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[Feature]: Add alignment and cigar getters #42

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@MillironX MillironX commented Apr 9, 2023

Closes #39

Types of changes

This PR implements the following changes:

  • ✨ 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

Add methods to BioAlignments.alignment and BioAlignments.cigar to pull a PairwiseAlignment and CIGAR string from a Haplotype, respectively.

See the updated docs for runnable examples.

☑️ 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 Apr 9, 2023

Codecov Report

Patch coverage: 100.00% and project coverage change: +3.53 🎉

Comparison is base (0116518) 86.52% compared to head (373e485) 90.06%.

Additional details and impacted files
@@            Coverage Diff             @@
##           master      #42      +/-   ##
==========================================
+ Coverage   86.52%   90.06%   +3.53%     
==========================================
  Files           7        7              
  Lines         282      312      +30     
==========================================
+ Hits          244      281      +37     
+ Misses         38       31       -7     
Flag Coverage Δ
unittests 90.06% <100.00%> (+3.53%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/SequenceVariation.jl 100.00% <ø> (ø)
src/Haplotype.jl 93.33% <100.00%> (+0.89%) ⬆️
src/Variation.jl 86.86% <100.00%> (+3.33%) ⬆️

... and 1 file with indirect coverage changes

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@MillironX MillironX changed the title feat: Add _cigar(::Variation) function [Feature]: Add alignment and cigar getters Apr 9, 2023
@MillironX MillironX requested review from jakobnissen and a team April 9, 2023 01:52
@MillironX MillironX marked this pull request as draft June 24, 2023 23:33
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[Feature]: Add getter for alignment of a haplotype to its reference
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