Till Hartmann

This PR adds a dinopy version of fqcnt, which uses some cythonization internally.

Add cosmic database download wrapper

6

This PR adds a wrapper for downloading files from [COSMIC](https://cancer.sanger.ac.uk/cosmic/download). It expects the following parameters to be set: - `build` (at the moment either "GRCh37" or "GRCh38") - `dataset` (at...

argument parser doesn't handle `=` in --arg=value

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Given an invocation of slivar such as `slivar expr --info="INFO.some_integer >= 2" -v slivar-example.vcf`, a syntax error occurs: > duko.nim(71) compile > Error: unhandled exception: SyntaxError: parse error (line 1)...

- [ ] Handle `FORMAT` properly (and make it easy to use) - [x] Swap order access from `FORMAT[sample][field]` to `FORMAT[field][sample]` (#65) - [ ] Parse genotyping info from `FORMAT`...

feat!: Sequence ontology support

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## Description Include support for sequence ontology terms. This allows filtering by SO relationships. For example, to filter for variants where the consequence is [`intron_variant`](http://www.sequenceontology.org/browser/current_release/term/SO:0001627) *or any descendant thereof*: ```bash...

fix: allow multiple references in mehari server run

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Support multiple references in `mehari server run`, e.g. ``` mehari server run \ --transcripts GRCh38-ensembl.bin.zst \ --transcripts GRCh37-ensembl.bin.zst \ --reference GCF_000001405.40_GRCh38.p14_genomic.fna \ --reference GCF_000001405.25_GRCh37.p13_genomic.fna ``` Note that this relies on...

feat: Plugin system (#426)

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This draft PR adds a plugin system based on [extism](https://extism.org/) (#426). To that end, the project is converted to a workspace with (currently) three members: `mehari`, `mehari-plugins` and `mehari-plugin-vep-nmd`. -...

Compare mehari annotation with VEP annotation

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- build mehari transcript DB (ensembl): - download cdot for ensembl and grch37 / grch38 - download ensembl FASTA for transcripts - create / fill seqrepo with ENSEMBL FASTAs -...