formatting

docs/query-types/variantRequestParameters.md

@@ -5,15 +5,18 @@
     The parameters currently implemented can be looked up in the Beacon v2
     default model'e [`genomicVariations/requestParameters`](https://github.com/ga4gh-beacon/beacon-v2/blob/main/models/src/beacon-v2-default-model/genomicVariations/requestParameters.yaml).
 
+    Quoted text below reflects the v2 definitions, some of which might be subject
+    toc change (e.g. as result of the scouts' process).
+
 ## Beacon v2 Variant Request Parameters
 
 ### `assemblyId`
 
 In the original Beacon v2 specification `assemblyId` parameter refers to the
 
-    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.
+> 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.
 
 #### Scouts TODO
 
@@ -27,17 +30,17 @@ In the original Beacon v2 specification `assemblyId` parameter refers to the
 
 The `referenceName` parameter matches the 
 
-    sequence id for genomic sequence (e.g. chromosome) in which variant coordinates
-    (`start`, `end` ...) are given. Preferably a RefSeqId or alternatively common
-    synonymus or aliases.
+> sequence id for genomic sequence (e.g. chromosome) in which variant coordinates
+> (`start`, `end` ...) are given. Preferably a RefSeqId or alternatively common
+> synonymus or aliases.
 
 #### Examples
 
-	- "refseq:NC_000009.12"
-	- NC_000009.12
-	- Chr9
-	- "9"
-	- NC_012920.1
+- refseq:NC_000009.12
+- NC_000009.12
+- Chr9
+- 9
+- NC_012920.1
 
 #### Scouts TODO
 
@@ -62,27 +65,27 @@ are many practical cases for translocation/fusion events).
 Precise or fuzzy start coordinate position(s) for a variation locus (0-based, inclusive).
 The use depends on the query type:
 
-* `start` only:
-	- for single positions, e.g. the start of a specified sequence
-	  alteration where the size is given through the specified `alternateBases`
-	- typical use are queries for SNV and small InDels
-	- the use of `start` without an `end` parameter requires the use of
-	  `alternateBases`
-* `start` and `end`:
-	- for searching any variant falling fully or partially within the range
-	  between `start` and `end` (a.k.a. "range query")
-	- additional use of `variantType` OR `alternateBases` can limit the
-	  scope of the query
-	- by convention, partial overlaps of variants with the indicated genomic
-	  range are accepted; for specific overlap requirements the 4-parameter
-	  "Bracket Queries" should be employed
-* 2 values in both `start` and `end` for constructing a "Bracket Query":
-	- can be used to match any contiguous genomic interval, e.g. for querying
-	  imprecise positions
-	- identifies all structural variants starting between `start[0]` and `start[1]`,
-	  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`
+> * `start` only:
+> 	  - for single positions, e.g. the start of a specified sequence
+> 	  alteration where the size is given through the specified `alternateBases`
+> 	  - typical use are queries for SNV and small InDels
+> 	  - the use of `start` without an `end` parameter requires the use of
+> 	  `alternateBases`
+> * `start` and `end`:
+> 	  - for searching any variant falling fully or partially within the range
+> 	  between `start` and `end` (a.k.a. "range query")
+> 	  - additional use of `variantType` OR `alternateBases` can limit the
+> 	  scope of the query
+> 	  - by convention, partial overlaps of variants with the indicated genomic
+> 	  range are accepted; for specific overlap requirements the 4-parameter
+> 	  "Bracket Queries" should be employed
+> * 2 values in both `start` and `end` for constructing a "Bracket Query":
+> 	  - can be used to match any contiguous genomic interval, e.g. for querying
+> 	  imprecise positions
+> 	  - identifies all structural variants starting between `start[0]` and `start[1]`,
+> 	  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`
 
 #### Scouts TODO
 
@@ -94,17 +97,21 @@ Precise or fuzzy end coordinate position(s) for a variation locus (0-based, incl
 This is commonly used for variations w/o specified sequence (although e.g. a range
 and a sequence motif could be combined).
 
+#### Scouts TODO
+
+* as above
+
 ### `alternateBases`
 
 Sequence of bases for this variation (starting from `start`).
 
-* Accepted values: [ACGTN]
-* N is a wildcard, that denotes the position of any base and can be used as
-a standalone base of any type or within a partially known 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.
-* an _empty value_ is used in the case of deletions with the maximally
-trimmed, deleted sequence being indicated in `referenceBases`
+> * Accepted values: [ACGTN]
+> * N is a wildcard, that denotes the position of any base and can be used as
+> a standalone base of any type or within a partially known 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.
+> * an _empty value_ is used in the case of deletions with the maximally
+> trimmed, deleted sequence being indicated in `referenceBases`
 
 #### Scouts TODO
 
@@ -131,18 +138,20 @@ query type using non-sequence parameters (e.g. `aminoacidChange`).
 
 The Beacon v2 schema uses some "VCF-like" examples w/o being prescriptive:
 
-      Examples here are e.g. structural variants:
-      * DUP
-        - increased allelic count of material from the genomic region between
-          `start` and `end` positions
-        - no assumption about the placement of the additional sequences is being
-          made (i.e. no _in situ_ requirement as tandem duplications)
-      * DEL: deletion of sequence following `start`
-      * BND: breakend, i.e. termination of the allele at position `start` or in
-        the `startMin` => `startMax` interval, or fusion of the sequence to distant
-        partner
-      Either `alternateBases` or `variantType` is required, with the exception
-      of range queries (single `start` and `end` parameters).
+> Examples here are e.g. structural variants:
+>
+> * DUP
+>     - increased allelic count of material from the genomic region between
+>   `start` and `end` positions
+>     - no assumption about the placement of the additional sequences is being
+>   made (i.e. no _in situ_ requirement as tandem duplications)
+> * DEL: deletion of sequence following `start`
+> * BND: breakend, i.e. termination of the allele at position `start` or in
+> the `startMin` => `startMax` interval, or fusion of the sequence to distant
+> partner
+>
+> Either `alternateBases` or `variantType` is required, with the exception
+> of range queries (single `start` and `end` parameters).
 
 #### Scouts TODO
 
@@ -160,7 +169,7 @@ The Beacon v2 schema uses some "VCF-like" examples w/o being prescriptive:
   that length based queries should also be supported for variants with indicated 
   eferenceBases and alternateBases, to enable length-specific wildcard queries.
 
- #### Scouts TODO
+#### Scouts TODO
 
 * check definition
 

mkdocs.yml

@@ -12,7 +12,7 @@ schemas_path: /blob/main/schemas/
 nav:
   - 'Home': /
   - Variation Types: variant-types
-  - Request PArameters: query-types/variantRequestParameters
+  - Request Parameters: query-types/variantRequestParameters
   - Query Types: query-types
   - Query Schema Source Files: https://github.com/ga4gh-beacon/variant-query-types/tree/main/schemas