Fix for #519 - add support for HGVS repeats

[markwoon]

Took a stab at implementing support for repeats as documented at https://varnomen.hgvs.org/recommendations/DNA/variant/repeated/.

I hope the new class names sufficiently aligns with what you expect.

I considered renaming the NucleotideShortSequenceRepeatVariability over to LegacyNucleotideShortSequenceRepeatVariability but figured this would be a breaking change. I'm not sure how you want to distinguish between the current spec and the old spec at https://www.hgvs.org/mutnomen/.

[holtgrewe]

Dear @markwoon, thanks for this 👏. I glanced over this quickly and I have to say: good job, in particular getting into the Antlr part is not trivial IMO. I will need to take some time to review this (next week).

Cheers!

[markwoon]

Learning antlr was fun.

I am torn between writing my own parser and using jannovar. I'd like to just use jannovar but I'm starting to need the parts of the spec that jannovar doesn't cover.

I'm happy to contribute, but I'm not sure what your plan is for fully supporting the current spec, and how/if you plan on supporting the older spec. I would be interested in working on a version that only has to care about the current spec.

[holtgrewe]

Looks good to me!

[holtgrewe]

Hi Mark,

thanks again, i just merged it.

Maybe we continue the discussion on HGVS support in #519?

Cheers!

[holtgrewe]

Oh, by the way, do you need a release from this or are you building yourself anyway?

[markwoon]

Would prefer an official release, but I'm using my own build in the meantime.

[holtgrewe]

@markwoon Then let's see where #519 takes us. I'm a bit reluctant to release for such small features (Jannovar build infrastructure is not properly setup for such small-stepped builds) but would do a release if we don't expect any changes of the code base in the next weeks.

edit: s/days/weeks/