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.
tgv 0.1.0 release: github.com/zeqianli/tgv
- Rich CIGAR and base visualization
- Allele frequency visualization
- VCF and BED file support
- Mouse dragging and hovering
- Filter alignment
Now 90% of what I need from IGV can be done in the terminal.
Some interesting behind-the-scenes:
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.
tgv 0.1.0 release: github.com/zeqianli/tgv
- Rich CIGAR and base visualization
- Allele frequency visualization
- VCF and BED file support
- Mouse dragging and hovering
- Filter alignment
Now 90% of what I need from IGV can be done in the terminal.
Some interesting behind-the-scenes:
Come on Claude, I give you one more chance. This is just a simple refactoring. I wrote instructions in comments. I'll write a good prompt. I'll use your PRO model with MAX reasoning. You got it. No mistake.
> Deletes all the code
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 :(
Types are cool but how do I explain this
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...
tgv is becoming so good. Next release gonna be epic.
On a side note, I stopped using AI all together a month ago (except occasionally turning on tabbing for boilerplate). I'm so much happier. Coding is much more flowy and I'm learning a ton. Vim motion boosts productivity way more than any AI.
Anyone uses marimo notebooks regularly? What do you use it for?
New tgv release: local cache!
tgv download hg38
Download UCSC reference genomes to a local sqlite db for much faster browsing. Awesome Rust tools (twobit, bigtools) made this simple.
github.com/zeqianli/tgv
This is still at an early stage. This is the best I got 😅: github.com/zeqianli/tgv...
I started tgv to learn Rust and building it has been unbelievably fun! If you wanna pick up a super fast and fun programming language, tgv is open for contribution! There aren't many bioinformatics tools built entirely by the community. If tgv can become one, I'll be so psyched
Thanks for posting! tgv is still at a very early stage so expect bugs :)
Congratulations!
