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8a71715cd9
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Change v::Haplotype function arguments to h::Haplotype
`v` made sense for a `Variant`, but doesn't for a `Haplotype`, so pretty
things up.
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2023-01-05 11:58:29 -06:00 |
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4e0d88039d
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Update CHANGELOG
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2023-01-05 11:58:29 -06:00 |
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1384783fcc
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Update documentation wording to reflect new type names
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2023-01-05 11:58:29 -06:00 |
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46c84b06bb
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Rename variants.md to haplotypes.md
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2023-01-05 11:58:29 -06:00 |
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5839de3ce1
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Rename Variant type to Haplotype
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2023-01-05 11:58:29 -06:00 |
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44aa41e628
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Rename Variant.jl to Haplotype.jl
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2023-01-05 11:58:29 -06:00 |
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3ef4a92ba2
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Update CHANGELOG
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2023-01-04 11:56:45 -06:00 |
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8ae09aa9a1
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Add linting workflow for PRs
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2023-01-04 11:56:45 -06:00 |
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d29764d2bc
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Apply Blue style to tests file
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2023-01-04 11:56:45 -06:00 |
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fb9ab68cca
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Apply Blue style to docs file
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2023-01-04 11:56:45 -06:00 |
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cb53defe9a
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Add Aqua tests
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2023-01-04 11:56:45 -06:00 |
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1942090cd6
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Remove Windows and Mac CI tests
There is no platform-specific code in this package, so this just slows down
CI with no benefit
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2023-01-04 11:56:45 -06:00 |
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6510ee3fc0
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Add tutorial-type documentation
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2023-01-04 11:56:45 -06:00 |
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134ee771b9
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Correct package install directions in docs
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2023-01-04 11:56:45 -06:00 |
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6f7110caec
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Organize API docs
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2023-01-04 11:56:45 -06:00 |
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2a7d61e43d
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Add docstrings for Variation functions
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2023-01-04 11:56:45 -06:00 |
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673481b40f
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Add docstring for Variation
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2023-01-04 11:56:45 -06:00 |
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ea25ab87dc
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Add docstrings for Variant methods
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2023-01-04 11:56:45 -06:00 |
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f49220782b
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Add docstring for Variant
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2023-01-04 11:56:45 -06:00 |
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f1baf27865
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Add docstring for lendiff(::Edit)
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2023-01-04 11:56:45 -06:00 |
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82ba838614
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Add docstring for mutation(::Edit)
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2023-01-04 11:56:45 -06:00 |
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1f2b116518
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Mark is_valid(::Variation) as private function
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2023-01-04 11:56:45 -06:00 |
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386acba8ab
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Mark edits(::Variant) as private API
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2023-01-04 11:56:45 -06:00 |
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a573693737
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Mark edit(::Variation) as private function
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2023-01-04 11:56:45 -06:00 |
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2f4f5fb5ae
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Mark is_valid(::Variant) as private function
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2023-01-04 11:56:45 -06:00 |
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2719c438f3
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Mark lendiff(::Edit) as private API
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2023-01-04 11:56:45 -06:00 |
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e8457e4241
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Mark mutation(::Edit) as private API
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2023-01-04 11:56:45 -06:00 |
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cb1c429610
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Update getter usage in translate function
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2023-01-04 11:56:45 -06:00 |
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ef4460bbbf
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Replace field accession with getter function usage
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2023-01-04 11:56:45 -06:00 |
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dd405c5f4b
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Refactor _lendiff to use multiple dispatch
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2023-01-04 11:56:45 -06:00 |
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cab3029bc6
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Refactor Edit length to use dispatch instead of type checking
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2023-01-04 11:56:45 -06:00 |
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22d460b15a
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Remove unused argument names from base getters for edits
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2023-01-04 11:56:45 -06:00 |
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da2cbbd528
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Add equals functionality to Deletion
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2023-01-04 11:56:45 -06:00 |
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f08d6eb991
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Add length method for Substitution
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2023-01-04 11:56:45 -06:00 |
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3b2730b5c1
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Add export for translate and reconstruct!
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2023-01-04 11:56:45 -06:00 |
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25c63906dc
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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
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2023-01-04 11:56:45 -06:00 |
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9f9d0899bd
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Move Insertion-related code to edits/Insertion.jl
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2023-01-04 11:56:45 -06:00 |
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b36ab69c72
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Move Deletion-related code to edits/Deletion.jl
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2023-01-04 11:56:45 -06:00 |
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ba9f0e8fb1
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Move Substitution-related code to edits/Substitution.jl
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2023-01-04 11:56:45 -06:00 |
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8c2dd271f3
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Move Variation-related code to Variation.jl
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2023-01-04 11:56:45 -06:00 |
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37965ac7eb
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Move Variant-related code to Variant.jl
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2023-01-04 11:56:45 -06:00 |
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3f631ace8f
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Move Edit-related code to Edit.jl
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2023-01-04 11:56:45 -06:00 |
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a6ad47a568
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Declare Blue style formatting for all new documents
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2023-01-04 11:56:45 -06:00 |
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fb5b7dfacf
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Remove commented-out code
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2023-01-04 11:56:45 -06:00 |
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73d2781ee9
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Update CHANGELOG
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2022-12-17 22:59:39 +00:00 |
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6ba583de4f
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Bump version number in Project.toml
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2022-12-17 22:59:39 +00:00 |
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17f4cd6f39
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Update CHANGELOG
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2022-12-17 22:02:15 +00:00 |
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128a5445ad
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Switch alignment validation to after edit construction
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2022-12-17 22:02:15 +00:00 |
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f9058c5cb3
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Update ranges to allow end position insertions
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2022-12-17 22:02:15 +00:00 |
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5be4dce200
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Add check for soft clips when construction Variants from alignment
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2022-12-17 22:02:15 +00:00 |
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