44aa41e628
Rename Variant.jl to Haplotype.jl
2023-01-05 11:58:29 -06:00
3ef4a92ba2
Update CHANGELOG
2023-01-04 11:56:45 -06:00
8ae09aa9a1
Add linting workflow for PRs
2023-01-04 11:56:45 -06:00
d29764d2bc
Apply Blue style to tests file
2023-01-04 11:56:45 -06:00
fb9ab68cca
Apply Blue style to docs file
2023-01-04 11:56:45 -06:00
cb53defe9a
Add Aqua tests
2023-01-04 11:56:45 -06:00
1942090cd6
Remove Windows and Mac CI tests
...
There is no platform-specific code in this package, so this just slows down
CI with no benefit
2023-01-04 11:56:45 -06:00
6510ee3fc0
Add tutorial-type documentation
2023-01-04 11:56:45 -06:00
134ee771b9
Correct package install directions in docs
2023-01-04 11:56:45 -06:00
6f7110caec
Organize API docs
2023-01-04 11:56:45 -06:00
2a7d61e43d
Add docstrings for Variation functions
2023-01-04 11:56:45 -06:00
673481b40f
Add docstring for Variation
2023-01-04 11:56:45 -06:00
ea25ab87dc
Add docstrings for Variant methods
2023-01-04 11:56:45 -06:00
f49220782b
Add docstring for Variant
2023-01-04 11:56:45 -06:00
f1baf27865
Add docstring for lendiff(::Edit)
2023-01-04 11:56:45 -06:00
82ba838614
Add docstring for mutation(::Edit)
2023-01-04 11:56:45 -06:00
1f2b116518
Mark is_valid(::Variation) as private function
2023-01-04 11:56:45 -06:00
386acba8ab
Mark edits(::Variant) as private API
2023-01-04 11:56:45 -06:00
a573693737
Mark edit(::Variation) as private function
2023-01-04 11:56:45 -06:00
2f4f5fb5ae
Mark is_valid(::Variant) as private function
2023-01-04 11:56:45 -06:00
2719c438f3
Mark lendiff(::Edit) as private API
2023-01-04 11:56:45 -06:00
e8457e4241
Mark mutation(::Edit) as private API
2023-01-04 11:56:45 -06:00
cb1c429610
Update getter usage in translate function
2023-01-04 11:56:45 -06:00
ef4460bbbf
Replace field accession with getter function usage
2023-01-04 11:56:45 -06:00
dd405c5f4b
Refactor _lendiff to use multiple dispatch
2023-01-04 11:56:45 -06:00
cab3029bc6
Refactor Edit length to use dispatch instead of type checking
2023-01-04 11:56:45 -06:00
22d460b15a
Remove unused argument names from base getters for edits
2023-01-04 11:56:45 -06:00
da2cbbd528
Add equals functionality to Deletion
2023-01-04 11:56:45 -06:00
f08d6eb991
Add length method for Substitution
2023-01-04 11:56:45 -06:00
3b2730b5c1
Add export for translate and reconstruct!
2023-01-04 11:56:45 -06:00
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
2023-01-04 11:56:45 -06:00
9f9d0899bd
Move Insertion-related code to edits/Insertion.jl
2023-01-04 11:56:45 -06:00
b36ab69c72
Move Deletion-related code to edits/Deletion.jl
2023-01-04 11:56:45 -06:00
ba9f0e8fb1
Move Substitution-related code to edits/Substitution.jl
2023-01-04 11:56:45 -06:00
8c2dd271f3
Move Variation-related code to Variation.jl
2023-01-04 11:56:45 -06:00
37965ac7eb
Move Variant-related code to Variant.jl
2023-01-04 11:56:45 -06:00
3f631ace8f
Move Edit-related code to Edit.jl
2023-01-04 11:56:45 -06:00
a6ad47a568
Declare Blue style formatting for all new documents
2023-01-04 11:56:45 -06:00
fb5b7dfacf
Remove commented-out code
2023-01-04 11:56:45 -06:00
73d2781ee9
Update CHANGELOG
2022-12-17 22:59:39 +00:00
6ba583de4f
Bump version number in Project.toml
2022-12-17 22:59:39 +00:00
17f4cd6f39
Update CHANGELOG
2022-12-17 22:02:15 +00:00
128a5445ad
Switch alignment validation to after edit construction
2022-12-17 22:02:15 +00:00
f9058c5cb3
Update ranges to allow end position insertions
2022-12-17 22:02:15 +00:00
5be4dce200
Add check for soft clips when construction Variants from alignment
2022-12-17 22:02:15 +00:00
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.
2022-12-17 22:02:15 +00:00
91c3acc85e
Add equality function for Variant
2022-12-17 22:02:15 +00:00
f9e76d60d6
Add test for ending substitutions being invalid
2022-12-17 22:02:15 +00:00
3b61ccefb5
Add test for ending insertion
2022-12-17 22:02:15 +00:00
abff6692d4
Add test for combined clips
2022-12-17 22:02:15 +00:00
