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Implement pack CLI command for matrix packing and layer compaction

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Adds the `pack` subcommand to `obikmer2` for persisting presence and count matrices in sparse or dense formats. Introduces the `compact_layer` module in `obikrebuild` to merge multiple partition layers into a single layer in-place via atomic operations. Updates dependencies across `obikdump`, `obikmer2`, and `obikrebuild` to resolve new local crate references. Shifts the architecture from multi-layer accumulation to in-place compaction, removing legacy rebuild modules.
This commit is contained in:
Eric Coissac
2026-08-26 14:48:44 +02:00
parent 96dfb5300b
commit 904d85f33b
12 changed files with 252 additions and 382 deletions
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src/obikdump/Cargo.toml
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@@ -10,4 +10,6 @@ obikidxcache = { path = "../obikidxcache" }
obikseq = { path = "../obikseq" }
obidebruinj = { path = "../obidebruinj" }
obifastwrite = { path = "../obifastwrite" }
obicompactvec = { path = "../obicompactvec" }
obisys = { path = "../obisys" }
rayon = "1"