Merge pull request #1404 from nextstrain/chore/cleanup-3

Author: ivan-aksamentov

packages/nextclade/Cargo.toml

@@ -82,10 +82,6 @@ rstest_reuse = "=0.5.0"
 name = "bench_create_stripes"
 harness = false
 
-[[bench]]
-name = "bench_seed_match"
-harness = false
-
 [[bench]]
 name = "bench_seed_alignment"
 harness = false

packages/nextclade/benches/bench_create_stripes.rs

@@ -1,6 +1,6 @@
 use criterion::{black_box, criterion_group, criterion_main, Criterion, Throughput};
 use nextclade::align::seed_alignment::create_alignment_band;
-use nextclade::align::seed_match2::SeedMatch2;
+use nextclade::align::seed_match::SeedMatch2;
 
 pub fn bench_create_stripes(c: &mut Criterion) {
   let seed_matches = black_box(vec![

packages/nextclade/benches/bench_seed_alignment.rs

@@ -4,7 +4,7 @@ use std::path::PathBuf;
 use criterion::{black_box, criterion_group, criterion_main, Criterion};
 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::align::seed_match::{get_seed_matches_maybe_reverse_complement, CodonSpacedIndex, SeedMatchesResult};
 use nextclade::alphabet::nuc::to_nuc_seq;
 
 pub fn bench_seed_alignment(c: &mut Criterion) {

packages/nextclade/benches/bench_seed_match.rs

@@ -1,10 +1,10 @@
 use crate::align::backtrace::{backtrace, AlignmentOutput};
 use crate::align::band_2d::Stripe;
 use crate::align::band_2d::{full_matrix, simple_stripes};
-use crate::align::params::AlignPairwiseParams;
 use crate::align::score_matrix::{score_matrix, ScoreMatrixResult};
 use crate::align::seed_alignment::create_alignment_band;
-use crate::align::seed_match2::{get_seed_matches_maybe_reverse_complement, CodonSpacedIndex, SeedMatchesResult};
+use crate::align::params::AlignPairwiseParams;
+use crate::align::seed_match::{get_seed_matches_maybe_reverse_complement, CodonSpacedIndex, SeedMatchesResult};
 use crate::alphabet::aa::Aa;
 use crate::alphabet::letter::Letter;
 use crate::alphabet::nuc::Nuc;

packages/nextclade/src/align/align.rs

@@ -10,4 +10,3 @@ pub mod score_matrix_aa;
 pub mod score_matrix_nuc;
 pub mod seed_alignment;
 pub mod seed_match;
-pub mod seed_match2;

packages/nextclade/src/align/mod.rs

@@ -1,21 +1,12 @@
-use crate::align::band_2d::full_matrix;
 use crate::align::band_2d::Stripe;
-use crate::align::params::AlignPairwiseParams;
-use crate::align::seed_match::seed_match;
-use crate::align::seed_match2::{get_seed_matches2, CodonSpacedIndex, SeedMatch2};
+use crate::align::seed_match::SeedMatch2;
 use crate::alphabet::letter::Letter;
-use crate::alphabet::nuc::Nuc;
-use crate::coord::position::LocalSpace;
-use crate::make_error;
-use crate::utils::collections::first;
 use eyre::Report;
 use log::trace;
 use num_traits::abs;
 use num_traits::clamp;
-use num_traits::clamp_min;
 use std::cmp::max;
 use std::cmp::min;
-use std::collections::BTreeMap;
 
 /// generate a vector of query sequence positions that are followed by at least `seed_length`
 /// valid characters. Positions in this vector are thus "good" positions to start a query k-mer.