Brent Pedersen

Vcfexpress: flexible, rapid user-expressions to filter and format VCFs AbstractMotivation. Variant Call Format (VCF) files are the standard output format for various software tools that identify genetic variation from DNA sequ

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...

06.03.2025 15:05 — 👍 25    🔁 8    💬 1    📌 1

vcfexpress/examples at main · brentp/vcfexpress expressions on VCFs. Contribute to brentp/vcfexpress development by creating an account on GitHub.

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

04.02.2025 17:05 — 👍 4    🔁 1    💬 0    📌 0

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...

28.01.2025 17:45 — 👍 3    🔁 0    💬 0    📌 0

awesome! it'll take me some time to digest this but this gives me a great start. thank you!

27.01.2025 17:48 — 👍 1    🔁 0    💬 1    📌 0

and thanks for your offer to help!

27.01.2025 17:17 — 👍 0    🔁 0    💬 1    📌 0

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(&region); | ^^^^^^^^^^^^^^^ 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.

27.01.2025 17:17 — 👍 0    🔁 0    💬 1    📌 0

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.

27.01.2025 15:42 — 👍 4    🔁 2    💬 1    📌 0

with Jason K from @aaronquinlan.bsky.social lab, I have been dusting off fraguracy, which evaluates sequencing error rates using the portion of bases from paired end reads that overlap. New release adds, among other niceties, tracking for distance to homopolymers
github.com/brentp/fragu...

25.11.2024 17:48 — 👍 5    🔁 1    💬 1    📌 0

also see BITS alg by Ryan Layer and @aaronquinlan.bsky.social academic.oup.com/bioinformati...

20.11.2024 22:59 — 👍 4    🔁 0    💬 1    📌 0