Gavin's work on read alignment

[learner-long-life]

Gavin mentioned in Discord that his last work this spring when attempting to process the whole transcriptome into a suffix tree was on read_alignment branch.

During last week's Smarty Plants meeting, we discovered that the main method in rusty-plants/main.rs was commented out, as well as algorithms/better_align.rs so this started our exploration of how anyone of us can kickstart suffix tree building on our own machines.

This is the start of making a "Hello Plants" tutorial for anyone to try out Smarty Plants for themselves, it may be interesting for your work @EvergreenSpock .

[learner-long-life]

@AbyssalRemark has agreed to be the primary reviewer of rebasing @Gavin-Bowers read_alignment branch off of main , so that we can merge with the directory rename to rusty-plants. I may have borked something up, so please have a look and double-check.

I also installed git-lfs with Homebrew and ran git lfs pull in the repo to resolve data/ large files.

It should be 9.9M lines in the full version as shown below. If you see it as 3 lines, that's just the ref in git LFS that needs to be downloaded.

 wc ../data/ref_genome.fna 
 9965732 9966398 807222515 ../data/ref_genome.fna

It built and ran, and is currently still running on my MacBook Pro with M1 (ARM).

[learner-long-life]

Seems fine. I don't like this commenting out dead code but that's what happens when your try to measure contribution.

GitHub counts both deletions and additions. We could talk about passing the same test with net code deletions as one way to show refactoring.