `
 * `EFO:0030069`        
 
 ### `Start` 

diff --git a/docs/generated/requestProfiles.md b/docs/generated/requestProfiles.md
@@ -55,9 +55,9 @@ This represents the generic collection of variant parameters supported in Beacon
     - `start`: `'$ref': './common/requestParameterComponents.yaml#/$defs/Start'`      
     - `referenceBases`: `'$ref': './common/requestParameterComponents.yaml#/$defs/ReferenceBases'`      
     - `alternateBases`: `'$ref': './common/requestParameterComponents.yaml#/$defs/AlternateBases'`    
-**required:** 
-* `referenceName`
-* `start`
+**required:**     
+* `referenceName    `
+* `start    `
 * `alternateBases`        
 
 ### `BV2bracketRequest` 
@@ -74,10 +74,10 @@ A typical Beacon v2 request for matching variations where start and end fall in
     - `variantType`: `'$ref': './common/requestParameterComponents.yaml#/$defs/VariantType'`      
     - `variantMinLength`: `'$ref': './common/requestParameterComponents.yaml#/$defs/VariantMinLength'`      
     - `variantMaxLength`: `'$ref': './common/requestParameterComponents.yaml#/$defs/VariantMaxLength'`    
-**required:** 
-* `referenceName`
-* `start`
-* `end`
+**required:**     
+* `referenceName    `
+* `start    `
+* `end    `
 * `variantType`        
 
 ### `BV2rangeRequest` 
@@ -94,9 +94,9 @@ Beacon Range Queries are supposed to return matches of any variant with at least
     - `variantType`: `'$ref': './common/requestParameterComponents.yaml#/$defs/VariantType'`      
     - `variantMinLength`: `'$ref': './common/requestParameterComponents.yaml#/$defs/VariantMinLength'`      
     - `variantMaxLength`: `'$ref': './common/requestParameterComponents.yaml#/$defs/VariantMaxLength'`    
-**required:** 
-* `referenceName`
-* `start`
+**required:**     
+* `referenceName    `
+* `start    `
 * `end`        
 
 ### `BV2variantIdRequest` 
@@ -111,7 +111,7 @@ Beacon Range Queries are supposed to return matches of any variant with at least
     - `requestProfileId`: `'const': 'BV2aminoacidChangeRequest'`      
     - `aminoacidChange`: `'$ref': './common/requestParameterComponents.yaml#/$defs/AminoacidChange'`      
     - `geneId`: `'$ref': './common/requestParameterComponents.yaml#/$defs/GeneId'`    
-**required:** 
+**required:**     
 * `aminoacidChange`        
 
 ### `BV2genomicAlleleShortFormRequest` 
@@ -131,7 +131,7 @@ A typical Beacon v2.n request for gene queries, e.g. for the retrieval of all va
     - `variantType`: `'$ref': './common/requestParameterComponents.yaml#/$defs/VariantType'`      
     - `variantMinLength`: `'$ref': './common/requestParameterComponents.yaml#/$defs/VariantMinLength'`      
     - `variantMaxLength`: `'$ref': './common/requestParameterComponents.yaml#/$defs/VariantMaxLength'`    
-**required:** 
+**required:**     
 * `geneId`        
 
 ### `VQSsequenceRequest` 
@@ -142,9 +142,9 @@ A typical Beacon v2.n request for gene queries, e.g. for the retrieval of all va
     - `start`: `'$ref': './common/requestParameterComponents.yaml#/$defs/SequenceStart'`      
     - `end`: `'$ref': './common/requestParameterComponents.yaml#/$defs/SequenceEnd'`      
     - `sequence`: `'$ref': './common/requestParameterComponents.yaml#/$defs/Sequence'`    
-**required:** 
-* `referenceAccession`
-* `start`
+**required:**     
+* `referenceAccession    `
+* `start    `
 * `sequence`        
 
 ### `VQScopyChangeRequest` 
@@ -160,10 +160,10 @@ A typical Beacon v2.n request for copy number variations (CNVs) queries approxim
     - `copyChange`: `'$ref': './common/requestParameterComponents.yaml#/$defs/CopyChange'`      
     - `variantMinLength`: `'$ref': './common/requestParameterComponents.yaml#/$defs/VariantMinLength'`      
     - `variantMaxLength`: `'$ref': './common/requestParameterComponents.yaml#/$defs/VariantMaxLength'`    
-**required:** 
-* `referenceAccession`
-* `start`
-* `end`
+**required:**     
+* `referenceAccession    `
+* `start    `
+* `end    `
 * `copyChange`        
 
