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Yay! My first rust code is now in sourmash! https://github.com/dib-lab/sourmash/pull/856 … - 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
@luizirber for bearing with!Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
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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Another Pythonic compiled language? Curious how this stacks up against Nim. https://github.com/seq-lang/seq https://dl.acm.org/doi/pdf/10.1145/3360551?download=true …
#Seqlang#Nim#BioinformaticsPrikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
ducktapeprogrammer proslijedio/la je Tweet
#dlang First prototype of D's Ownership/Borrowing system incorporated today!https://github.com/dlang/dmd/pull/10586 …Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
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. https://github.com/sstadick/py-lapper …
#python#bioinformaticsHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
ducktapeprogrammer proslijedio/la je Tweet
Want to call
#rust code from@nim_lang? 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 :)https://github.com/arnetheduck/nbindgen …Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
ducktapeprogrammer proslijedio/la je Tweet
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.pic.twitter.com/0uBY9XRc76
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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. https://github.com/sstadick/scivs https://index.scala-lang.org/sstadick/scivs/scivs …
#scala#bioinformaticsHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
ducktapeprogrammer proslijedio/la je Tweet
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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ducktapeprogrammer proslijedio/la je Tweet
sourmash 3.0.0 released! Officially migrated from C++ to
#RustLang
Release notes: https://sourmash.readthedocs.io/en/v3.0.1/release-notes/sourmash-3.0.html …
PyPI: https://pypi.org/project/sourmash/3.0.0 …
$ pip install sourmash==3.0.0
Bioconda:
$ conda install -c conda-forge -c bioconda sourmash=3.0.0Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
ducktapeprogrammer proslijedio/la je Tweet
Introducing --gc:arc, the new frontier for Nim's memory management. https://forum.nim-lang.org/t/5734
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ducktapeprogrammer proslijedio/la je Tweet
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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Great demo on Python + Rust for text processing. Hopefully performance oriented bioinformatics code starts to lean this way. https://youtu.be/G_43eu6Ascs
#Python#pydataberlin#Bioinformatics#rustlangHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
ducktapeprogrammer proslijedio/la je Tweet
Join us in January for our next series of DNAnexus Essentials Webinars. Register for a walkthrough of platform fundamentals to make onboarding a breeze. http://ow.ly/g8hH50xxYde pic.twitter.com/l1MPkvlOOg
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ducktapeprogrammer proslijedio/la je Tweet
The long awaited release of 1.10 of Samtools, BCFtools and HTSlib is now available from the GitHub. See https://htslib.org/download/ for links to tarballs and release notes.
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Looking for a faster umi-tools? Give rumi a try! (and then submit any issues you find :) https://github.com/sstadick/rumi A rust implementation of the core directional adjacency algorithm from umi-tools. It is faster, actual fair benchmarks tbd.
#bioinformatics#umitools#umi#rustlangHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
ducktapeprogrammer proslijedio/la je Tweet
miniwdl beta can run
@humancellatlas and@EncodeDCC WDL workflows and maybe yours too. Try it out and let us know!https://medium.com/czi-technology/miniwdl-17ecdaf40944 …Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
To clarify intent: A faster umi-tools for deduplication
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Beta release of rumi: https://crates.io/crates/rumi A rust implementation of directional adjacency deduplication as described in https://genome.cshlp.org/content/early/2017/01/18/gr.209601.116.abstract …. Improvements: - Granular test suite - Multi-core support (one per chromosome) It needs real life reps!
#bioinformaticsPrikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
ducktapeprogrammer proslijedio/la je Tweet
FFI::Platypus 1.00 is out: http://blogs.perl.org/users/graham_ollis/2019/11/platypus-next-generation.html …
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