fix: group deletions into ranges correctly

packages/nextclade/src/analyze/aa_del.rs

@@ -1,8 +1,9 @@
-use crate::alphabet::aa::Aa;
+use crate::alphabet::aa::{to_aa, Aa};
 use crate::analyze::aa_sub::AaSub;
 use crate::analyze::abstract_mutation::{AbstractMutation, CloneableMutation, MutParams, Pos, QryLetter, RefLetter};
 use crate::coord::position::AaRefPosition;
 use crate::coord::range::AaRefRange;
+use eyre::Report;
 use serde::{Deserialize, Serialize};
 use std::fmt::{Display, Formatter};
 
@@ -45,6 +46,14 @@ impl Pos<AaRefPosition> for AaDel {
 }
 
 impl AaDel {
+  pub fn from_raw(cds: impl AsRef<str>, pos: usize, ref_nuc: char) -> Result<Self, Report> {
+    Ok(Self {
+      cds_name: cds.as_ref().to_owned(),
+      pos: pos.into(),
+      ref_aa: to_aa(ref_nuc)?,
+    })
+  }
+
   /// Converts deletion to substitution to Gap
   #[inline]
   pub fn to_sub(&self) -> AaSub {

packages/nextclade/src/analyze/group_adjacent_deletions.rs

@@ -12,12 +12,12 @@ pub fn group_adjacent<P: PositionLike>(dels: &[impl Pos<P>]) -> Vec<Range<P>> {
     let mut end = begin;
     for del in dels.iter().skip(1) {
       if del.pos().as_isize() != end.as_isize() + 1 {
-        ranges.push(Range::new(begin, end));
+        ranges.push(Range::from_isize(begin.as_isize(), end.as_isize() + 1));
         begin = del.pos();
       }
       end = del.pos();
     }
-    ranges.push(Range::new(begin, end));
+    ranges.push(Range::from_isize(begin.as_isize(), end.as_isize() + 1));
   } else {
     return vec![];
   }
@@ -42,8 +42,10 @@ pub fn group_adjacent_aa_dels(dels: &[AaDel]) -> Vec<AaDelRange> {
 #[cfg(test)]
 mod tests {
   use super::*;
+  use crate::analyze::aa_del::{AaDel, AaDelRange};
   use crate::analyze::nuc_del::{NucDel, NucDelRange};
   use eyre::Report;
+  use pretty_assertions::assert_eq;
 
   #[test]
   fn test_group_adjacent_empty_input() -> Result<(), Report> {
@@ -57,7 +59,7 @@ mod tests {
   fn test_group_adjacent_single_deletion() -> Result<(), Report> {
     let dels = vec![NucDel::from_raw(5, 'A')?];
     let ranges = group_adjacent_nuc_dels(&dels);
-    assert_eq!(ranges, vec![NucDelRange::from_usize(5, 5)]);
+    assert_eq!(ranges, vec![NucDelRange::from_usize(5, 6)]);
     Ok(())
   }
 
@@ -72,9 +74,9 @@ mod tests {
     assert_eq!(
       ranges,
       vec![
-        NucDelRange::from_usize(1, 1),
-        NucDelRange::from_usize(3, 3),
-        NucDelRange::from_usize(5, 5)
+        NucDelRange::from_usize(1, 2),
+        NucDelRange::from_usize(3, 4),
+        NucDelRange::from_usize(5, 6),
       ]
     );
     Ok(())
@@ -88,7 +90,7 @@ mod tests {
       NucDel::from_raw(3, 'G')?,
     ];
     let ranges = group_adjacent_nuc_dels(&dels);
-    assert_eq!(ranges, vec![NucDelRange::from_usize(1, 3)]);
+    assert_eq!(ranges, vec![NucDelRange::from_usize(1, 4)]);
     Ok(())
   }
 
