Better document "slow" options that should be avoided
(Zhang, 2019) used -a
(the option is now --out-reads
), that is far from optimal, taking time to output all reads vdj#919
Since !434 (merged), options were renamed and are more explicit. However, we should ensure that the non-recommended options are clearly docuemted as such:
- in
-h
/-H
(we could also move options from-h
to advanced usage-H
) - with
Warning for non-optimal use
on stdout (we have already some) - in
doc/vidjil-algo.md