I would guess that soon, every tool will have one of these. It is more interactive than just documentation and better than waiting for a grumpy maintainer to answer the same question in a github issue or personal email.
Feeding my markdown docs to this, then using it in anger shows where the docs need to be bolstered and provides a nice reference for users:
help.openai.com/en/articles/...
here's one for bedder: chatgpt.com/g/g-69a6027f...
I had a similar, less principled way of doing this, but this does seem to work quite well after trying a couple of large changes with it: boristane.com/blog/how-i-u...
(I use codex, but same idea)
AGENTS.md > skills
vercel.com/blog/agents-...
it does support more than 2 sets of intervals, but now, a single --b-piece controls all of them. I'll have a look at this and your other comments. thank you!
scratch that. better to use gemini-cli, turn on preview features and then get gemini 3.0 pro and flash for free for a decent amount each day.
cerebras is so fast it makes the human <-> agent loop (or one-shot) very quick
and crush will also detect your GEMINI/OPENAI/OPENROUTER/CLAUDE env API vars as well
crush coding agent with a free plan from cerebras using glm4.7 model is an easy way to start with coding cli tools.
inference-docs.cerebras.ai/support/rate...
github.com/charmbracele...
crush is static binary that detects your CEREBRAS_API_KEY. GLM 4.7 isn't as good as Opus, but it is very solid.
another reminder about htsvcf which allows either
1. rust library to support javascript expressions (filtering/modification) on variants from VCF/BCF
2. javascript (node/bun) library for reading/writing/modifying variants from vcf/bcf.
both very performant.
github.com/brentp/htsvcf
a post about how, with LLMs, I wrote a new set of libraries.
Wrapping htslib is my hello-world but doing it in rust to allow javascript expressions handled by V8 was more substantial project.
The tools and LLMs are now getting quite good:
brentp.github.io/latest/blog/...
let me know what you think
my LLM-coded version of the single-page year calendar that's been going around. This one can be scripted with javascript to highlight cells, change the borders and texts. It also allows saving and sharing via url:
brentp.github.io/single-page-...
with code here:
github.com/brentp/singl...
exactly! and with Plan mode in opencode (or architect in kilo code) this becomes even more mind-blowing
so Opus 4.5 is excellent for coding. I've been using these LLMs for coding for a while and it felt like slow improvement with each new model and sometimes more work to guide the model. Opus 4.5 just works. It solves hard problems and has good taste.
Anyone else notice this?
I'll write more about this later, but as an experiment in LLM coding (GPT-5.2 and Opus 4.5), I wrote a JS wrapper for rust-htslib to read/write modify VCFs:
www.npmjs.com/package/htsvcf
works on linux (x64/aarch64) and OSX.
brentp.github.io/htsvcf/lates...
Get bedder v0.1.8 and r๐ฒ๐ฎ๐ฑ ๐๐ต๐ฒ ๐ฑ๐ผ๐ฐ๐๐บ๐ฒ๐ป๐๐ฎ๐๐ถ๐ผ๐ป here: github.com/quinlan-lab/...
We are looking for researchers to kick the tires, integrate bedder into their pipelines, and provide feedback on the Python functions, performance, and overall user experience! Please share and give us your feedback.
We are thrilled to announce the first official release (v0.1.8) of #๐ฏ๐ฒ๐ฑ๐ฑ๐ฒ๐ฟ, the successor to one of our flagship tool, #๐ฏ๐ฒ๐ฑ๐๐ผ๐ผ๐น๐! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
thank you. I'll have a look next week!
thanks Matt! Is this: docs.rs/aardvark-bio...
the entry point if I want to compare, e.g. 2 STR variants with slightly different positions to see if they are identical?
(Would be nice to have a quick example ๐)
yep! that's what I was thinking of. Thank you! (for software and pointer)
I vaguely recall seeing #bioinformatics tool that could compare variants (or set of variants) using haplotypes rather than simply normalize and check for equality. That murky description is about as specific as I can get. Any pointers? IIRC, it's not just a truth-set evaluation tool. Has API
how do we feel about putting JSON in the INFO field of a VCF?
This is very cool work and I'm happy to see it published. Vcfexpress by @brent-p.bsky.social and @aaronquinlan.bsky.social allows building (essentially) arbitrary VCF filters expressed in lua code with parsing & eval powered by rust!
academic.oup.com/bioinformati...
vcfexpress applies simple user expressions variants in a VCF.
it can replace one-off python scripts to manipulate VCFs, likely with better performance.
we'd like to collect use-cases here: github.com/brentp/vcfex...
if you have a use-case and want some pointers, open an issue
vcfexpress is a command-line tool built in rust that lets users apply lua expressions to modify or filter a vcf from the command-line
github.com/brentp/vcfex...
new release with better docs github.com/brentp/vcfex...
and examples github.com/brentp/vcfex...
awesome! it'll take me some time to digest this but this gives me a great start. thank you!
and thanks for your offer to help!
![error[E0599]: the method `indexed_records` exists for struct `Query<'_, &mut Reader<BufReader<File>>>`, but its trait bounds were not satisfied
--> src/lib.rs:374:27
|
374 | let q = q.indexed_records(&header).filter_by_region(®ion);
| ^^^^^^^^^^^^^^^ method cannot be called on `Query<'_, &mut Reader<BufReader<File>>>` due to unsatisfied trait bounds
|
= note: the following trait bounds were not satisfied:
`&mut noodles::noodles_bgzf::Reader<BufReader<File>>: noodles::noodles_bgzf::io::BufRead`
`&mut noodles::noodles_bgzf::Reader<BufReader<File>>: noodles::noodles_bgzf::io::Seek`](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:b4x3jqelv3boot7op2yo7kkw/bafkreifwvimn7r32ddejzdsu6yqyzp7uyo3lcrs24k7qnt5de2o647a4ge@jpeg)
error[E0599]: the method `indexed_records` exists for struct `Query<'_, &mut Reader<BufReader<File>>>`, but its trait bounds were not satisfied --> src/lib.rs:374:27 | 374 | let q = q.indexed_records(&header).filter_by_region(®ion); | ^^^^^^^^^^^^^^^ method cannot be called on `Query<'_, &mut Reader<BufReader<File>>>` due to unsatisfied trait bounds | = note: the following trait bounds were not satisfied: `&mut noodles::noodles_bgzf::Reader<BufReader<File>>: noodles::noodles_bgzf::io::BufRead` `&mut noodles::noodles_bgzf::Reader<BufReader<File>>: noodles::noodles_bgzf::io::Seek`
I think it might require more interactive help, but here's the error. I understand why, but not how to architect my code to fix.
I am looking for a mentor for the rust programming language. My latest issue is with trait bounds (github.com/brentp/simpl...) but I have a few things I generally hit. I can compensate with $$ or interesting problems. :)
Please share with relevant people and feel free to DM.
