Richard Neher

[WIP] Feat/read mitigations

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## Related issues and PRs preparatory PR for crowdsourced mitigation measures. ## Description Use data from countries and regions to prepopulate the scenarios with measures. ## Impacted Areas in the...

Step-by-step guide for parameter adjustment

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# 🙋 Feature Request Some guidance on how to develop a new scenario and adjust parameters to fit existing data would help many users. Especially once we have case count...

Default run doesn't work

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We used to be able to run an example workflow by simply doing ``` snakemake -j1 ``` Now not even `clean` works anymore without specifying a profile with inputs: ```...

DO NOT MERGE: don't award matches with unknown state the full match score

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We currently award a match `score_match` (3) and penalize a mismatch with `mismatch_penalty` (1). Ambiguous characters (`N`) match every other character and are thus always award the full score. In...

Spike only sequences from VOC alpha aren't assigned the 20I (Alpha) but 20B

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The presence of recombinant lineage `XA` with Alpha spike in a non-alpha background attracts Spike only Alpha sequences. Unsure how to handle this, but as a stop-gap solution we could...

Improve polytomy resolution

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## The problem TreeTime has currently a very rudimentary way of resolving polytomies (multi-furcations in the tree). When this was initially put in place it was never meant to resolve...

Export fails if node-data contains unhashable items.

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If `node_data` contains data such as lists, validation of the output json in export fails here: https://github.com/nextstrain/augur/blob/cc3b7bdb6faf370c496efc798b10e4a3d014bef4/augur/export_v2.py#L185 While we typically don't have such data, it is a rather difficult to...

Augur's `align` command currently only support `mafft` called as `mafft --reorder --anysymbol --nomemsave --adjustdirection --thread` and the possibility to add to an existing alignment with the option `--add`. The latter...