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docs: Update installation instructions and add new CLI arguments by fxwiegand · Pull Request #374 · alignoth/alignoth · GitHub

docs: Update installation instructions and add new CLI arguments - #374

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fxwiegand merged 1 commit into
mainfrom
update-readme
Oct 16, 2025
Merged

fxwiegand merged 1 commit into
mainfrom
update-readme

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This pull request updates the documentation for alignoth in the README.md file, focusing on clarifying available options and improving installation instructions. The most important changes include enhanced descriptions for highlighting options, and the addition of new installation methods and guidance.

Improvements to visualization options:

  • Updated the highlight option to support named intervals and single base positions, providing clearer examples for users.
  • Added descriptions for new vcf and bed options, allowing users to highlight regions or variants from VCF and BED files in visualizations.

Installation instructions:

  • Added a new installation method using pixi, with a direct command for global installation.
  • Improved Bioconda installation instructions by specifying channel order and highlighting its importance for successful installation.

fxwiegand merged commit f0a594a into main Oct 16, 2025
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fxwiegand deleted the update-readme branch October 16, 2025 10:34

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 50.08%. Comparing base (1998228) to head (3242fa8).
⚠️ Report is 2 commits behind head on main.
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Additional details and impacted files
@@           Coverage Diff           @@
##             main     #374   +/-   ##
=======================================
  Coverage   50.08%   50.08%           
=======================================
  Files           6        6           
  Lines         617      617           
=======================================
  Hits          309      309           
  Misses        308      308           

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