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Precompute deletion penalties and log values #21

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@bmesuere bmesuere commented Feb 3, 2026

This PR precomputes deletion penalties and logvalues.

Benchmark on my laptop:

Benchmark: Short reads (NC_000913-454.fna)
Benchmark 1: /Users/bart/Code/FragGeneScanRs/target/release/FragGeneScanRs -s /Users/bart/Code/FragGeneScanRs/example/NC_000913-454.fna -t 454_10 -w 0 -o /var/folders/j3/38fskpy159v07np8syk3p_2m0000gn/T/tmp.LcYOUWUb39/NC_000913-454
  Time (mean ± σ):     393.5 ms ±   3.8 ms    [User: 380.9 ms, System: 9.7 ms]
  Range (min … max):   387.8 ms … 404.9 ms    20 runs


Benchmark: Complete genome (NC_000913.fna)
Benchmark 1: /Users/bart/Code/FragGeneScanRs/target/release/FragGeneScanRs -s /Users/bart/Code/FragGeneScanRs/example/NC_000913.fna -t complete -w 1 -o /var/folders/j3/38fskpy159v07np8syk3p_2m0000gn/T/tmp.LcYOUWUb39/NC_000913
  Time (mean ± σ):     620.2 ms ±   6.8 ms    [User: 499.1 ms, System: 116.3 ms]
  Range (min … max):   613.1 ms … 640.1 ms    20 runs


Benchmark: Long reads (contigs.fna)
Benchmark 1: /Users/bart/Code/FragGeneScanRs/target/release/FragGeneScanRs -s /Users/bart/Code/FragGeneScanRs/example/contigs.fna -t complete -w 1 -o /var/folders/j3/38fskpy159v07np8syk3p_2m0000gn/T/tmp.LcYOUWUb39/contigs
  Time (mean ± σ):      3.861 s ±  0.021 s    [User: 3.797 s, System: 0.050 s]
  Range (min … max):    3.826 s …  3.900 s    10 runs

short reads: 393.5 ms ± 3.8 ms
complete genome: 620.2 ms ± 6.8 ms
long reads: 3.861 s ± 0.021 s

See #17 for a comparison.

@bmesuere bmesuere mentioned this pull request Feb 3, 2026
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