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feature/alignment

feature/niave-abstract-types

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• 74363b5505
  
  wip: Remove includes from Edit.jl feature/niave-abstract-types Thomas A. Christensen II 2024-11-06 11:06:39 -0600
• 3b04aabe9c
  
  wip: Convert Variation to abstract type Thomas A. Christensen II 2024-11-06 11:06:12 -0600
• 21b0a4f526
  
  wip: formatting glitches from git absorb Thomas A. Christensen II 2024-10-01 11:36:03 -0500
• 43a2708a1e
  
  fix: Remove excess type annotations from *Edit types Thomas A. Christensen II 2024-10-01 11:09:32 -0500
• 8814882507
  
  refactor: Use types to power _lendiff function Thomas A. Christensen II 2024-10-01 11:07:46 -0500
• be731665bc
  
  refactor: Replace BioGenerics functions for Edit with stubs Thomas A. Christensen II 2024-10-01 11:01:43 -0500
• d702de31b6
  
  feat!: Remove _mutation getter Thomas A. Christensen II 2024-10-01 10:59:09 -0500
• f5bfd78020
  
  refactor: Change Edit parsing to return *Edit types Thomas A. Christensen II 2024-10-01 10:57:56 -0500
• 3eab426398
  
  feat: Add SubstitutionEdit type Thomas A. Christensen II 2024-10-01 10:54:43 -0500
• 9d882fb1d8
  
  feat: Add InsertionEdit type Thomas A. Christensen II 2024-10-01 10:48:06 -0500
• 7afeede80c
  
  feat: Add DeletionEdit type Thomas A. Christensen II 2024-10-01 10:40:15 -0500
• 1c80158d5b
  
  refactor: Add Base methods for generic Edit Thomas A. Christensen II 2024-10-01 10:38:47 -0500
• 0b10b9ae7b
  
  refactor: Change Edit to abstract type Thomas A. Christensen II 2024-10-01 10:20:44 -0500
• 373e485802
  
  chore: Update CHANGELOG feature/alignment Thomas A. Christensen II 2023-04-08 20:51:09 -0500
• 6b2bd018e2
  
  docs: Add examples of alignment getters Thomas A. Christensen II 2023-04-08 20:44:21 -0500
• 341faa45e3
  
  docs: Add autodocs for cigar Thomas A. Christensen II 2023-04-08 20:43:50 -0500
• 8458f74053
  
  docs: Add autodocs for alignment Thomas A. Christensen II 2023-04-08 20:43:30 -0500
• 2d16c0b7b6
  
  docs: Rename 'Variants' header to 'Haplotypes' Thomas A. Christensen II 2023-04-08 20:40:17 -0500
• db170730f0
  
  test: Add test for alignment(::Haplotype) Thomas A. Christensen II 2023-04-04 12:32:13 -0500
• 4817c8016a
  
  feat: Add alignment(::Haplotype) function Thomas A. Christensen II 2023-04-04 11:50:24 -0500
• 95ef4fdc62
  
  test: Add tests for cigar(::Haplotype) Thomas A. Christensen II 2023-04-04 11:36:27 -0500
• 719a123992
  
  feat: Add cigar(::Haplotype) function Thomas A. Christensen II 2023-04-04 11:34:35 -0500
• e84f765357
  
  feat: Add _cigar_between(::Variation, ::Variation) function Thomas A. Christensen II 2023-04-04 11:32:21 -0500
• c3a7788dbd
  
