John Lees

hhalignment: did not find [x] match states in sequence [i]

30

:exclamation: Make to check out our [User Guide](https://github.com/soedinglab/hh-suite/wiki). I am trying to run alphafold (using the docker image in the current readme), but an error is encountered when running the...

Turn exception handling off in nextclade_wasm/nextalign

2

Love the use of WASM for nextalign! I was wondering whether you had tried/considered turning exception handling off when compiling your code (`-s DISABLE_EXCEPTION_CATCHING=1 -fno-exceptions`)? Anecdotally, I've found this has...

Possibility of having a single header to include

3

We are using Seqan3 in a couple of projects, and it is generally working nicely. However, one issue we have is that over time our builds start failing when they...

bcftools csq cannot parse bacterial gff3 files

16

I have tried the bcftools csq command with the attached fasta, and three different gff files (one from ncbi, one ncbi modified to add transcripts, and one from ensembl bacteria)....

To build the API docs correctly, a newer version of sphinx is needed (otherwise autodoc mock imports doesn't work properly). Trying to add this in `docs/requirements.txt`

Meta: Refactor code base

2

Things to be done off the top of my head: - [ ] Remove dbFuncs (#166) - [x] Remove all `use_mash` instances, and the partial functions - [x] Redo command...

Nice suggestion from Ste on the distance plot: 'I think being able to colour/filter based on metadata (eg. MLST, lab, country) might be a quick way to understand the the...

Move ranges package from bedtools

4

There is a native python implementation of intervals here: https://github.com/vsbuffalo/BioRanges This might save on tmp files, dependencies and improve speed

Add --dbgwas option

2

Add an option to provide output in the right format for DBGWAS, so that pyseer can be used as an alternative option in their step2 association. This format is: ```...