Optimize the Nuc enum with bitwise operations and remove the lookup in trinucleotide

[bmesuere]

This PR optimizes the Nuc enum to use bitwise operations and replaces the trinucleotide function by direct calculation.

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.oLaKKc9LR3/NC_000913-454
  Time (mean ± σ):     532.2 ms ±   4.8 ms    [User: 520.0 ms, System: 9.4 ms]
  Range (min … max):   525.9 ms … 543.7 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.oLaKKc9LR3/NC_000913
  Time (mean ± σ):     695.9 ms ±   8.3 ms    [User: 576.6 ms, System: 111.8 ms]
  Range (min … max):   685.2 ms … 716.3 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.oLaKKc9LR3/contigs
  Time (mean ± σ):      4.488 s ±  0.015 s    [User: 4.438 s, System: 0.042 s]
  Range (min … max):    4.464 s …  4.511 s    10 runs

short reads: 532.2 ms ± 4.8 ms
complete genome: 695.9 ms ± 8.3 ms
long reads: 4.488 s ± 0.015 s

[Copilot]

Pull request overview

This PR optimizes the nucleotide (Nuc) representation to exploit bitwise operations and replaces the large pattern-matching trinucleotide lookup with a direct arithmetic calculation, yielding measurable performance improvements in the benchmarks provided.

Changes:

• Reworked Nuc to be a #[repr(u8)] enum with a documented bit layout (bit 0 as insertion flag, bits 1–2 as base encoding).
• Implemented bitwise-based helpers on Nuc (to_int, to_lower, is_insertion, rc) to replace large pattern matches.
• Replaced the exhaustive trinucleotide pattern-match table with a direct computed codon index based on base indices.

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[ninewise]

I'd not enumerate these here, they are right below in the definition.

[ninewise]

On its own, this change gives me a 1.11x on execution time (slower). I'm running only on NC_000913.fna though:

Benchmark 1: ./secondline -s /data/programming/unipept/FragGeneScanRs/example/NC_000913.fna -t complete -w 1 -o /tmp/asdf/NC_000913
  Time (mean ± σ):      1.557 s ±  0.102 s    [User: 0.990 s, System: 0.560 s]
  Range (min … max):    1.473 s …  1.754 s    10 runs
 
Benchmark 2: ./table -s /data/programming/unipept/FragGeneScanRs/example/NC_000913.fna -t complete -w 1 -o /tmp/asdf/NC_000913
  Time (mean ± σ):      1.725 s ±  0.024 s    [User: 1.134 s, System: 0.581 s]
  Range (min … max):    1.695 s …  1.767 s    10 runs
 
Benchmark 3: ./transmute -s /data/programming/unipept/FragGeneScanRs/example/NC_000913.fna -t complete -w 1 -o /tmp/asdf/NC_000913
  Time (mean ± σ):      1.736 s ±  0.026 s    [User: 1.124 s, System: 0.603 s]
  Range (min … max):    1.697 s …  1.786 s    10 runs
 
Summary
  ./secondline -s /data/programming/unipept/FragGeneScanRs/example/NC_000913.fna -t complete -w 1 -o /tmp/asdf/NC_000913 ran
    1.11 ± 0.07 times faster than ./table -s /data/programming/unipept/FragGeneScanRs/example/NC_000913.fna -t complete -w 1 -o /tmp/asdf/NC_000913
    1.11 ± 0.07 times faster than ./transmute -s /data/programming/unipept/FragGeneScanRs/example/NC_000913.fna -t complete -w 1 -o /tmp/asdf/NC_000913

(secondline is this version without this change, table is me trying out a constant table lookup, transmute is this version)

[ninewise]

Bitshifts here give a minor improvement for me.