Eric Coissac
ba49af6f9e
Introduce the `obipipeline` dependency and refactor merge and partition logic to leverage parallel execution. Update `merge_partitions` to use rayon with dynamic memory budgeting and concurrency control via a pilot run. Refactor Pass 1 to concurrently read unitigs, filter kmers through a shared `LayeredMap`, and populate the graph safely. Simplify diagnostics to report total kmer counts and replace manual flags with graph length validation.
33 lines
843 B
TOML
33 lines
843 B
TOML
[package]
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name = "obikpartitionner"
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version = "0.1.0"
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edition = "2024"
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[dev-dependencies]
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tempfile = "3"
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obikseq = { path = "../obikseq", features = ["test-utils"] }
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obiskbuilder = { path = "../obiskbuilder" }
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obiread = { path = "../obiread" }
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obikrope = { path = "../obikrope" }
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[dependencies]
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niffler = "3.0.0"
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remove_dir_all = "0.8"
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obikseq = { path = "../obikseq" }
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obiskio = { path = "../obiskio" }
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obidebruinj = { path = "../obidebruinj" }
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obilayeredmap = { path = "../obilayeredmap" }
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rayon = "1"
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sysinfo = "0.33"
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serde = { version = "1", features = ["derive"] }
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serde_json = "1"
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tracing = "0.1.44"
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cacheline-ef = "1.1"
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epserde = "0.8"
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memmap2 = "0.9.10"
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obicompactvec = { path = "../obicompactvec" }
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ptr_hash = "1.1"
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indicatif = "0.17"
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obisys = { path = "../obisys" }
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obipipeline = { path = "../obipipeline" }
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