Eric Coissac
878b63566f
Decouple k-mer counting from the partitioner by introducing a new `Counter` struct. The module exposes a fluent builder API with optional partial file retention, executes partition processing in parallel via Rayon with memory-aware chunk sizing, and integrates thread-safe progress callbacks. Update all callers to use the new counter, simplify test pipelines by removing serialization overhead, and clarify algorithm separation in module documentation.
62 lines
832 B
Plaintext
62 lines
832 B
Plaintext
.venv/
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.DS_Store
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.claude/
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.kilo/
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.serena/
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.zed/
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.ast-cache/
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memory/
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sandbox/
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src/target
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data-stress
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*.fasta
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*.fasta.gz
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*.fastq
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*.fastq.gz
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*.vcf
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*.zst
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*.zst.meta
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*.pb
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**/*.json
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*.bin
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*.log
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*.csv
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*.meta
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*.pfiv
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*.done
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*.efh
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*.efl
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*.bin.idx
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*.prsb
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Betula_exilis--IGA-24-33
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benchmark/genomes
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benchmark/genomes_orig
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benchmark/simulated_data
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benchmark/specimen_index_presence
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benchmark/specimen_index_count
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benchmark/global_index_presence
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benchmark/global_index_presence_orig
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benchmark/global_index_presence_sav
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benchmark/all_specific
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benchmark/global_index_count
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benchmark/stats
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benchmark/reference_index
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benchmark/reference_dist
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benchmark/obikmer_dist
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benchmark/specific_index_count
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benchmark/specific_index_presence
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benchmark/query_data
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TNT
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phyg
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biblio
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*.tnt
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*.tre
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*.phy
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*.treefile
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*.bionj
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*.iqtree
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*.mldist
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*.parstree
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*.ckp.gz
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*.model
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