Merge remote-tracking branch 'origin/master' into feat/ref-minimizer

nextstrain · Sep 8, 2023 · 619aab4 · 619aab4
2 parents e30adc0 + 119cd4a
commit 619aab4
Show file tree

Hide file tree

Showing 4 changed files with 13 additions and 14 deletions.
diff --git a/packages_rs/nextclade-cli/src/cli/nextclade_cli.rs b/packages_rs/nextclade-cli/src/cli/nextclade_cli.rs
@@ -57,7 +57,7 @@ pub struct NextcladeArgs {
   pub command: NextcladeCommands,
 
   /// Make output more quiet or more verbose
-  #[clap(flatten, next_help_heading = "  Verbosity")]
+  #[clap(flatten, next_help_heading = "Verbosity")]
   pub verbosity: Verbosity<WarnLevel>,
 }
 
@@ -280,7 +280,7 @@ pub struct NextcladeRunInputArgs {
   ///
   /// See: https://en.wikipedia.org/wiki/FASTA_format
   #[clap(value_hint = ValueHint::FilePath)]
-  #[clap(display_order = 1)]
+  #[clap(display_order = 0)]
   pub input_fastas: Vec<PathBuf>,
 
   /// REMOVED. Use positional arguments instead.
@@ -615,16 +615,16 @@ pub struct NextcladeRunOtherParams {
 
 #[derive(Parser, Debug, Clone)]
 pub struct NextcladeRunArgs {
-  #[clap(flatten, next_help_heading = "  Inputs")]
+  #[clap(flatten, next_help_heading = "Inputs")]
   pub inputs: NextcladeRunInputArgs,
 
-  #[clap(flatten, next_help_heading = "  Outputs")]
+  #[clap(flatten, next_help_heading = "Outputs")]
   pub outputs: NextcladeRunOutputArgs,
 
   #[clap(flatten)]
   pub params: NextcladeInputParamsOptional,
 
-  #[clap(flatten, next_help_heading = "  Other")]
+  #[clap(flatten, next_help_heading = "Other")]
   pub other_params: NextcladeRunOtherParams,
 }
 

diff --git a/packages_rs/nextclade/benches/bench_create_stripes.rs b/packages_rs/nextclade/benches/bench_create_stripes.rs
@@ -22,7 +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 minimal_bandwidth = black_box(1);
+  let minimal_bandwidth = black_box(0);
 
   let mut group = c.benchmark_group("create_stripes");
   group.throughput(Throughput::Bytes(qry_len as u64));

diff --git 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();

diff --git a/packages_rs/nextclade/src/run/params.rs b/packages_rs/nextclade/src/run/params.rs
@@ -8,13 +8,13 @@ use serde::{Deserialize, Serialize};
 #[derive(Parser, Debug, Default, Clone, Serialize, Deserialize, schemars::JsonSchema)]
 #[serde(rename_all = "camelCase")]
 pub struct NextcladeInputParamsOptional {
-  #[clap(flatten, next_help_heading = "  General parameters")]
+  #[clap(flatten, next_help_heading = "General parameters")]
   pub general: Option<NextcladeGeneralParamsOptional>,
 
-  #[clap(flatten, next_help_heading = "  Phylogenetic tree parameters")]
+  #[clap(flatten, next_help_heading = "Phylogenetic tree parameters")]
   pub tree_builder: Option<TreeBuilderParamsOptional>,
 
-  #[clap(flatten, next_help_heading = "  Alignment parameters")]
+  #[clap(flatten, next_help_heading = "Alignment parameters")]
   pub alignment: Option<AlignPairwiseParamsOptional>,
 }