59 lines
1.8 KiB
Rust
59 lines
1.8 KiB
Rust
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//! Throughput of the streaming superkmer pipeline (`RollingStat`'s hot path:
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//! minimizer selection + entropy tracking fused in a single pass).
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//!
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//! Reference point for the `obikentropy` extraction: the entropy bookkeeping
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//! that used to live inline in `RollingStat` was pulled out into a composed
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//! `EntropyTracker`. This benchmark is run before and after that change to
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//! confirm no regression.
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use criterion::{Criterion, Throughput, criterion_group, criterion_main};
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use obikrope::Rope;
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use obiskbuilder::SuperKmerIter;
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const K: usize = 21;
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const M: usize = 9;
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const LEVEL_MAX: usize = 6;
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const THETA: f64 = 0.7;
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const SEQ_LEN: usize = 200_000;
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/// Deterministic pseudo-random ACGT sequence — high enough complexity that
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/// the entropy filter rarely rejects, so the bench stays on the steady-state
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/// path rather than repeatedly resetting.
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fn make_sequence(len: usize) -> Vec<u8> {
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let mut state: u64 = 0x9E3779B97F4A7C15;
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(0..len)
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.map(|_| {
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state ^= state << 13;
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state ^= state >> 7;
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state ^= state << 17;
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b"ACGT"[(state % 4) as usize]
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})
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.collect()
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}
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fn make_rope(seq: &[u8]) -> Rope {
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let mut rope = Rope::new(None);
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rope.push(seq.to_vec());
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rope
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}
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fn bench_build_superkmers(c: &mut Criterion) {
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obikseq::set_k(K);
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obikseq::set_m(M);
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let seq = make_sequence(SEQ_LEN);
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let rope = make_rope(&seq);
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let mut group = c.benchmark_group("build_superkmers");
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group.throughput(Throughput::Bytes(SEQ_LEN as u64));
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group.bench_function("stream", |b| {
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b.iter(|| {
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SuperKmerIter::new(std::hint::black_box(&rope), K, LEVEL_MAX, THETA).count()
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});
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});
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group.finish();
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}
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criterion_group!(benches, bench_build_superkmers);
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criterion_main!(benches);
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