From 1124bd8b0f0421958a1edce78b0b4620a959756a Mon Sep 17 00:00:00 2001
From: Michael Baudis <675030+mbaudis@users.noreply.github.com>
Date: Sat, 16 Mar 2024 14:48:37 +0100
Subject: [PATCH] doc formatting ...

---
 docs/.DS_Store                                | Bin 0 -> 6148 bytes
 docs/{query-types.md => query-types/index.md} |  19 ++++++++++++------
 .../index.md}                                 |   0
 mkdocs.yml                                    |   2 +-
 4 files changed, 14 insertions(+), 7 deletions(-)
 create mode 100644 docs/.DS_Store
 rename docs/{query-types.md => query-types/index.md} (82%)
 rename docs/{variant-types.md => variant-types/index.md} (100%)

diff --git a/docs/.DS_Store b/docs/.DS_Store
new file mode 100644
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diff --git a/docs/query-types.md b/docs/query-types/index.md
similarity index 82%
rename from docs/query-types.md
rename to docs/query-types/index.md
index 299d1e3..c8fc226 100644
--- a/docs/query-types.md
+++ b/docs/query-types/index.md
@@ -8,36 +8,43 @@ As part of the 2024 Beacon Variant Scouts we work on a revison and potential
 extension of the available parameters, as well as on the definition of canonical
 _Query Types_ tailored to the retrieval of defined [_Variant Types_](variant-types).
 
-## _Sequence Queries_: `VariantSequenceRequest`[^1]
+## Beacon v2 Default Model Queries
+
+### _Sequence Queries_: `VariantSequenceRequest`[^1]
 
 _Sequence Queries_ query for the existence of a specified sequence at a given genomic
 position. Such queries roughly correspond to Beacon v1 queries and are used to match
 short, precisely defined genomic variants such as SNVs, MNVs and INDELs.
 
-## _Range Queries_: `VariantRangeRequest`[^1]
+### _Range Queries_: `VariantRangeRequest`[^1]
 
 Beacon _Range Queries_ are supposed to return matches of any variant with at least
 partial overlap of the sequence range specified by `referenceName`, `start` and `end`
 parameters.
 
-## _Bracket Queries_ ("CNV queries"): `VariantBracketRequest`[^1]
+### _Bracket Queries_ ("CNV queries"): `VariantBracketRequest`[^1]
 
 _Bracket Queries_ allow the specification of sequence ranges for both start and end
 positions of a genomic variation. The typical example here is the query for similar
 structural variants - particularly CNVs - affecting a genomic region but potentially
 differing in their exact extents.
 
-## _GeneId Queries_: `GeneRequest`[^1]
+### _GeneId Queries_: `GeneRequest`[^1]
 
 _GeneId Queries_ are in essence a variation of _Range Queries_ in which the coordinates
 are replaced by the [HGNC](https://www.genenames.org) gene symbol. It is left to the
 implementation if the matching is done on variants annotated for the gene symbol or if
 a positional translation is being applied.
 
-## ==TBC==
+### ==TBC==
+
+## Query Type Proposals
+
+
+
 
 
-[^1:] The names of the request type schemas should be considered "malleable".
+[^1]: The names of the request type schemas should be considered "malleable".
 
 
 
diff --git a/docs/variant-types.md b/docs/variant-types/index.md
similarity index 100%
rename from docs/variant-types.md
rename to docs/variant-types/index.md
diff --git a/mkdocs.yml b/mkdocs.yml
index 0885180..9cb1e59 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -9,7 +9,7 @@ edit_uri: edit/main/docs/
 ###############################################################################
 
 nav:
-  - 'Home': index
+  - 'Home': /
   - Variation Types: variant-types
   - Query Types: query-types
   - Query Schema Source Files: https://github.com/ga4gh-beacon/variant-query-types/tree/main/schemas