It supports Ns (genome.ucsc.edu/FAQ/FAQforma...), but I can see it being problematic when more letters are needed. But (a) it seems fixable given how long it's been around? (b) A good proportion of research is aligning short reads to reference DNA so those applications could have been more efficient

I wonder why the 2bit format wasn't more popular. It's been around for a while. It's fantastic for reference genome random access in tgv.

If you want to learn Rust, contributing to tgv is a great way! A genome viewer consists of many small, isolated components. Many improvements need <10 lines of code change. You can find them by searching "FIXME" comments. Let's make open source better together! bsky.app/profile/robp...

I learned so many things with tgv. Writing a mini-interpreter is one of them. Now you can filter reads by:

FILTER BASE(1234)=C

It will be extended to a SQL-like mini language:

ORDER by STRAND WHERE BASE(123)=C AND MAPQ>=30

The parse is built and the backend is under development.

The allele frequency stacked-bar is trickier: we need to calculate how stacks overlap and use the foreground/background trick + █▇▆▅▄▃▂▁ characters. This became a sweet ratatui widget: github.com/ratatui/rata...

The half-block trick is yet to be implemented to alignments. Contribution is open!

The minimal resolution of terminal graphics is one character. To visualize more information, we use Unicode tricks:

At 2x zoom, to render 2 bases per cell, we use the half-block trick: render the "▌" Unicode character with the foreground of first base color and the background being the second base.

These are needed by another library and not my enums 😂 I did find some helper function tho users.rust-lang.org/t/nom-how-to...

In this case it's a bunch of custom enums in the library unfortunately :(

I think ai is most helpful at making learning less scary (not sure I would have learned rust as fast as I did without help). But the actual learning still needs to happen.

My day job is mostly Python - @pola.rs is expressive enough that typing out exactly what I want is not much more keystrokes than asking AI. Hallucinations are getting so bad that it's hurting the science. The new Python type checkers (pyrefly or ty) are much bigger productivity boost.

These two weeks was an epic refactor to get rid of Claude's vibe-coded mess. I finally leaned how databases and requests actually work in Rust. It's so simple and nice.

github.com/zeqianli/tgv...

This is still at an early stage. This is the best I got 😅: github.com/zeqianli/tgv...

Thanks for posting! tgv is still at a very early stage so expect bugs :)

Congratulations!