OBIKmers/obikmer
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

refactor: rename rebuild subcommand to filter

Browse Source 
Rename the `rebuild` CLI subcommand to `filter` to better reflect its primary purpose of row-level selection and k-mer filtering. Update all associated CLI arguments, logging, error messages, and module registrations accordingly. Introduce a dedicated `Rebuild` subcommand for index compaction, fully decoupling it from the filtering logic. Also refine related documentation to align with the new naming and semantics.
This commit is contained in:
Eric Coissac
2026-06-09 15:22:57 +02:00
parent e66adef23d
commit 970460be42
6 changed files with 25 additions and 28 deletions
Download Patch File Download Diff File Expand all files Collapse all files
docmd/implementation/select.md
+2 -2
View File
@@ -56,8 +56,8 @@ first, then renames atomically, so an interrupted run leaves the index intact.
--group <name>:<pred>
```
Defines a named group of genomes using the same predicate syntax as
`filter`/`rebuild`. Repeatable; a genome can belong to several groups.
Defines a named group of genomes using the same predicate syntax as `filter`.
Repeatable; a genome can belong to several groups.
```sh
--group "pub:species=Betula_pubescens"