fix docs

Author: nickzoic

docs/included-plugins/index.md

@@ -271,11 +271,32 @@ The reference sequence can either be provided directly as a configuration parame
 
 *See also: [countess-minimap2 plugin](https://github.com/CountESS-Project/countess-minimap2), a variant caller which uses 'minimap2' to find sequences within a genome.*
 
+#### Parameters
+
+Input Column
+: the input column with the variant sequence
+
+Reference
+: (optional) select column which contains the reference sequence ...
+
+Sequence
+: (optional) ... or supply a reference sequence as a value
+
+Output Column
+: Column name for HGVS string
+
+Max Mutations
+: Maximum number of mutations, if no variant with this number or less mutations is found then return a null value for the output
+
+Drop
+: Drop rows which would have null values for output
+
 ### Variant Classifier
 
-Takes a column of protein variants and classifies them into types:
+Takes a column of protein variants and classifies them into broad types.
+This is easier than writing the regular expression yourself.
 
-Short designations:
+#### Short format:
 
 |---|---|---|
 |format | type | explanation |
@@ -286,36 +307,24 @@ Short designations:
 | `A107*` <br/>`A107X` | `N` | Nonsense |
 | `A107-` | `D` | Deletion |
 
-HGVS Protein designations:
+There is currently no support for insertions in short format.
+Invalid amino acid letters will generate a warning and the type will be set to `?`.
+
+#### HGVS format:
 
 |---|---|---|
 | format | type | explanation |
 | `p.=` | `W` | Wild type |
 | `p.Ala107His` | `M` | Missense |
 | `p.Ala107=` | `S` | Synonymous |
 | `p.Ala107Ter` | `N` | Nonsense |
-| `p.Ala107del` | `D` | Deletion |
-| `p.Ala107_Glu108insHis` <br/>`p.Ala107dup` <br/>`p.Ala107_Glu108dup` | `I` | Insertion / Duplication |
-
-Other variant formats or invalid amino acid codes will generate a warning and the type will be set to `?`.
-There is currently no support for insertions in short designations.
+| `p.Ala107del` <br/>`p.Ala107_His109del` | `D` | Deletion |
+| `p.Ala107dup` <br/>`p.Ala107_Glu108dup` <br/>`p.Ala107_Glu108insHis` | `I` | Insertion / Duplication |
 
-#### Parameters
-
-Input Column
-: the input column with the variant sequence
+Invalid amino acid codes will generate a warning and the type will be set to `?`.
+Other issues such as invalid locations will not necessarily be detected.
+More complicated scenarios, like `delins` and multiple changes, are not currently supported.
 
-Reference
-: (optional) select column which contains the reference sequence ...
+#### Unrecognized Formats
 
-Sequence
-: (optional) ... or supply a reference sequence as a value
-
-Output Column
-: Column name for HGVS string
-
-Max Mutations
-: Maximum number of mutations, if no variant with this number or less mutations is found then return a null value for the output
-
-Drop
-: Drop rows which would have null values for output
+Other variant formats will generate a warning and the type will be set to `?`.