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github.com/BioJulia/SequenceVariation.jl

Biological sequence variation
https://github.com/BioJulia/SequenceVariation.jl

Bump version number in Project.toml to 0.2.2

011651857f5ce1580b3a8ba60f692ea1cfa03b49 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG for v0.2.2

4f39d9c8229d9cac172fa894f633ccf4b4a4460c authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Fix validation code for `Haplotype`

282050d442e3e88fe60d0e9fac37d1c10bd07ae4 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for _is_valid(::Haplotype)

7bd39b1d54418040d69a420cc0e06ec573f52a11 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

4f046fef9f0e1bfd0e5f8d9ec0b191006d407d33 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Fix tests for _is_valid(::Haplotype)

57ebe391bfbe7590d71018aa503b69ec98b75d53 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for _is_valid(::Haplotype)

2a5a5389ecfd17d458139541ea017635197aff62 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Bump version number in Project.toml to 0.2.1

9776d5a31e042845f5a812d4f67b72177603ad90 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG for v0.2.1

d53acf0df94f284a86b2853203248d502574e3a6 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

b7d4831cf2bbdc101131c0ee6810239c5f592e53 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add more informative errors to `_is_valid`

2fa57827195b9a3e5d95ce7b883664a7a696d3eb authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add translate function for Haplotypes

a61a80d586bc878e283bb2dabea67f3b6ad6c22b authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Fix tests for `translate(::Variation)`

e251b292a721c739c2da5eed53902e5fe696c5c8 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for `translate(::Variation)`

239b366a1c2cd2f6f5867bb092f4a12537951cd8 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

4e6c781c602e4ad944802f37854122080b25c8df authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add documentation for haplotype reference switching

d0f55742d6d9b258c9d2f3da1a6e9477667ae57e authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update API documentation for different `translate` methods

ecaa995d2b63d82117f44f192298cf32d7887596 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for `translate(::Haplotype)`

6a4a39c85936236a63c9049bad40292c7ed78ebb authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Bump version number to 0.2.0 in Project.toml

f38f0edb00a1e6ef04b105ff7dd0e16379741939 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update test information in READMEs

a437409afcf8e02a5fd78e7eeaa06a1d313f402b authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG for v0.2.0

52d401d6237d7f553eaef36e5ffad5279a363832 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add Zenodo badge

381e4f97366f760ac7857f408e1d52f35a95d6d5 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

e621983dd53afd1758fc717ef2dbac38aaacea8e authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for Variation sorting

c360caf9bdc9edc27d024c78cf444092433bc369 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add `isless` function for `Variation`

0b2879b78cb8a8e5a2d8592347ddfa6462af6701 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for Edit sorting

6119368af373a5821f798e8371e0fd90361ab0bd authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add `isless` function for `Edit`

860ce56b3401686d9ffd98aa304f7aa19ccfb549 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Fix deletion equality function

Fixes: da2cbbd5282b ("Add equals functionality to Deletion")

Signed-off-by: Thomas A. Christens...

2ff4181dd8a4f5fc173d2b694194cac9fa690d21 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Rename reconstruct! function to reconstruct

The exclamation mark is conventionally used to mark mutating functions, but
reconstruct is no lo...

b80dd8c9501cff1e87760233f77cc823b7069ae5 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Refactor `reconstruct!` to use the built-in reference sequence

reconstruct! previously allow changing of _any_ sequence to match a
haplotype, with no check to ...

adbf0ce7f1eb27af9e0475e65c0486c11f324cd3 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

5bd939a15cce7159fcdb6e9123ae9a4c6f217465 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update documentation to reflect new reconstruct syntax

6c86782a2c0a9a162771cce0290420e1c464120c authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for reconstruct function

b87000782664c8ed5150e7466283c1e89eb8049c authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Change `v::Haplotype` function arguments to `h::Haplotype`

`v` made sense for a `Variant`, but doesn't for a `Haplotype`, so pretty
things up.

8a71715cd9fa3826da930f0caa965c109810232f authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

4e0d88039db141d7fc1edfe6c2f36e0c84380db6 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update documentation wording to reflect new type names

1384783fccdf5842c4ae1ee088abce566d8e741b authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Rename variants.md to haplotypes.md

46c84b06bb541e684c26d0c301b319e189809bb6 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Rename `Variant` type to `Haplotype`

5839de3ce1e406756953a4e55ce3a630349d7c9a authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Rename Variant.jl to Haplotype.jl

44aa41e6285ae3855f7e4495dd9baa582cef4116 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Refactor Edit length to use dispatch instead of type checking

cab3029bc6cdc8821eaa08c3b5d857a0d886b079 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Remove unused argument names from base getters for edits

22d460b15a8d366594e32a7c026ded20cfeb725c authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add equals functionality to Deletion

da2cbbd5282b93b6c8399c943734057fa55d61f0 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add length method for Substitution

f08d6eb99167f1a82185bf9626c425b701e874c8 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add export for translate and reconstruct!

3b2730b5c1432d41a35f835f0130ec8e737506de authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Move exports to top of file

Per Blue style, exports should be one per line, and appear immediately
after using statements. R...

