Commit graph

137 commits

Author SHA1 Message Date
c360caf9bd Add tests for Variation sorting 2023-01-10 12:00:50 -06:00
0b2879b78c Add isless function for Variation 2023-01-10 12:00:50 -06:00
6119368af3 Add tests for Edit sorting 2023-01-10 12:00:50 -06:00
860ce56b34 Add isless function for Edit 2023-01-10 12:00:50 -06:00
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
5bd939a15c Update CHANGELOG 2023-01-10 11:22:06 -06:00
6c86782a2c Update documentation to reflect new reconstruct syntax 2023-01-10 11:22:06 -06:00
b870007826 Add test for reconstruct function 2023-01-10 11:22:06 -06:00
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
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
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
4e0d88039d Update CHANGELOG 2023-01-05 11:58:29 -06:00
1384783fcc Update documentation wording to reflect new type names 2023-01-05 11:58:29 -06:00
46c84b06bb Rename variants.md to haplotypes.md 2023-01-05 11:58:29 -06:00
5839de3ce1 Rename Variant type to Haplotype 2023-01-05 11:58:29 -06:00
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