Thomas A. Christensen II
ea25ab87dc
Add docstrings for Variant methods
1 year ago
Thomas A. Christensen II
f49220782b
Add docstring for Variant
1 year ago
Thomas A. Christensen II
f1baf27865
Add docstring for `lendiff(::Edit)`
1 year ago
Thomas A. Christensen II
82ba838614
Add docstring for `mutation(::Edit)`
1 year ago
Thomas A. Christensen II
1f2b116518
Mark is_valid(::Variation) as private function
1 year ago
Thomas A. Christensen II
386acba8ab
Mark `edits(::Variant)` as private API
1 year ago
Thomas A. Christensen II
a573693737
Mark `edit(::Variation)` as private function
1 year ago
Thomas A. Christensen II
2f4f5fb5ae
Mark `is_valid(::Variant)` as private function
1 year ago
Thomas A. Christensen II
2719c438f3
Mark `lendiff(::Edit)` as private API
1 year ago
Thomas A. Christensen II
e8457e4241
Mark `mutation(::Edit)` as private API
1 year ago
Thomas A. Christensen II
cb1c429610
Update getter usage in translate function
1 year ago
Thomas A. Christensen II
ef4460bbbf
Replace field accession with getter function usage
1 year ago
Thomas A. Christensen II
dd405c5f4b
Refactor _lendiff to use multiple dispatch
1 year ago
Thomas A. Christensen II
cab3029bc6
Refactor Edit length to use dispatch instead of type checking
1 year ago
Thomas A. Christensen II
22d460b15a
Remove unused argument names from base getters for edits
1 year ago
Thomas A. Christensen II
da2cbbd528
Add equals functionality to Deletion
1 year ago
Thomas A. Christensen II
f08d6eb991
Add length method for Substitution
1 year ago
Thomas A. Christensen II
3b2730b5c1
Add export for translate and reconstruct!
1 year ago
Thomas A. Christensen II
25c63906dc
Move exports to top of file
...
Per Blue style, exports should be one per line, and appear immediately
after using statements. Reorganize module file to comply
1 year ago
Thomas A. Christensen II
9f9d0899bd
Move Insertion-related code to edits/Insertion.jl
1 year ago
Thomas A. Christensen II
b36ab69c72
Move Deletion-related code to edits/Deletion.jl
1 year ago
Thomas A. Christensen II
ba9f0e8fb1
Move Substitution-related code to edits/Substitution.jl
1 year ago
Thomas A. Christensen II
8c2dd271f3
Move Variation-related code to Variation.jl
1 year ago
Thomas A. Christensen II
37965ac7eb
Move Variant-related code to Variant.jl
1 year ago
Thomas A. Christensen II
3f631ace8f
Move Edit-related code to Edit.jl
1 year ago
Thomas A. Christensen II
a6ad47a568
Declare Blue style formatting for all new documents
1 year ago
Thomas A. Christensen II
fb5b7dfacf
Remove commented-out code
1 year ago
Thomas A. Christensen II
73d2781ee9
Update CHANGELOG
1 year ago
Thomas A. Christensen II
6ba583de4f
Bump version number in Project.toml
1 year ago
Thomas A. Christensen II
17f4cd6f39
Update CHANGELOG
1 year ago
Thomas A. Christensen II
128a5445ad
Switch alignment validation to after edit construction
1 year ago
Thomas A. Christensen II
f9058c5cb3
Update ranges to allow end position insertions
1 year ago
Thomas A. Christensen II
5be4dce200
Add check for soft clips when construction Variants from alignment
1 year ago
Thomas A. Christensen II
d8435be115
Add Variation-level validation for Variants
...
Testing indicates that some Variants (particularly those with insertions
and/or clips at the send of the query sequence) will validate fine as a
Variant, but will fail validation as a Variation. This problem is
particularly annoying when constructing Variants in the REPL, as the
creation will complete successfully, but the show of the Variant will
error out. To fix this, leverage the existing validation of Variation to
check each Edit within a Variant upon construction.
1 year ago
Thomas A. Christensen II
91c3acc85e
Add equality function for Variant
1 year ago
Thomas A. Christensen II
f9e76d60d6
Add test for ending substitutions being invalid
1 year ago
Thomas A. Christensen II
3b61ccefb5
Add test for ending insertion
1 year ago
Thomas A. Christensen II
abff6692d4
Add test for combined clips
1 year ago
Thomas A. Christensen II
dd00231840
Add test for soft clips
1 year ago
Thomas A. Christensen II
b45081a56e
Update CHANGELOG for v0.1.3
2 years ago
Thomas A. Christensen II
00495d4e14
Bump version number in Project.toml
2 years ago
Thomas A. Christensen II
3ed27f0c4e
Update CHANGELOG
2 years ago
Thomas A. Christensen II
3b33c85d00
Add type parameterization to variations getter
...
I have encountered some cases where having a non-parameterized vector can
crash a downstream process. I don't yet know how to make a MWE of that, but
adding type parameters fixes my problem, and doesn't break any tests here.
2 years ago
Thomas A. Christensen II
752b482a0b
Update CHANGELOG for v0.1.2
2 years ago
Thomas A. Christensen II
4de936cc83
Update project version number to v0.1.2
2 years ago
Thomas A. Christensen II
780a5add8a
Update CHANGELOG
2 years ago
Thomas A. Christensen II
b20d603f95
Add ranged dependency compats
2 years ago
Thomas A. Christensen II
f7278bd7d7
Remove unused AminoAcidSeq reference
2 years ago
Thomas A. Christensen II
c945dc63dd
Release v0.1.1 ( #19 )
2 years ago
Thomas A. Christensen II
1bbb85153c
Add constructor for Variant based on Variations
...
A Variant is a collection of Variations, right? Unfortunately there was no
way to convert a collection of Variations into a Variant, so I added one.
2 years ago
