ducktapeprogrammer

@ducktapeprogra1

Bioinformatics. Rust, Nim, Perl, and Python. I like strings and I like making things go fast.

Vrijeme pridruživanja: siječanj 2019.

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  1. proslijedio/la je Tweet
    26. sij

    Yay! My first rust code is now in sourmash! - I wrote most of it by monkey-see-monkey-do coding, of course. Ended up being a sizable diff because I had to read and understand a lot of behavior (which I then doc/test). Thx to for bearing with!

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  2. 22. sij

    After playing with it a bit I have two conclusions: 1) Their benchmarks are highly suspect. 2) They could have just implemented a few Nim macros + a library and gotten better results AND have an ecosystem. But who knows, maybe it will grow into something awesome.

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  3. 21. sij

    Another Pythonic compiled language? Curious how this stacks up against Nim.

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  4. proslijedio/la je Tweet
    17. sij

    First prototype of D's Ownership/Borrowing system incorporated today!

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  5. 17. sij

    The lapper comes to Python! Pure python interval lib based on nim-lapper. Prepping for wrapping rust-lapper and scailist for use in Python and doing some benchmarking.

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  6. proslijedio/la je Tweet
    14. sij

    Want to call code from ? Just pushed an early preview of `nbindgen` that can generate Nim bindings for rust FFI code, allowing you to reuse those sweet and safe libraries without all the braces :)

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  7. proslijedio/la je Tweet
    12. sij

    I always think of std::vector::size() as cheap. As in, it just reads the size member, or something. Of course, I'm wrong. size() is always all that cheap. In principle, it involves a division, although the compiler will likely strength reduce it a constant multiply, etc.

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  8. 7. sij

    My first Scala package! So. Painful. To. Publish. A collection of datastructures for working with genomic intervals, including an AIList impl, and a Scala port of nim-lapper.

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  9. proslijedio/la je Tweet
    4. sij
    Odgovor korisnicima

    We are experimenting with rust too. Initial (small-scale) results are very promising. The language is *so* much better, and the compiler prevents *so* many more avoidable errors. Hopefully, when a project is done and out, I'll write up some thoughts.

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  10. proslijedio/la je Tweet
    4. sij

    sourmash 3.0.0 released! Officially migrated from C++ to 🎉 Release notes: PyPI: $ pip install sourmash==3.0.0 Bioconda: $ conda install -c conda-forge -c bioconda sourmash=3.0.0

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  11. proslijedio/la je Tweet
    26. pro 2019.

    Introducing --gc:arc, the new frontier for Nim's memory management.

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  12. proslijedio/la je Tweet
    21. pro 2019.

    I remind people every year: If you're giving someone a console for the holidays, today: - Open it up (CAREFULLY. Save all the packaging.) - Set it up - Boot it - Update it and configure it - Install a few games (especially if they're digital) - Pack it back up and wrap it.

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  13. Great demo on Python + Rust for text processing. Hopefully performance oriented bioinformatics code starts to lean this way.

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  14. proslijedio/la je Tweet
    17. pro 2019.

    Join us in January for our next series of DNAnexus Essentials Webinars. Register for a walkthrough of platform fundamentals to make onboarding a breeze.

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  15. proslijedio/la je Tweet
    6. pro 2019.

    The long awaited release of 1.10 of Samtools, BCFtools and HTSlib is now available from the GitHub. See for links to tarballs and release notes.

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  16. Looking for a faster umi-tools? Give rumi a try! (and then submit any issues you find :) A rust implementation of the core directional adjacency algorithm from umi-tools. It is faster, actual fair benchmarks tbd.

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  17. proslijedio/la je Tweet
    25. stu 2019.

    miniwdl beta can run and WDL workflows and maybe yours too. Try it out and let us know!

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  18. To clarify intent: A faster umi-tools for deduplication

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  19. Beta release of rumi: A rust implementation of directional adjacency deduplication as described in . Improvements: - Granular test suite - Multi-core support (one per chromosome) It needs real life reps!

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