v0.16.0
0.16.0 (2024-01-29)
This release makes relatively few surface level changes, but represents a minor (rather than patch) version bump because it sets piscem as the default index and mapper, and paves the way to remove the --use-piscem flag in the future. In the current release, the --use-piscem flag is still accepted, but it is the default behavior, and need not be explicitly provided. Additionally, a --no-piscem flag has been added to the index and quant commands, and the --no-piscem flag is necessary to use the alevin-fry associated flags and options to those commands.
The plan in future release (likely from 0.17 forward) will be to remove the --use-piscem flag entirely, and just keep the --no-piscem flag, as this will simplify argument parsing and also remove redundant flags.
This flag also fixed a bug with the parsing of , separated lists to the --decoy-paths flag, and fixed a few typos in error messages.
Features
- make piscem default, add --no-piscem flag (1642732)