Update variant notation docs

Author: mathieulemieux

docs/variant_notation/continuous.md

@@ -8,7 +8,7 @@ All continuous notation follows a similar pattern that is loosely defined as:
 ```
 
 The `reference feature` would be the gene (chromosome, transcript, etc.)  name that the variant
-occurs on. The prefix denotes the coordinate type (see [prefixes](#prefixes)). The range is the
+occurs on. The prefix denotes the coordinate type (see [prefixes](./coordinate_systems)). The range is the
 position or positions of the variant. For a deletion, this is the range that is deleted. For an
 insertion, this is the two positions the sequence is inserted between. The sequence element will
 depend on the type of variant being described, but often this is the untemplated/inserted sequence.
@@ -23,9 +23,9 @@ specificity.
 
 ### Substitution
 
-[Genomic/CDS substitution variants](http://varnomen.hgvs.org/recommendations/DNA/variant/substitution/)
+[Genomic/CDS substitution variants](https://hgvs-nomenclature.org/stable/recommendations/DNA/substitution/)
 differ from
-[protein substitution variants](http://varnomen.hgvs.org/recommendations/protein/variant/substitution/).
+[protein substitution variants](https://hgvs-nomenclature.org/stable/recommendations/protein/substitution/).
 Therefore examples of both will be given.
 
 A protein missense mutation where G is replaced with D
@@ -42,7 +42,7 @@ chr11:g.1234A>C
 
 ### Indel
 
-A [protein deletion](http://varnomen.hgvs.org/recommendations/protein/variant/deletion/) of amino
+A [protein deletion](https://hgvs-nomenclature.org/stable/recommendations/protein/deletion/) of amino
 acids GH and insertion of three amino acids TTA
 
 ```text
@@ -60,7 +60,7 @@ Insertions must be a range to specify between which two coordinates the insertio
 avoids the problem
 when only a single coordinate is given of which side it is inserted on.
 
-An [protein insertion](http://varnomen.hgvs.org/recommendations/protein/variant/insertion/) of four
+An [protein insertion](https://hgvs-nomenclature.org/stable/recommendations/protein/insertion/) of four
 amino acids between G123 and H124. The sequence element here is optional and can also be described
 as a number if the number of bases inserted is known but the sequence is not given.
 
@@ -95,7 +95,7 @@ EGFR:p.R10_G14dupRSTGG
 
 ### Frameshift
 
-[Frameshifts](http://varnomen.hgvs.org/recommendations/protein/variant/frameshift/) are only
+[Frameshifts](https://hgvs-nomenclature.org/stable/recommendations/protein/frameshift/) are only
 applicable to variants denoted with protein coordinates. Frameshift notation follows the pattern
 below
 

docs/variant_notation/index.md

@@ -40,11 +40,11 @@ The expected variant types are given below. Some types are only applicable to ce
 
 ### Unsupported HGVS Features
 
-There are a few elements of the [HGVS v15.11](http://varnomen.hgvs.org/) notation that are not yet supported ([contributions are welcome!](https://github.com/bcgsc/pori_graphkb_parser)). These include:
+Some elements of the [HGVS v15.11](http://varnomen.hgvs.org/) notation that are not yet supported ([contributions are welcome!](https://github.com/bcgsc/pori_graphkb_parser)). These include, but are not limited to:
 
-- [mosacism](http://varnomen.hgvs.org/recommendations/DNA/variant/complex/)
-- [chimerism](http://varnomen.hgvs.org/recommendations/DNA/variant/complex/)
-- [RNA variants](http://varnomen.hgvs.org/recommendations/RNA/)
+- [methylation](https://hgvs-nomenclature.org/stable/recommendations/DNA/other/?h=methylation)
+- [mosaicism](https://hgvs-nomenclature.org/stable/recommendations/DNA/other/?h=mosaicism)
+- [chimerism](https://hgvs-nomenclature.org/stable/recommendations/DNA/other/?h=chimerism)
 - [conversions](http://varnomen.hgvs.org/recommendations/DNA/variant/conversion/)
 - [alleles](http://varnomen.hgvs.org/recommendations/DNA/variant/alleles/)
 - [v20 Complex Variants](https://varnomen.hgvs.org/recommendations/DNA/variant/complex/)

docs/variant_notation/split.md

@@ -50,3 +50,21 @@ a translocation might be described
 
 Above we are describing a translocation from chr8:1234 to chr7:4567 where AAT is the untemplated
 sequence inserted between the breakpoints.
+
+
+### Fusion nomenclature using the ```::``` delimiter
+
+As of v2.1.0 of the [pori_graphkb_parser](https://github.com/bcgsc/pori_graphkb_parser), some support has been added for [VICC](https://fusions.cancervariants.org/en/latest/index.html)-like fusion nomenclature using the ```::``` delimiter.
+
+Fusion variants can follow the pattern below
+
+```text
+<feature>:<prefix>.<start_range_pos>_<end_range_pos>::<feature>:<prefix>.<start_range_pos>_<end_range_pos>
+```
+
+Previous example ```(EWSR1,FLI1):fusion(e.4,e.7)``` can be written as:
+```text
+EWSR1:e.?_4::FLI1:e.7_?
+```
+
+Note that positions need to be given as a range. Use '?' when the starting and/or the ending position is unknowned.