feat: implement alignment param presets

Define some hard-coded presets of alignment parameters additionally to the default one.

The `--alignment-preset` arg allows users to toggle between presets.

Example:

```bash
nextclade run --dataset-name=sars-cov-2 -O tmp/sars-cov-2 sequences.fasta --alignment-preset=high-diversity --verbosity=info
```

packages/nextclade/src/align/params.rs

@@ -30,6 +30,10 @@ impl Default for GapAlignmentSide {
 #[derive(Parser, Debug, Clone, Eq, PartialEq, Serialize, Deserialize, schemars::JsonSchema)]
 #[serde(rename_all = "camelCase")]
 pub struct AlignPairwiseParams {
+  /// Alignment param preset
+  #[clap(long, default_value = ALIGNMENT_PRESET_DEFAULT)]
+  pub alignment_preset: String,
+
   /// Minimum length of nucleotide sequence to consider for alignment.
   ///
   /// If a sequence is shorter than that, alignment will not be attempted and a warning will be emitted. When adjusting this parameter, note that alignment of short sequences can be unreliable.
@@ -150,9 +154,13 @@ pub struct AlignPairwiseParams {
   pub seed_spacing: Option<AnyType>,
 }
 
+pub const ALIGNMENT_PRESET_DEFAULT: &str = "default";
+
 impl Default for AlignPairwiseParams {
   fn default() -> Self {
     Self {
+      alignment_preset: ALIGNMENT_PRESET_DEFAULT.to_owned(),
+
       min_length: 100,
       penalty_gap_extend: 0,
       penalty_gap_open: 6,
@@ -188,6 +196,29 @@ impl Default for AlignPairwiseParams {
 }
 
 impl AlignPairwiseParams {
+  pub fn from_preset(preset_name: impl AsRef<str>) -> Result<AlignPairwiseParams, Report> {
+    let preset_name = preset_name.as_ref();
+    match preset_name {
+      "default" => Ok(AlignPairwiseParams::default()),
+      "high-diversity" => Ok(AlignPairwiseParams {
+        alignment_preset: o!("high-diversity"),
+        penalty_gap_extend: 0,
+        penalty_gap_open: 999999,             // FIXME: dummy values
+        penalty_gap_open_in_frame: 88888,     // FIXME: dummy values
+        penalty_gap_open_out_of_frame: 77777, // FIXME: dummy values
+        penalty_mismatch: 6666,               // FIXME: dummy values
+        score_match: 33333,                   // FIXME: dummy values
+        ..AlignPairwiseParams::default()
+      }),
+      "short-sequences" => Ok(AlignPairwiseParams {
+        alignment_preset: o!("short-sequences"),
+        min_length: 0, // FIXME: dummy values
+        ..AlignPairwiseParams::default()
+      }),
+      _ => make_error!("Alignment params preset not found: {preset_name}"),
+    }
+  }
+
   pub fn validate(&self) -> Result<(), Report> {
     #[rustfmt::skip]
   let deprecated = BTreeMap::from([

packages/nextclade/src/run/params.rs

@@ -1,4 +1,4 @@
-use crate::align::params::{AlignPairwiseParams, AlignPairwiseParamsOptional};
+use crate::align::params::{AlignPairwiseParams, AlignPairwiseParamsOptional, ALIGNMENT_PRESET_DEFAULT};
 use crate::analyze::aa_changes_find_for_cds::{AaChangesParams, AaChangesParamsOptional};
 use crate::analyze::virus_properties::VirusProperties;
 use crate::run::params_general::{NextcladeGeneralParams, NextcladeGeneralParamsOptional};
@@ -52,9 +52,16 @@ impl NextcladeInputParams {
       general_params
     };
 
+    let preset_name: String = params
+      .alignment
+      .as_ref()
+      .and_then(|a| a.alignment_preset.as_ref())
+      .cloned()
+      .unwrap_or_else(|| ALIGNMENT_PRESET_DEFAULT.to_owned());
+
     let alignment = {
       // Start with defaults
-      let mut alignment_params = AlignPairwiseParams::default();
+      let mut alignment_params = AlignPairwiseParams::from_preset(preset_name)?;
       // Merge params coming from virus_properties
       if let Some(alignment_params_from_file) = &virus_properties.alignment_params {
         alignment_params.merge_opt(alignment_params_from_file.clone());