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refactor: implement RoutableSuperKmer and update k-mer indexing pipeline

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Replace raw SuperkMer routing with a new RoutableSuperKimer type that embeds canonical sequences and precomputed minimizers, enabling direct partition routing via hash. Update the build pipeline to yield RoutableSuperKmers throughout (builder, scatterer), refactor FASTA/unitig export commands to use the new type and compressed outputs (.fasta.gz, .unitigs.fasta.zst), revise SuperKmer header to store n_kmers instead of seql (avoiding 256-byte wrap), and update documentation to reflect minimizer-based theory, two evidence-encoding strategies for unitig-MPHF indexing (global offset vs. ID+rank), and the new obipipeline library architecture with parallel workers, biased scheduling, and error handling.
This commit is contained in:
Eric Coissac
2026-04-29 22:52:42 +02:00
parent 4e26e3bd40
commit 27f5e88a7b
72 changed files with 10093 additions and 1626 deletions
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.gitignore
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@@ -2,10 +2,10 @@
src/target
data-stress
*.fasta
*.fasta.gz
*.zst
*.zst.meta
*.pb
*.json
./**/*.json
*.bin
*.bin
*.json
Betula_exilis--IGA-24-33