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Add unitig extraction command to obikdump and obikmer2

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Introduces a new unitig extraction feature that reads k-mers from an index, filters them by group metadata, and partitions the computation using rayon. The implementation constructs per-partition de Bruijn graphs, merges them, computes node degrees, and writes the resulting sequences as FASTA. A corresponding CLI command is added to obikmer2 to expose this functionality with configurable filtering and progress reporting.
This commit is contained in:
Eric Coissac
2026-08-26 14:40:02 +02:00
parent 768fa0183d
commit 96dfb5300b
7 changed files with 129 additions and 5 deletions
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src/obikdump/Cargo.toml
+7 -5
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@@ -4,8 +4,10 @@ version = "0.1.0"
edition = "2024"
[dependencies]
obikindex = { path = "../obikindex" }
obikfilter = { path = "../obikfilter" }
obikidxcache = { path = "../obikidxcache" }
obikseq = { path = "../obikseq" }
rayon = "1"
obikindex = { path = "../obikindex" }
obikfilter = { path = "../obikfilter" }
obikidxcache = { path = "../obikidxcache" }
obikseq = { path = "../obikseq" }
obidebruinj = { path = "../obidebruinj" }
obifastwrite = { path = "../obifastwrite" }
rayon = "1"