formatting; page cleanup

ga4gh-beacon · Feb 7, 2025 · ba895dd · ba895dd
1 parent 862550b
commit ba895dd
Show file tree

Hide file tree

Showing 3 changed files with 23 additions and 56 deletions.
diff --git a/docs/generated/requestProfiles_VQSadjacencyRequest.md b/docs/generated/requestProfiles_VQSadjacencyRequest.md
@@ -4,13 +4,14 @@ A typical Beacon v2.n request for sequence adjacency queries, e.g. for the retri
 
 ### Find  t(8;14)(q24;q32) translocations
 #### Solution for `VQSrequest` using genomic ranges (`VQSadjacencyRequest`)
-This is a query for translocations between the MYC and IgH loci, where the breakpoints are loosely defined through there well known cytogenetic bands. The query here follows the VRS adjacency model. In contrast to the VRS representational model, here:
-* VRS uses an array of 2 genomic locations while Beacon names the location
-  parameters individually (using "adjacency..." for the second partner)
-* VRS explicitely encodes directionality by using either `start` or `end`
+This is a query for translocations between the MYC and IgH loci, where the breakpoints are loosely defined through there well known cytogenetic bands. The query here follows the VRS adjacency model. In contrast to the VRS representational model, here:    
+
+- VRS uses an array of 2 genomic locations while Beacon names the location
+  parameters individually (using "adjacency..." for the second partner)    
+- VRS explicitely encodes directionality by using either `start` or `end`
   position parameters (integers or ranges) while this query example creates
   non-directional ranges on both sides since directionality might not be known,
-  the storage system might not encode this or all options could be of interest
+  the storage system might not encode this or all options could be of interest    
 #### Request 
 
 * `requestProfileId`: `VQSadjacencyRequest`    

diff --git a/docs/generated/requestProfiles_VQSrequest.md b/docs/generated/requestProfiles_VQSrequest.md
@@ -135,13 +135,14 @@ The query uses `"copyChange": "EFO:0020073"` for `high-level copy number loss` a
 
 ### Find  t(8;14)(q24;q32) translocations
 #### Solution for `VQSrequest` using genomic ranges (`VQSadjacencyRequest`)
-This is a query for translocations between the MYC and IgH loci, where the breakpoints are loosely defined through there well known cytogenetic bands. The query here follows the VRS adjacency model. In contrast to the VRS representational model, here:
-* VRS uses an array of 2 genomic locations while Beacon names the location
-  parameters individually (using "adjacency..." for the second partner)
-* VRS explicitely encodes directionality by using either `start` or `end`
+This is a query for translocations between the MYC and IgH loci, where the breakpoints are loosely defined through there well known cytogenetic bands. The query here follows the VRS adjacency model. In contrast to the VRS representational model, here:    
+
+- VRS uses an array of 2 genomic locations while Beacon names the location
+  parameters individually (using "adjacency..." for the second partner)    
+- VRS explicitely encodes directionality by using either `start` or `end`
   position parameters (integers or ranges) while this query example creates
   non-directional ranges on both sides since directionality might not be known,
-  the storage system might not encode this or all options could be of interest
+  the storage system might not encode this or all options could be of interest    
 #### Request 
     
 * `requestProfileId`: `VQSadjacencyRequest`    

diff --git a/docs/variant-types.md b/docs/variant-types.md
@@ -7,55 +7,20 @@ manifestations.
 
 !!! info "Under Construction"
 
-	For a start please see the previous [Beacon Scouts: Genomic Variants Use Cases & Examples](https://docs.google.com/document/d/1cwwRQ2PtlN1dBffCugdkbSHWCPmLgLkADd-5mu-rVAw/edit).
+	This page is currently under construction and will be updated with the types
+	of variants supported in teh different Beacon flavours.
 
-!!! bug "Beacon Scouts To Do"
+	Currently (February 2025, towards GA4GH Connect 2025) there is rapid development
+	which is reflected in the version specific pages:
 
-	We will add and document the variation concepts during the 2024 Beacon Variation
-	Scouts process.
-
-
-## Implemented
-
-### Allelic Sequence Variations
-
-==TBD==
-
-### Genomic Deletions
-
-#### Sequence-defined deletions
-
-==TBD==
-
-#### Copy Number Variations (CNVs)
-
-==TBD==
-
-### Genomic Duplications
+	- [Beacon v2 Query Solutions](generated/requestProfiles_g_variant) for demonstrating options provided by Beacon v2
+	- [Beacon v2+ Query Proposals](generated/requestProfiles_VQSrequest) for proposed parameters and solutions in a Beacon v2+ "Variant Query Standard" **VQS**
 
-==TBD==
 
-#### Copy Number Variations (CNVs)
+	For additional background see the previous [Beacon Scouts: Genomic Variants Use Cases & Examples](https://docs.google.com/document/d/1cwwRQ2PtlN1dBffCugdkbSHWCPmLgLkADd-5mu-rVAw/edit).
 
-==TBD==
+<!-- !!! bug "Beacon Scouts To Do"
 
-#### Tandem Duplications
-
-==TBD==
-
-### Genomic Fusions
-
-
-
-## For Consideration
-
-### Cytogenetic fusions and translocations
-
-### Variants by effect or annotation
-
-### Quantitative parameters related to regions and elements
-
-* expression
-* methylation
-
-... ==TBD==
+	We will add and document the variation concepts during the 2024/25 Beacon Variation
+	Scouts process.
+ -->