Open nickzoic opened 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, ®s[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
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.