diff --git a/packages_rs/nextclade/benches/bench_create_stripes.rs b/packages_rs/nextclade/benches/bench_create_stripes.rs index e10348d55..728485685 100644 --- a/packages_rs/nextclade/benches/bench_create_stripes.rs +++ b/packages_rs/nextclade/benches/bench_create_stripes.rs @@ -22,9 +22,7 @@ pub fn bench_create_stripes(c: &mut Criterion) { let excess_bandwidth = black_box(2); let qry_len = black_box(30); let ref_len = black_box(40); - let max_indel = black_box(400); - let allowed_mismatches = black_box(2); - let max_band_area = black_box(500_000_000); + let minimal_bandwidth = black_box(0); let mut group = c.benchmark_group("create_stripes"); group.throughput(Throughput::Bytes(qry_len as u64)); @@ -36,8 +34,7 @@ pub fn bench_create_stripes(c: &mut Criterion) { ref_len, terminal_bandwidth, excess_bandwidth, - allowed_mismatches, - max_band_area, + minimal_bandwidth, ) }); }); diff --git a/packages_rs/nextclade/benches/bench_seed_alignment.rs b/packages_rs/nextclade/benches/bench_seed_alignment.rs index 8ce268981..66c7c85ad 100644 --- a/packages_rs/nextclade/benches/bench_seed_alignment.rs +++ b/packages_rs/nextclade/benches/bench_seed_alignment.rs @@ -6,7 +6,6 @@ use nextclade::align::params::AlignPairwiseParams; use nextclade::align::seed_alignment::create_alignment_band; use nextclade::align::seed_match2::{get_seed_matches_maybe_reverse_complement, CodonSpacedIndex, SeedMatchesResult}; use nextclade::alphabet::nuc::to_nuc_seq; -use nextclade::gene::gene_map::GeneMap; pub fn bench_seed_alignment(c: &mut Criterion) { let params = AlignPairwiseParams::default(); @@ -20,6 +19,8 @@ pub fn bench_seed_alignment(c: &mut Criterion) { let seed_index = CodonSpacedIndex::from_sequence(&ref_seq); + let minimal_bandwidth = black_box(0); + let mut group = c.benchmark_group("seed_alignment"); group.bench_function("seed_match", |b| { b.iter(|| { @@ -32,10 +33,8 @@ pub fn bench_seed_alignment(c: &mut Criterion) { ref_seq.len() as isize, params.terminal_bandwidth as isize, params.excess_bandwidth as isize, - params.allowed_mismatches as isize, - params.max_band_area, - ) - .unwrap(); + minimal_bandwidth, + ); }); }); group.finish();