millironx/SequenceVariation.jl
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Author SHA1 Message Date
Thomas A. Christensen II
3b04aabe9c
wip: Convert Variation to abstract type 2024-11-06 11:06:12 -06:00
Thomas A. Christensen II
21b0a4f526
wip: formatting glitches from git absorb 2024-10-01 11:43:29 -05:00
Thomas A. Christensen II
43a2708a1e
fix: Remove excess type annotations from *Edit types 2024-10-01 11:43:26 -05:00
Thomas A. Christensen II
8814882507
refactor: Use types to power _lendiff function 2024-10-01 11:35:16 -05:00
Thomas A. Christensen II
be731665bc
refactor: Replace BioGenerics functions for Edit with stubs 2024-10-01 11:35:15 -05:00
Thomas A. Christensen II
d702de31b6
feat!: Remove _mutation getter 2024-10-01 11:35:14 -05:00
Thomas A. Christensen II
f5bfd78020
refactor: Change Edit parsing to return *Edit types 2024-10-01 11:35:13 -05:00
Thomas A. Christensen II
3eab426398
feat: Add SubstitutionEdit type 2024-10-01 11:35:12 -05:00
Thomas A. Christensen II
9d882fb1d8
feat: Add InsertionEdit type 2024-10-01 11:35:10 -05:00
Thomas A. Christensen II
7afeede80c
feat: Add DeletionEdit type 2024-10-01 11:35:08 -05:00
Thomas A. Christensen II
1c80158d5b
refactor: Add Base methods for generic Edit 2024-10-01 10:38:47 -05:00
Thomas A. Christensen II
0b10b9ae7b
refactor: Change Edit to abstract type 2024-10-01 10:20:44 -05:00
Thomas A. Christensen II
011651857f Bump version number in Project.toml to 0.2.2 2023-01-28 20:07:48 +00:00
Thomas A. Christensen II
4f39d9c822 Update CHANGELOG for v0.2.2 2023-01-28 20:07:48 +00:00
Thomas A. Christensen II
4f046fef9f Update CHANGELOG 2023-01-28 19:57:10 +00:00
Thomas A. Christensen II
282050d442 Fix validation code for Haplotype 2023-01-28 19:57:10 +00:00
Thomas A. Christensen II
7bd39b1d54 Add tests for _is_valid(::Haplotype) 2023-01-28 19:57:10 +00:00
Thomas A. Christensen II
57ebe391bf Fix tests for _is_valid(::Haplotype) 2023-01-28 19:57:10 +00:00
Thomas A. Christensen II
2a5a5389ec Add tests for _is_valid(::Haplotype) 2023-01-28 19:57:10 +00:00
Thomas A. Christensen II
9776d5a31e Bump version number in Project.toml to 0.2.1 2023-01-11 17:32:15 -06:00
Thomas A. Christensen II
d53acf0df9 Update CHANGELOG for v0.2.1 2023-01-11 17:32:15 -06:00
Thomas A. Christensen II
b7d4831cf2 Update CHANGELOG 2023-01-11 17:17:10 -06:00
Thomas A. Christensen II
2fa5782719 Add more informative errors to _is_valid 2023-01-11 17:17:10 -06:00
Thomas A. Christensen II
4e6c781c60 Update CHANGELOG 2023-01-11 15:01:43 -06:00
Thomas A. Christensen II
d0f55742d6 Add documentation for haplotype reference switching 2023-01-11 15:01:43 -06:00
Thomas A. Christensen II
ecaa995d2b Update API documentation for different translate methods 2023-01-11 15:01:43 -06:00
Thomas A. Christensen II
6a4a39c859 Add tests for translate(::Haplotype) 2023-01-11 15:01:43 -06:00
Thomas A. Christensen II
a61a80d586 Add translate function for Haplotypes 2023-01-11 15:01:43 -06:00
Thomas A. Christensen II
e251b292a7 Fix tests for translate(::Variation) 2023-01-11 15:01:43 -06:00
Thomas A. Christensen II
239b366a1c Add tests for translate(::Variation) 2023-01-11 15:01:43 -06:00
Thomas A. Christensen II
f38f0edb00 Bump version number to 0.2.0 in Project.toml 2023-01-10 12:29:04 -06:00
Thomas A. Christensen II
a437409afc Update test information in READMEs 2023-01-10 12:29:04 -06:00
Thomas A. Christensen II
52d401d623 Update CHANGELOG for v0.2.0 2023-01-10 12:29:04 -06:00
Thomas A. Christensen II
381e4f9736
Add Zenodo badge 2023-01-10 18:12:03 +00:00
Thomas A. Christensen II
e621983dd5 Update CHANGELOG 2023-01-10 12:00:50 -06:00
Thomas A. Christensen II
c360caf9bd Add tests for Variation sorting 2023-01-10 12:00:50 -06:00
Thomas A. Christensen II
0b2879b78c Add isless function for Variation 2023-01-10 12:00:50 -06:00
Thomas A. Christensen II
6119368af3 Add tests for Edit sorting 2023-01-10 12:00:50 -06:00
Thomas A. Christensen II
860ce56b34 Add isless function for Edit 2023-01-10 12:00:50 -06:00
Thomas A. Christensen II
2ff4181dd8
Fix deletion equality function 
Fixes: da2cbbd528 ("Add equals functionality to Deletion")

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
 2023-01-10 11:41:08 -06:00
Thomas A. Christensen II
5bd939a15c Update CHANGELOG 2023-01-10 11:22:06 -06:00
Thomas A. Christensen II
6c86782a2c Update documentation to reflect new reconstruct syntax 2023-01-10 11:22:06 -06:00
Thomas A. Christensen II
b870007826 Add test for reconstruct function 2023-01-10 11:22:06 -06:00
Thomas A. Christensen II
b80dd8c950 Rename reconstruct! function to reconstruct 
The exclamation mark is conventionally used to mark mutating functions, but
reconstruct is no longer mutating, so change the notation.
 2023-01-10 11:22:06 -06:00
Thomas A. Christensen II
adbf0ce7f1 Refactor reconstruct! to use the built-in reference sequence 
reconstruct! previously allow changing of _any_ sequence to match a
haplotype, with no check to see if that sequence is compatible with the
reference sequence the haplotype is based on. Change that to only allow
reconstructing sequences from the reference sequence itself, making this a
non-mutating function.
 2023-01-10 11:22:06 -06:00
Thomas A. Christensen II
8a71715cd9 Change v::Haplotype function arguments to h::Haplotype 
`v` made sense for a `Variant`, but doesn't for a `Haplotype`, so pretty
things up.
 2023-01-05 11:58:29 -06:00
Thomas A. Christensen II
4e0d88039d Update CHANGELOG 2023-01-05 11:58:29 -06:00
Thomas A. Christensen II
1384783fcc Update documentation wording to reflect new type names 2023-01-05 11:58:29 -06:00
Thomas A. Christensen II
46c84b06bb Rename variants.md to haplotypes.md 2023-01-05 11:58:29 -06:00
Thomas A. Christensen II
5839de3ce1 Rename Variant type to Haplotype 2023-01-05 11:58:29 -06:00