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Rename CLI to obikmer2, add phylo commands, and unify index caching

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Restructure the workspace and rename the CLI application to obikmer2. Replace direct KmerIndex usage across all commands with Arc-wrapped IndexCache to enable shared ownership. Introduce builder patterns for algorithmic operations and integrate explicit progress tracking. Add new Phylo, NameTree, and Convert subcommands with expanded CLI flags. Consolidate module structure, update dependency specifications, and remove legacy directories.
This commit is contained in:
Eric Coissac
2026-08-28 22:34:46 +02:00
parent e101f629e6
commit 95fa0c93b2
61 changed files with 1034 additions and 6797 deletions
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src/Cargo.toml
+1 -1
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@@ -1,5 +1,5 @@
[workspace]
resolver = "3"
members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikmer2","obikrope","obipipeline", "obiskio","obidebruinj", "obicompactvec", "obisys", "obikindex", "obikindexer", "obikquery", "obikdump", "obikfilter", "obikselect", "obikrebuild", "obikmerge", "obikstats", "obikidxcache", "obitaxonomy", "obikentropy", "obikphylo", "obikalgorithm"]
members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obiskio","obidebruinj", "obicompactvec", "obisys", "obikindex", "obikindexer", "obikquery", "obikdump", "obikfilter", "obikselect", "obikrebuild", "obikmerge", "obikstats", "obikidxcache", "obitaxonomy", "obikentropy", "obikphylo", "obikalgorithm"]
[profile.release]
debug = 1