Incorrect HGVS output

[nickzoic]

See CountESS-Project/CountESS#32 and 0b464fb but there's still issues about different possible ways of representing the change in HGVS.

[nickzoic]

Possibly this could be fixed with better CS output, which minimap can do if called with --cs=long

python API Alignment.map() gets the CS string from cmappy.mm_gen_cs(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq, 1)
that last parameter is int no_iden which gets passed through to write_cs_ds_core where it controls output of matching sequences as either =(bases) or :(length) sequences.

So to get the equivalent I'd have to pass some other flag into Alignment.map(cs=mappy.CS_LONG) or whatever, and then pass that through in minimap.

Could write a minimap2 PR for this but note lh3/minimap2#292