Klangina commented 1 month ago

Refactored and merged R/tree.R CreateFA2Tree and ConvertFA2Tree.
- Parametrized every hardcoded value and path in ConvertFA2Tree
- Refactored convertAlignment2Trees to support running both modes.
- Backward compatible
- Updated all documentation for R/tree.R

Description

What kind of change(s) are included?

[ ] Feature (adds or updates new capabilities)
[ ] Bug fix (fixes an issue).
[x] Enhancement (adds functionality).
[ ] Breaking change (these changes would cause existing functionality to not work as expected).

Please ensure that all boxes are checked before indicating that this pull request is ready for review.

[x] I have read and followed the CONTRIBUTING.md guidelines.
[x] I have searched for existing content to ensure this is not a duplicate.
[x] I have performed a self-review of these additions (including spelling, grammar, and related).
[x] I have added comments to my code to help provide understanding.
[ ] I have added a test which covers the code changes found within this PR.
[x] I have deleted all non-relevant text in this pull request template.
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Klangina commented 1 month ago

@jananiravi I have made the changes. Kindly review/guide me for further steps if required in this Issue.

Klangina commented 1 month ago

FIxed the commit message to reflect the correct issue number

Klangina commented 4 weeks ago

@epbrenner @jananiravi : Made changes as per recommendations before. Kindly review.