Chris Wright

With version 2023.0.0.20221201 I had to also remove the conditional definition of `__cpuidex` in `ksw2_ext2_avx.c`, as with the code I received: ``` ksw2_dispatch.c:17:6: error: definition of builtin function '__cpuidex' void...

I don't think it correct to require that all QUAL fields be numeric, there is no constraint in the VCF specification to this end. A QUAL of `.` is perfectly...

Thanks @OscarAspelin, I suspect you're correct, the code doesn't consider the fact that there might be fastq comments that are not formatted as a tab separated list of SAM tags...

If you are making a submission to an academic journal, how you cite will depend on the journal's own rules. The may allow simply a URL to https://github.com/nanoporetech/pod5-file-format. From our...

Closing this issue as its gotten rather off-topic.

From the fact that you shell prompt contains both `(medaka)` and `(base)` I would guess that you have created a python virtual environment inside a base conda environment. I would...

Can you please provide the full output of the pip install command having created a new virtual environment.

I'm not entirely sure what is happening here. Pip is seemingly referencing three different versions of medaka in that logging before finally settling on a rather old version. It references...

You should not need to install libdeflate through brew in order for medaka to work --- its is intended to be included within the medaka code. I will try to...

@bentsherman Why do you say > joining on a closure doesn't really make sense I came passed here because I was searching for issues as I want to do exactly...