@@ -116,17 +118,104 @@ mod tests {
     assert_eq!(
       ranges,
       vec![
-        NucDelRange::from_usize(1, 1),
-        NucDelRange::from_usize(3, 4),
-        NucDelRange::from_usize(6, 6),
-        NucDelRange::from_usize(8, 10),
-        NucDelRange::from_usize(12, 12),
-        NucDelRange::from_usize(14, 14),
-        NucDelRange::from_usize(16, 17),
-        NucDelRange::from_usize(19, 19),
-        NucDelRange::from_usize(21, 21),
-        NucDelRange::from_usize(23, 24),
-        NucDelRange::from_usize(26, 26)
+        NucDelRange::from_usize(1, 2),
+        NucDelRange::from_usize(3, 5),
+        NucDelRange::from_usize(6, 7),
+        NucDelRange::from_usize(8, 11),
+        NucDelRange::from_usize(12, 13),
+        NucDelRange::from_usize(14, 15),
+        NucDelRange::from_usize(16, 18),
+        NucDelRange::from_usize(19, 20),
+        NucDelRange::from_usize(21, 22),
+        NucDelRange::from_usize(23, 25),
+        NucDelRange::from_usize(26, 27),
+      ]
+    );
+    Ok(())
+  }
+
+  #[test]
+  fn test_group_adjacent_aa_dels_empty_input() -> Result<(), Report> {
+    let dels = vec![];
+    let ranges = group_adjacent_aa_dels(&dels);
+    assert!(ranges.is_empty());
+    Ok(())
+  }
+
+  #[test]
+  fn test_group_adjacent_aa_dels_single_deletion() -> Result<(), Report> {
+    let dels = vec![AaDel::from_raw("Gene1", 5, 'A')?];
+    let ranges = group_adjacent_aa_dels(&dels);
+    assert_eq!(ranges, vec![AaDelRange::from_usize(5, 6)]);
+    Ok(())
+  }
+
+  #[test]
+  fn test_group_adjacent_aa_dels_multiple_non_adjacent_deletions() -> Result<(), Report> {
+    let dels = vec![
+      AaDel::from_raw("Gene1", 1, 'A')?,
+      AaDel::from_raw("Gene1", 3, 'T')?,
+      AaDel::from_raw("Gene1", 5, 'G')?,
+    ];
+    let ranges = group_adjacent_aa_dels(&dels);
+    assert_eq!(
+      ranges,
+      vec![
+        AaDelRange::from_usize(1, 2),
+        AaDelRange::from_usize(3, 4),
+        AaDelRange::from_usize(5, 6),
+      ]
+    );
+    Ok(())
+  }
+
+  #[test]
+  fn test_group_adjacent_aa_dels_multiple_adjacent_deletions() -> Result<(), Report> {
+    let dels = vec![
+      AaDel::from_raw("Gene1", 1, 'A')?,
+      AaDel::from_raw("Gene1", 2, 'T')?,
+      AaDel::from_raw("Gene1", 3, 'G')?,
+    ];
+    let ranges = group_adjacent_aa_dels(&dels);
+    assert_eq!(ranges, vec![AaDelRange::from_usize(1, 4)]);
+    Ok(())
+  }
+
+  #[test]
+  fn test_group_adjacent_aa_dels_complex_mixed_deletions() -> Result<(), Report> {
+    let dels = vec![
+      AaDel::from_raw("Gene1", 1, 'A')?,
+      AaDel::from_raw("Gene1", 3, 'T')?,
+      AaDel::from_raw("Gene1", 4, 'G')?,
+      AaDel::from_raw("Gene1", 6, 'C')?,
+      AaDel::from_raw("Gene1", 8, 'A')?,
+      AaDel::from_raw("Gene1", 9, 'T')?,
+      AaDel::from_raw("Gene1", 10, 'G')?,
+      AaDel::from_raw("Gene1", 12, 'C')?,
+      AaDel::from_raw("Gene1", 14, 'A')?,
+      AaDel::from_raw("Gene1", 16, 'T')?,
+      AaDel::from_raw("Gene1", 17, 'G')?,
+      AaDel::from_raw("Gene1", 19, 'C')?,
+      AaDel::from_raw("Gene1", 21, 'A')?,
+      AaDel::from_raw("Gene1", 23, 'T')?,
+      AaDel::from_raw("Gene1", 24, 'G')?,
+      AaDel::from_raw("Gene1", 26, 'C')?,
+    ];
+    let ranges = group_adjacent_aa_dels(&dels);
+    assert_eq!(
+      ranges,
+      vec![
+        AaDelRange::from_usize(1, 2),
+        AaDelRange::from_usize(3, 5),
+        AaDelRange::from_usize(6, 7),
+        AaDelRange::from_usize(8, 11),
+        AaDelRange::from_usize(12, 13),
+        AaDelRange::from_usize(14, 15),
+        AaDelRange::from_usize(16, 18),
+        AaDelRange::from_usize(19, 20),
+        AaDelRange::from_usize(21, 22),
+        AaDelRange::from_usize(23, 25),
+        AaDelRange::from_usize(26, 27),
       ]
     );
     Ok(())