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CountESS-Project / countess-minimap2

Sequence Alignment Plugin for CountESS, based on Minimap2
BSD 3-Clause "New" or "Revised" License
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Incorrect HGVS output #1

Open nickzoic opened 7 months ago

nickzoic commented 7 months ago

See https://github.com/CountESS-Project/CountESS/issues/32 and 0b464fbe2ae6b5289331cdad5f3edf9fbd4c0cd2 but there's still issues about different possible ways of representing the change in HGVS.

nickzoic commented 7 months ago

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 https://github.com/lh3/minimap2/issues/292