adding imprecise SVs

[pnrobinson]

Addresses #259

Not entirely clear to me what the testing is for functionality. For instance, why do we want this function to return None? Please document! :-0

    def test_find_large_structural(
        self,
        fpath_test_genomic_interpretations: str,
        pp_vc_finder: PhenopacketVariantCoordinateFinder,
    ):
        fpath_pp = os.path.join(fpath_test_genomic_interpretations, 'chromosomal_deletion.ANKRD11.json')
        gi = read_genomic_interpretation_json(fpath_pp)

        vc = pp_vc_finder.find_coordinates(gi)
        assert vc is None

[ielis]

Hi @pnrobinson,

thank you for pointing this out. The topic of breakends/translocations has not yet been addressed by GPSEA and it seems like there is a need.

The PR looks OK, there are few things that I'd like to clarify though. Please see below.

[ielis]

Isn't this redundant with BND above?

[ielis]

Depending on my comment in _variant.py, this may need to be changed to VariantClass.BND.

[pnrobinson]

I think BND is broader than just translocation ("BND can be used to represent reciprocal translocations or non-reciprocal break ends. ") but in any case, BND is a technical description rather than a biological one, and so I do not think we should actually keep BND as a Variant Category

[ielis]

So do you recommend (effectively) renaming BND to TRANSLOCATION?

[pnrobinson]

That would work, yes, I am guessing it has not been used in any other context yet (if at al!)!

[ielis]

It has not been used, and I kind of planned to use BND as a translocation. Let's then keep TRANSLOCATION and remove BND.

[pnrobinson]

@ielis Using TRANSLOCATION instead of BND seems good. Probably we can merge this?

[ielis]

Awesome!