Kyle Beauchamp

FWIW, I've generally updated the HTSLib bioconda recipes once things have been pulled into pysam (by @andreasheger) and stabilized. I also find that using miniconda+bioconda helps folks get their CI...

Good list of issues, one more I would add is just ensuring version consistency between the tree of HTSLib dependent children, and clarifying when tools are static builds versus relying...

From the paper abtract: "We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000...

Conda (https://conda.io/docs/): "Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. Conda quickly installs, runs and updates packages and their...

I have also observed good performance on ZSTD, although it appears that the CRAM compressor is also a very modern approach. See my issue here on the "unifying compressor API"...

In particular, I was able to convince the squash benchmark folks to add the genome FASTA data to their compressor benchmark. I then ran the benchmark on chr1 and observed...

Cool. I'm not actually an HTSLib developer :) but I wanted to voice my support for any project that improves the compression ratio and/or read throughput of HTSLib-supported formats (particularly...

Thanks, this is helpful information in terms of the challenges and also what's been tried. I suspected someone did a lot of benchmarking at some point.

I think I've found a related issue. It seems that the only way to specify a formula is to call the .fit() function. However, this seems to be incompatible with...

There's a lot of legacy python applications that are not going to be migrated to py3 on the year timescale. I think we should ask ourselves "will a sizable fraction...