Reece Hart comments

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                                            Reece Hart

untangle lru_cache and persistent cache

Outcomes that I'd like to see: * `interface` module should be about the *interface* only. It shouldn't mix caching, etc. * use existing caching and persistence tools where possible *...

hgvs should optionally use seqrepo namespaces

SeqRepo doesn't require a namespace to lookup a sequence. The logic is: * For a fully qualified search (e.g., NCBI:NM_000551.3), SeqRepo searches explicitly. This will either exist and refer to...

In-frame del at the end of a transcript throws Index Error

Confirmed on master (hgvs 1.2.5). :-( I agree that this is likely related to the issues you saw previously.

AttributeError: 'AARefAlt' object has no attribute 'ref_n'

Confirmed. This is a bug. Ultimately, this stems from the issues discussed in #333 . I'm currently looking for funding to address issues like this. Until then, I'll gladly accept...

strict_bounds parameter for AssemblyMapper

@cassiemk : Your understanding is unfortunately correct: you cannot currently set strict_bounds for a single projection. I remember disliking this limitation when implementing it. I would welcome a per-invocation option....

Make the HGVS parser as a separate package

There's good separation of the parser and models from the algorithmic components, so splitting the package is possible and useful. However, it'd be a bit of work that I don't...

implement linters / static analyzers

Also: https://requires.io/ https://landscape.io/ https://scrutinizer-ci.com/ https://codeclimate.com https://app.codacy.com/

bioconda recipe?

Thanks for giving it a shot. I don't use conda, so don't have the personal motivation for that particular solution. I have a couple of disconnected thoughts: * My understanding...

Ambiguous genome-transcript alignments cause ambiguous variant projections

Angie- I totally agree that the convention should be to right shift alignment gaps, with the addition that shifting should be with respect to the transcript. Than main reason for...