 ### `VQSadjacencyRequest` 
@@ -194,7 +194,7 @@ A typical Beacon v2.n request for gene queries, e.g. for the retrieval of all va
     - `variantMaxLength`: `'$ref': './common/requestParameterComponents.yaml#/$defs/VariantMaxLength'`      
     - `molecularEffect`: `'$ref': './common/requestParameterComponents.yaml#/$defs/molecularEffect'`      
     - `clinicalRelevance`: `'$ref': './common/requestParameterComponents.yaml#/$defs/clinicalRelevance'`    
-**required:** 
+**required:**     
 * `geneId`        
 
 ### `BV2multivarsRequest` 

diff --git a/docs/generated/requestProfiles_BV2bracketRequest.md b/docs/generated/requestProfiles_BV2bracketRequest.md
@@ -8,10 +8,10 @@ Here sequence variants (insertions or deletions) involving a specific region on
 ### Request 
 **assemblyId:** `GRCh38`    
 **referenceName:** `17`    
-**start:** 
-* `43045703`
+**start:**     
+* `43045703    `
 * `43045709`        
-**end:** 
-* `43045715`
+**end:**     
+* `43045715    `
 * `43045720`        
 **variantType:** `INDEL`    
diff --git a/docs/generated/requestProfiles_BV2rangeRequest.md b/docs/generated/requestProfiles_BV2rangeRequest.md
@@ -9,9 +9,9 @@ CAVE: Since no variant type is indicated such a query can potentially match a la
 ### Request 
 **assemblyId:** `GRCh38`    
 **referenceName:** `17`    
-**start:** 
+**start:**     
 * `345675`        
-**end:** 
+**end:**     
 * `345681`        
 
 
@@ -20,9 +20,9 @@ CAVE: Since no variant type is indicated such a query can potentially match a la
 Query for a deletion involving TP53 using the maximum extent of the gene's coding region (known from somewhere...). The deletion to be found are expected to have an overlap with the queried range; however, the extent of the overlap is not pre-defined (most endpoints woul respond to a **recommended** "any" overlap but this is not a strict requirement imposed by the schema). Here positions refer to chromosome 17 on GRCh38 as indicated by the referenceName RefSeq ID.
 ### Request 
 **referenceName:** `refseq:NC_0000017.11`    
-**start:** 
+**start:**     
 * `7669608`        
-**end:** 
+**end:**     
 * `7676593`        
 **variantType:** `DEL`    
 
@@ -33,8 +33,8 @@ For this query the mapping position of TP53 (17:7669607-7676593) has to be known
 The "insertion" type is here provided through the Sequence Ontology term `SO:0000667` and for the chromosome the full, prefixed RefSeq term is being used.
 ### Request 
 **referenceName:** `refseq:NC_0000017.11`    
-**start:** 
+**start:**     
 * `7664000`        
-**end:** 
+**end:**     
 * `7682000`        
 **variantType:** `SO:0000667`    
diff --git a/docs/generated/requestProfiles_g_variant.md b/docs/generated/requestProfiles_g_variant.md
@@ -8,11 +8,11 @@ Here sequence variants (insertions or deletions) involving a specific region on
 ### Request 
 **assemblyId:** `GRCh38`    
 **referenceName:** `17`    
-**start:** 
-* `43045703`
+**start:**     
+* `43045703    `
 * `43045709`        
-**end:** 
-* `43045715`
+**end:**     
+* `43045715    `
 * `43045720`        
 **variantType:** `INDEL`    
 
@@ -24,9 +24,9 @@ CAVE: Since no variant type is indicated such a query can potentially match a la
 ### Request 
 **assemblyId:** `GRCh38`    
 **referenceName:** `17`    
-**start:** 
+**start:**     
 * `345675`        
-**end:** 
+**end:**     
 * `345681`        
 
 
@@ -35,9 +35,9 @@ CAVE: Since no variant type is indicated such a query can potentially match a la
 Query for a deletion involving TP53 using the maximum extent of the gene's coding region (known from somewhere...). The deletion to be found are expected to have an overlap with the queried range; however, the extent of the overlap is not pre-defined (most endpoints woul respond to a **recommended** "any" overlap but this is not a strict requirement imposed by the schema). Here positions refer to chromosome 17 on GRCh38 as indicated by the referenceName RefSeq ID.
 ### Request 
 **referenceName:** `refseq:NC_0000017.11`    
-**start:** 
+**start:**     
 * `7669608`        
-**end:** 
+**end:**     
 * `7676593`        
 **variantType:** `DEL`    
 
@@ -48,9 +48,9 @@ For this query the mapping position of TP53 (17:7669607-7676593) has to be known
 The "insertion" type is here provided through the Sequence Ontology term `SO:0000667` and for the chromosome the full, prefixed RefSeq term is being used.
 ### Request 
 **referenceName:** `refseq:NC_0000017.11`    
-**start:** 
+**start:**     
 * `7664000`        
-**end:** 
+**end:**     
 * `7682000`        
 **variantType:** `SO:0000667`