Eric Coissac
1a470eab9e
Replaces the explicit `SiblingInfo` struct and 3-bit minorant flags with a derived 4-bit presence mask (`FamilyMask`) that tracks observed bases per family. This eliminates redundant file I/O overhead by introducing a `PartitionCache` for batch lookups, simplifies serialization, and updates all downstream builders, stats computation, and tests to operate on the new bitmask representation. Adjusts CLI output to report deduplicated family sizes instead of histograms, ignores generated CSV files, and updates documentation to reflect the fixed canonical reference and new theory.
27 lines
473 B
Plaintext
27 lines
473 B
Plaintext
.venv/
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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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*.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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Betula_exilis--IGA-24-33
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benchmark/genomes
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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/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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