  feat: Add _cigar(::Variation) function Thomas A. Christensen II 2023-04-04 11:30:59 -0500
• 011651857f Bump version number in Project.toml to 0.2.2 master Thomas A. Christensen II 2023-01-28 14:03:02 -0600
• 4f39d9c822 Update CHANGELOG for v0.2.2 Thomas A. Christensen II 2023-01-28 14:02:13 -0600
• 4f046fef9f Update CHANGELOG Thomas A. Christensen II 2023-01-28 13:47:37 -0600
• 282050d442 Fix validation code for Haplotype Thomas A. Christensen II 2023-01-24 12:04:29 -0600
• 7bd39b1d54 Add tests for _is_valid(::Haplotype) Thomas A. Christensen II 2023-01-21 18:10:04 -0600
• 57ebe391bf Fix tests for _is_valid(::Haplotype) Thomas A. Christensen II 2023-01-21 18:10:46 -0600
• 2a5a5389ec Add tests for _is_valid(::Haplotype) Thomas A. Christensen II 2023-01-21 18:10:04 -0600
• 9776d5a31e Bump version number in Project.toml to 0.2.1 Thomas A. Christensen II 2023-01-11 17:26:29 -0600
• d53acf0df9 Update CHANGELOG for v0.2.1 Thomas A. Christensen II 2023-01-11 17:25:38 -0600
• b7d4831cf2 Update CHANGELOG Thomas A. Christensen II 2023-01-11 16:21:59 -0600
• 2fa5782719 Add more informative errors to _is_valid Thomas A. Christensen II 2023-01-11 16:21:16 -0600
• 4e6c781c60 Update CHANGELOG Thomas A. Christensen II 2023-01-11 14:58:00 -0600
• d0f55742d6 Add documentation for haplotype reference switching Thomas A. Christensen II 2023-01-05 14:58:27 -0600
• ecaa995d2b Update API documentation for different translate methods Thomas A. Christensen II 2023-01-05 13:10:24 -0600
• 6a4a39c859 Add tests for translate(::Haplotype) Thomas A. Christensen II 2023-01-05 14:45:31 -0600
• a61a80d586 Add translate function for Haplotypes Thomas A. Christensen II 2023-01-05 13:09:12 -0600
• e251b292a7 Fix tests for translate(::Variation) Thomas A. Christensen II 2023-01-05 14:34:22 -0600
• 239b366a1c Add tests for translate(::Variation) Thomas A. Christensen II 2023-01-05 14:32:26 -0600
• f38f0edb00 Bump version number to 0.2.0 in Project.toml Thomas A. Christensen II 2023-01-10 12:19:48 -0600
• a437409afc Update test information in READMEs Thomas A. Christensen II 2023-01-10 12:19:26 -0600
• 52d401d623 Update CHANGELOG for v0.2.0 Thomas A. Christensen II 2023-01-10 12:17:42 -0600
• 381e4f9736
  Add Zenodo badge Thomas A. Christensen II 2023-01-10 18:12:03 +0000
• e621983dd5 Update CHANGELOG Thomas A. Christensen II 2023-01-10 11:09:10 -0600
• c360caf9bd Add tests for Variation sorting Thomas A. Christensen II 2023-01-10 11:19:58 -0600
• 0b2879b78c Add isless function for Variation Thomas A. Christensen II 2023-01-10 11:07:30 -0600
• 6119368af3 Add tests for Edit sorting Thomas A. Christensen II 2023-01-10 11:17:26 -0600
• 860ce56b34 Add isless function for Edit Thomas A. Christensen II 2023-01-10 11:17:08 -0600
• 2ff4181dd8
  
