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@alyst alyst commented Nov 25, 2021

Update docs with alignment position

This template is rather extensive. Fill out all that you can, if are a new contributor or you're unsure about any section, leave it unchanged and a reviewer will help you 😄. This template is simply a tool to help everyone remember the BioJulia guidelines, if you feel anything in this template is not relevant, simply delete it.

Types of changes

This PR implements the following changes:
No functional changes, just update the documentation with AlignmentAnchor.alnpos introduced by #44.
Also serves as a gentle reminder to tag a new minor version, since this anchor functionality is only available in the master branch ;)

  • ✨ New feature (A non-breaking change which adds functionality).
  • 🐛 Bug fix (A non-breaking change, which fixes an issue).
  • 💥 Breaking change (fix or feature that would cause existing functionality to change).

📋 Additional detail

  • If you have implemented new features or behaviour

    • Provide a description of the addition in as many details as possible.

    • Provide justification of the addition.

    • Provide a runnable example of use of your addition. This lets reviewers
      and others try out the feature before it is merged or makes it's way to release.

  • If you have changed current behaviour...

    • Describe the behaviour prior to you changes

    • Describe the behaviour after your changes and justify why you have made the changes,
      Please describe any breakages you anticipate as a result of these changes.

    • Does your change alter APIs or existing exposed methods/types?
      If so, this may cause dependency issues and breakages, so the maintainer
      will need to consider this when versioning the next release.

    • If you are implementing changes that are intended to increase performance, you
      should provide the results of a simple performance benchmark exercise
      demonstrating the improvement. Especially if the changes make code less legible.

☑️ Checklist

  • 🎨 The changes implemented is consistent with the julia style guide.
  • 📘 I have updated and added relevant docstrings, in a manner consistent with the documentation styleguide.
  • 📘 I have added or updated relevant user and developer manuals/documentation in docs/src/.
  • 🆗 There are unit tests that cover the code changes I have made.
  • 🆗 The unit tests cover my code changes AND they pass.
  • 📝 I have added an entry to the [UNRELEASED] section of the manually curated CHANGELOG.md file for this repository.
  • 🆗 All changes should be compatible with the latest stable version of Julia.
  • 💭 I have commented liberally for any complex pieces of internal code.

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codecov bot commented Nov 25, 2021

Codecov Report

Merging #61 (f0ab859) into master (5a3354e) will increase coverage by 0.31%.
The diff coverage is n/a.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #61      +/-   ##
==========================================
+ Coverage   87.64%   87.95%   +0.31%     
==========================================
  Files          16       16              
  Lines        1052     1121      +69     
==========================================
+ Hits          922      986      +64     
- Misses        130      135       +5     
Impacted Files Coverage Δ
src/pairwise/algorithms/banded_needleman_wunsch.jl 75.00% <0.00%> (-1.36%) ⬇️
src/pairwise/algorithms/needleman_wunsch.jl 83.59% <0.00%> (-0.71%) ⬇️
src/anchors.jl 100.00% <0.00%> (ø)
src/pairwise/algorithms/edit_distance.jl 100.00% <0.00%> (ø)
src/pairwise/algorithms/hamming_distance.jl 100.00% <0.00%> (ø)
src/pairwise/alignment.jl 98.26% <0.00%> (+0.04%) ⬆️
src/submat.jl 98.29% <0.00%> (+0.21%) ⬆️
src/pairwise/algorithms/common.jl 90.62% <0.00%> (+0.30%) ⬆️
src/models.jl 85.50% <0.00%> (+0.43%) ⬆️
src/pairwise/algorithms/smith_waterman.jl 89.00% <0.00%> (+0.45%) ⬆️
... and 4 more

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@TransGirlCodes
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Thanks @alyst!

@TransGirlCodes TransGirlCodes merged commit 36a5e75 into BioJulia:master Nov 25, 2021
@alyst
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alyst commented Nov 25, 2021

Sorry, I've realized that the alignment anchor SVG figure also have to be updated. I'm working on it at the moment.

@alyst alyst mentioned this pull request Nov 25, 2021
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