Merge dev into main. The main focus of this release is to move to piscem as the default backend for indexing and mapping. The --use-piscem flag is no longer necessary as this is the default, but the flag is still supported for the time being, so as to not break existing pipelines (at some non-trivial cost to code complexity given the way that clap handles such things). However, in the future, we expect that the --use-piscem flag will be removed, and there will simply be a --no-piscem flag if the user wants to override the default behavior and use the salmon-alevin index and mapper.
Merge dev into main. The main focus of this release is to move to
piscemas the default backend for indexing and mapping. The--use-piscemflag is no longer necessary as this is the default, but the flag is still supported for the time being, so as to not break existing pipelines (at some non-trivial cost to code complexity given the way that clap handles such things). However, in the future, we expect that the--use-piscemflag will be removed, and there will simply be a--no-piscemflag if the user wants to override the default behavior and use thesalmon-alevinindex and mapper.