millironx/SequenceVariation.jl
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Author SHA1 Message Date
Thomas A. Christensen II
22d460b15a Remove unused argument names from base getters for edits 2023-01-04 11:56:45 -06:00
Thomas A. Christensen II
da2cbbd528 Add equals functionality to Deletion 2023-01-04 11:56:45 -06:00
Thomas A. Christensen II
f08d6eb991 Add length method for Substitution 2023-01-04 11:56:45 -06:00
Thomas A. Christensen II
3b2730b5c1 Add export for translate and reconstruct! 2023-01-04 11:56:45 -06:00
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
 2023-01-04 11:56:45 -06:00
Thomas A. Christensen II
9f9d0899bd Move Insertion-related code to edits/Insertion.jl 2023-01-04 11:56:45 -06:00
Thomas A. Christensen II
b36ab69c72 Move Deletion-related code to edits/Deletion.jl 2023-01-04 11:56:45 -06:00
Thomas A. Christensen II
ba9f0e8fb1 Move Substitution-related code to edits/Substitution.jl 2023-01-04 11:56:45 -06:00
Thomas A. Christensen II
8c2dd271f3 Move Variation-related code to Variation.jl 2023-01-04 11:56:45 -06:00
Thomas A. Christensen II
37965ac7eb Move Variant-related code to Variant.jl 2023-01-04 11:56:45 -06:00
Thomas A. Christensen II
3f631ace8f Move Edit-related code to Edit.jl 2023-01-04 11:56:45 -06:00
Thomas A. Christensen II
a6ad47a568 Declare Blue style formatting for all new documents 2023-01-04 11:56:45 -06:00
Thomas A. Christensen II
fb5b7dfacf Remove commented-out code 2023-01-04 11:56:45 -06:00
Thomas A. Christensen II
73d2781ee9 Update CHANGELOG 2022-12-17 22:59:39 +00:00
Thomas A. Christensen II
6ba583de4f Bump version number in Project.toml 2022-12-17 22:59:39 +00:00
Thomas A. Christensen II
17f4cd6f39 Update CHANGELOG 2022-12-17 22:02:15 +00:00
Thomas A. Christensen II
128a5445ad Switch alignment validation to after edit construction 2022-12-17 22:02:15 +00:00
Thomas A. Christensen II
f9058c5cb3 Update ranges to allow end position insertions 2022-12-17 22:02:15 +00:00
Thomas A. Christensen II
5be4dce200 Add check for soft clips when construction Variants from alignment 2022-12-17 22:02:15 +00:00
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.
 2022-12-17 22:02:15 +00:00
Thomas A. Christensen II
91c3acc85e Add equality function for Variant 2022-12-17 22:02:15 +00:00
Thomas A. Christensen II
f9e76d60d6 Add test for ending substitutions being invalid 2022-12-17 22:02:15 +00:00
Thomas A. Christensen II
3b61ccefb5 Add test for ending insertion 2022-12-17 22:02:15 +00:00
Thomas A. Christensen II
abff6692d4 Add test for combined clips 2022-12-17 22:02:15 +00:00
Thomas A. Christensen II
dd00231840 Add test for soft clips 2022-12-17 22:02:15 +00:00
Thomas A. Christensen II
b45081a56e Update CHANGELOG for v0.1.3 2022-11-22 18:07:53 +00:00
Thomas A. Christensen II
00495d4e14 Bump version number in Project.toml 2022-11-22 18:07:53 +00:00
Thomas A. Christensen II
3ed27f0c4e Update CHANGELOG 2022-11-22 17:55:41 +00:00
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.
 2022-11-22 17:55:41 +00:00
Thomas A. Christensen II
752b482a0b Update CHANGELOG for v0.1.2 2022-10-04 11:55:58 -05:00
Thomas A. Christensen II
4de936cc83 Update project version number to v0.1.2 2022-10-04 11:55:58 -05:00
Thomas A. Christensen II
780a5add8a Update CHANGELOG 2022-10-04 11:41:42 -05:00
Thomas A. Christensen II
b20d603f95 Add ranged dependency compats 2022-10-04 11:41:42 -05:00
Thomas A. Christensen II
f7278bd7d7 Remove unused AminoAcidSeq reference 2022-10-04 11:41:42 -05:00
Thomas A. Christensen II
c945dc63dd
Release v0.1.1 (#19) 2022-07-21 12:59:47 +00:00
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.
 2022-07-21 12:33:35 +00:00
Thomas A. Christensen II
6a77d6d589
Merge pull request #16 from MillironX/feature/getbases 2022-07-14 15:00:10 +00:00
Thomas A. Christensen II
1cfe128070
Update CHANGELOG 2022-07-13 16:52:11 -05:00
Thomas A. Christensen II
97e1d193a6
Add VCF spec tests for reference and alternate bases 2022-07-13 16:50:00 -05:00
Thomas A. Christensen II
b8e44c7b81
Add public alternate base getter for Variation 2022-07-13 16:49:59 -05:00
Thomas A. Christensen II
cab314ec0b
Add public reference base getter for Variation 2022-07-13 16:49:58 -05:00
Thomas A. Christensen II
ccbe6eed62
Add private alternate base getter for Insertion 2022-07-13 16:49:57 -05:00
Thomas A. Christensen II
1b7c7f86d7
Add private reference base getter for Insertion 2022-07-13 16:49:56 -05:00
Thomas A. Christensen II
145e9e5f88
Add private alternate base getter for Deletion 2022-07-13 16:49:56 -05:00
Thomas A. Christensen II
bc073eaf20
Add private reference base getter for Deletion 2022-07-13 16:49:55 -05:00
Thomas A. Christensen II
c1f47c7b22
Add private alternate base getter for Substitution 2022-07-13 16:49:54 -05:00
Thomas A. Christensen II
73c2c2764f
Add private reference base getter for Substitution 2022-07-13 16:49:53 -05:00
Thomas A. Christensen II
a80ff869ce
Fix reference(::Variation) 
`reference(::Variation)` used the wrong field name. Fix that so I can use
it downstream.
 2022-07-13 16:49:52 -05:00
Thomas A. Christensen II
ece50c1ee9
Remove 32-bit arches from unit testing CI workflow 
32-bit is causing problems in an upstream package, and I'm not sure why, so remove it for now.
 2022-07-11 19:07:07 +00:00
Thomas A. Christensen II
467fa4d261
Fix iterator error in API auto-documentation 2022-07-11 19:04:20 +00:00