  Fix deletion equality function Thomas A. Christensen II 2023-01-10 11:41:08 -0600
• 5bd939a15c Update CHANGELOG Thomas A. Christensen II 2023-01-05 12:41:46 -0600
• 6c86782a2c Update documentation to reflect new reconstruct syntax Thomas A. Christensen II 2023-01-05 12:41:35 -0600
• b870007826 Add test for reconstruct function Thomas A. Christensen II 2023-01-05 12:33:05 -0600
• b80dd8c950 Rename reconstruct! function to reconstruct Thomas A. Christensen II 2023-01-05 12:32:54 -0600
• adbf0ce7f1 Refactor reconstruct! to use the built-in reference sequence Thomas A. Christensen II 2023-01-05 12:30:03 -0600
• 8a71715cd9 Change v::Haplotype function arguments to h::Haplotype Thomas A. Christensen II 2023-01-04 14:16:48 -0600
• 4e0d88039d Update CHANGELOG Thomas A. Christensen II 2023-01-04 13:15:36 -0600
• 1384783fcc Update documentation wording to reflect new type names Thomas A. Christensen II 2023-01-04 13:05:56 -0600
• 46c84b06bb Rename variants.md to haplotypes.md Thomas A. Christensen II 2023-01-04 12:48:54 -0600
• 5839de3ce1 Rename Variant type to Haplotype Thomas A. Christensen II 2023-01-04 12:45:25 -0600
• 44aa41e628 Rename Variant.jl to Haplotype.jl Thomas A. Christensen II 2023-01-04 12:38:51 -0600
• 3ef4a92ba2 Update CHANGELOG Thomas A. Christensen II 2023-01-04 11:13:38 -0600
• 8ae09aa9a1 Add linting workflow for PRs Thomas A. Christensen II 2023-01-03 22:02:09 -0600
• d29764d2bc Apply Blue style to tests file Thomas A. Christensen II 2023-01-03 21:59:42 -0600
• fb9ab68cca Apply Blue style to docs file Thomas A. Christensen II 2023-01-03 21:59:31 -0600
• cb53defe9a Add Aqua tests Thomas A. Christensen II 2023-01-03 16:22:04 -0600
• 1942090cd6 Remove Windows and Mac CI tests Thomas A. Christensen II 2023-01-03 16:03:47 -0600
• 6510ee3fc0 Add tutorial-type documentation Thomas A. Christensen II 2023-01-03 16:01:59 -0600
• 134ee771b9 Correct package install directions in docs Thomas A. Christensen II 2022-12-31 15:16:34 -0600
• 6f7110caec Organize API docs Thomas A. Christensen II 2022-12-31 15:15:44 -0600
• 2a7d61e43d Add docstrings for Variation functions Thomas A. Christensen II 2022-12-31 14:45:33 -0600
• 673481b40f Add docstring for Variation Thomas A. Christensen II 2022-12-31 13:39:56 -0600
• ea25ab87dc Add docstrings for Variant methods Thomas A. Christensen II 2023-01-03 21:34:28 -0600
• f49220782b Add docstring for Variant Thomas A. Christensen II 2022-12-30 15:48:47 -0600
• f1baf27865 Add docstring for lendiff(::Edit) Thomas A. Christensen II 2023-01-03 20:03:37 -0600
• 82ba838614 Add docstring for mutation(::Edit) Thomas A. Christensen II 2023-01-03 20:01:13 -0600
• 1f2b116518 Mark is_valid(::Variation) as private function Thomas A. Christensen II 2022-12-31 14:46:23 -0600
• 386acba8ab Mark edits(::Variant) as private API Thomas A. Christensen II 2023-01-03 21:35:16 -0600
• a573693737 Mark edit(::Variation) as private function Thomas A. Christensen II 2023-01-03 21:28:20 -0600
• 2f4f5fb5ae Mark is_valid(::Variant) as private function Thomas A. Christensen II 2023-01-03 20:19:58 -0600
• 2719c438f3 Mark lendiff(::Edit) as private API Thomas A. Christensen II 2023-01-03 20:02:56 -0600
• e8457e4241 Mark mutation(::Edit) as private API Thomas A. Christensen II 2023-01-03 20:00:42 -0600
• cb1c429610 Update getter usage in translate function Thomas A. Christensen II 2023-01-03 15:01:31 -0600
• ef4460bbbf Replace field accession with getter function usage Thomas A. Christensen II 2023-01-03 20:07:31 -0600
• dd405c5f4b Refactor _lendiff to use multiple dispatch Thomas A. Christensen II 2023-01-03 20:11:08 -0600
• cab3029bc6 Refactor Edit length to use dispatch instead of type checking Thomas A. Christensen II 2022-12-30 14:54:03 -0600
• 22d460b15a Remove unused argument names from base getters for edits Thomas A. Christensen II 2022-12-30 14:47:50 -0600
• da2cbbd528 Add equals functionality to Deletion Thomas A. Christensen II 2022-12-30 14:46:42 -0600
• f08d6eb991 Add length method for Substitution Thomas A. Christensen II 2022-12-30 14:45:31 -0600
• 3b2730b5c1 Add export for translate and reconstruct! Thomas A. Christensen II 2023-01-03 16:01:37 -0600
• 25c63906dc Move exports to top of file Thomas A. Christensen II 2022-12-30 14:29:08 -0600
• 9f9d0899bd Move Insertion-related code to edits/Insertion.jl Thomas A. Christensen II 2022-12-30 14:43:55 -0600
• b36ab69c72 Move Deletion-related code to edits/Deletion.jl Thomas A. Christensen II 2022-12-30 14:38:59 -0600
• ba9f0e8fb1 Move Substitution-related code to edits/Substitution.jl Thomas A. Christensen II 2022-12-30 14:35:55 -0600
• 8c2dd271f3 Move Variation-related code to Variation.jl Thomas A. Christensen II 2022-12-30 14:25:14 -0600
• 37965ac7eb Move Variant-related code to Variant.jl Thomas A. Christensen II 2022-12-30 14:22:45 -0600
• 3f631ace8f Move Edit-related code to Edit.jl Thomas A. Christensen II 2022-12-30 14:20:03 -0600
• a6ad47a568 Declare Blue style formatting for all new documents Thomas A. Christensen II 2022-12-30 14:10:19 -0600