25c63906dc60ac2efc94be67d8a273a04b7b9251 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Move Insertion-related code to edits/Insertion.jl

9f9d0899bdff26f936bc90e2b99ec2b395bf5071 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Move Deletion-related code to edits/Deletion.jl

b36ab69c728bf287219e5ff9fea1926cb0cdb7ae authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Move Substitution-related code to edits/Substitution.jl

ba9f0e8fb155b810771ea6261b6526145d8e6215 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Move Variation-related code to Variation.jl

8c2dd271f3f51c14b945fb1a3d6c8e416f8a4a27 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Move Variant-related code to Variant.jl

37965ac7eb80992a0580d86b7e4d9a67b65e752f authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Move Edit-related code to Edit.jl

3f631ace8fc1979ddf3104c143f4582760c97b4e authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Declare Blue style formatting for all new documents

a6ad47a5687b89e15de444582200d8924deadf1a authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Remove commented-out code

fb5b7dfacf695a5df5540271d068690afec0e3e1 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

3ef4a92ba268faa509547bb9774d070aba38cdd5 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add linting workflow for PRs

8ae09aa9a1bbd0376d51483b4134d968b242863e authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Apply Blue style to tests file

d29764d2bce83822b83e4d8581d7eceb25b43f63 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Apply Blue style to docs file

fb9ab68cca925e138fd9dc1ebbccdb23c6257f89 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add Aqua tests

cb53defe9adaa652af8caf5ff1709ca5566a2fd4 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Remove Windows and Mac CI tests

There is no platform-specific code in this package, so this just slows down
CI with no benefit

1942090cd610108a8056d6b955b17519ab2e3bb1 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add tutorial-type documentation

6510ee3fc030992f93562c4c072b57f2b2c621c2 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Correct package install directions in docs

134ee771b9963819b336655c552b70278eeab775 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Organize API docs

6f7110caec1894d89b5a41b4d5688d4fd8701760 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add docstrings for Variation functions

2a7d61e43d61d8ace9cfbe7fb157a5e707683945 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add docstring for Variation

673481b40f98049c0d4c37f50a9e28a01c4d4965 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add docstrings for Variant methods

ea25ab87dcc6d8c03748af9db830c05dc485b45d authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add docstring for Variant

f49220782b8c6535d864ae55815c11389c605e9f authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add docstring for `lendiff(::Edit)`

f1baf27865125b6d86ff991ce2e8a62740d5eb19 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add docstring for `mutation(::Edit)`

82ba8386147f6b60d0dc58dd868f941e2d2bf4ce authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Mark is_valid(::Variation) as private function

1f2b116518ebea297c71e69e026d25fc4efbbffc authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Mark `edits(::Variant)` as private API

386acba8ab0a17879ac4e1afb884d38fcd8be87a authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Mark `edit(::Variation)` as private function

a573693737e2ca4edc3f11d65e652b2fd0ce0d1e authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Mark `is_valid(::Variant)` as private function

2f4f5fb5aeeeaf42d23dd740de8e6d124c7499cb authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Mark `lendiff(::Edit)` as private API

2719c438f3261d6b0345e70afd3ffff6a97b7543 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Mark `mutation(::Edit)` as private API

e8457e4241467448d449387bae6d6d0b2a50fef3 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update getter usage in translate function

cb1c429610e214de017cb57726ecc539669dc24b authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Replace field accession with getter function usage

ef4460bbbf0172cf68edb65397616dba8b7fa0f0 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Refactor _lendiff to use multiple dispatch

dd405c5f4b75d8d201a684165da1747eac039db0 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

73d2781ee945ebc64f6b5599ef0838f4cab585e9 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Bump version number in Project.toml

6ba583de4f42f0fc711085705c024e441b265d67 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

17f4cd6f395610f30ee0856f55a473b830378455 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Switch alignment validation to after edit construction

128a5445ad566ee4c0bf9f9d0331ec1cd1e5e41c authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update ranges to allow end position insertions

f9058c5cb393a2a616535843eba15a3c2ed0f3b4 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add check for soft clips when construction Variants from alignment

5be4dce200ad3e4f9ea121c9159e5ec30d7c6eb1 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add Variation-level validation for Variants

Testing indicates that some Variants (particularly those with insertions
and/or clips at the sen...

d8435be115d38d450a283f2ed4a8b212b192dce0 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add equality function for Variant

91c3acc85ee9c9aec558b94f3b41fa38d9d84931 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for ending substitutions being invalid

f9e76d60d6d23530b449062e4e5ac7998f25a978 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for combined clips

abff6692d49052e88966d40fdb92194a7290b0e9 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for soft clips

dd00231840f0288a30c6da2c63925a581e559204 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for ending insertion

3b61ccefb5eb783d819468680bc77bb8d198ec3d authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG for v0.1.3

b45081a56e1602dc546ee0f75787611b57726418 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Bump version number in Project.toml

00495d4e14537454a5f0a952d5e9fc29d24e1279 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

3ed27f0c4e53c2662da4ddd1af224fed733de44c authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add type parameterization to variations getter

I have encountered some cases where having a non-parameterized vector can
crash a downstream pro...

3b33c85d00db3437998fdc93075b37399204ff42 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG for v0.1.2

752b482a0b7ba9374ec43032b7499b65ab721762 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Update project version number to v0.1.2

4de936cc83abfdcd037c2eb9874f885bd8db9df1 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

780a5add8a01b0b0db1467ff8ce1639deba6c983 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add ranged dependency compats

b20d603f95e624aed55e1c2698f043eadc0d2da4 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Remove unused AminoAcidSeq reference

f7278bd7d7345aafe399c0a7622027de12bc800a authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Release v0.1.1 (#19)

c945dc63ddabdbcc7b0953afd8033d2b70d7fe1c authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add constructor for Variant based on Variations

A Variant is a collection of Variations, right? Unfortunately there was no
way to convert a coll...

1bbb85153c176ff1fb4c909136b0e8ea8369de9e authored over 2 years ago by Thomas A. Christensen II <[email protected]>