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
dd00231840
Add test for soft clips
2022-12-17 22:02:15 +00:00
b45081a56e
Update CHANGELOG for v0.1.3
2022-11-22 18:07:53 +00:00
00495d4e14
Bump version number in Project.toml
2022-11-22 18:07:53 +00:00
3ed27f0c4e
Update CHANGELOG
2022-11-22 17:55:41 +00:00
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.
2022-11-22 17:55:41 +00:00
752b482a0b
Update CHANGELOG for v0.1.2
2022-10-04 11:55:58 -05:00
4de936cc83
Update project version number to v0.1.2
2022-10-04 11:55:58 -05:00
780a5add8a
Update CHANGELOG
2022-10-04 11:41:42 -05:00
b20d603f95
Add ranged dependency compats
2022-10-04 11:41:42 -05:00
f7278bd7d7
Remove unused AminoAcidSeq reference
2022-10-04 11:41:42 -05:00
c945dc63dd
Release v0.1.1 ( #19 )
2022-07-21 12:59:47 +00:00
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.
2022-07-21 12:33:35 +00:00
6a77d6d589
Merge pull request #16 from MillironX/feature/getbases
2022-07-14 15:00:10 +00:00
1cfe128070
Update CHANGELOG
2022-07-13 16:52:11 -05:00
97e1d193a6
Add VCF spec tests for reference and alternate bases
2022-07-13 16:50:00 -05:00
