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fix: treat deletions as undetermined in nearest node distance #1765

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Merged
ivan-aksamentov merged 2 commits into from
Apr 28, 2026
+131 −13
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fix: treat deletions as undetermined in nearest node distance #1765

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d9d1caa
fix(tree): treat deletions as undetermined in nearest node distance
ivan-aksamentov Apr 28, 2026
3004cda
test(tree): add test for deletion-aware nearest node distance
ivan-aksamentov Apr 28, 2026
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3 changes: 2 additions & 1 deletion packages/nextclade/src/run/nextclade_run_one.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -327,7 +327,8 @@ pub fn nextclade_run_one(
nearest_node_name,
nearest_nodes,
} = if let Some(graph) = graph {
let nearest_node_candidates = graph_find_nearest_nodes(graph, &substitutions, &missing, &alignment_range)?;
let nearest_node_candidates =
graph_find_nearest_nodes(graph, &substitutions, &missing, &deletions, &alignment_range)?;
let nearest_node_id = nearest_node_candidates[0].node_key;
let nearest_node = graph.get_node(nearest_node_id)?.payload();
let nearest_node_name = nearest_node.name.clone();
Expand Down
141 changes: 129 additions & 12 deletions packages/nextclade/src/tree/tree_find_nearest_node.rs
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
use crate::alphabet::nuc::Nuc;
use crate::analyze::is_sequenced::is_nuc_sequenced;
use crate::analyze::letter_ranges::NucRange;
use crate::analyze::nuc_del::NucDelRange;
use crate::analyze::nuc_sub::NucSub;
use crate::coord::range::NucRefGlobalRange;
use crate::graph::node::GraphNodeKey;
Expand All @@ -21,6 +22,7 @@ pub fn graph_find_nearest_nodes(
graph: &AuspiceGraph,
qry_nuc_subs: &[NucSub],
qry_missing: &[NucRange],
qry_deletions: &[NucDelRange],
aln_range: &NucRefGlobalRange,
) -> Result<Vec<TreePlacementInfo>, Report> {
let masked_ranges = graph.data.meta.placement_mask_ranges();
Expand All @@ -29,7 +31,14 @@ pub fn graph_find_nearest_nodes(
let nodes_by_placement_score = DftPre::new(graph.get_exactly_one_root()?, |node| graph.iter_children_of(node))
.map(|(_, node)| {
let node_payload = node.payload();
let distance = tree_calculate_node_distance(node_payload, qry_nuc_subs, qry_missing, aln_range, masked_ranges);
let distance = tree_calculate_node_distance(
node_payload,
qry_nuc_subs,
qry_missing,
qry_deletions,
aln_range,
masked_ranges,
);
let prior = get_prior(node_payload);
TreePlacementInfo {
node_key: node.key(),
Expand Down Expand Up @@ -69,6 +78,7 @@ fn tree_calculate_node_distance(
node: &AuspiceGraphNodePayload,
qry_nuc_subs: &[NucSub],
qry_missing: &[NucRange],
qry_deletions: &[NucDelRange],
aln_range: &NucRefGlobalRange,
masked_ranges: &[NucRefGlobalRange],
) -> i64 {
Expand Down Expand Up @@ -105,11 +115,13 @@ fn tree_calculate_node_distance(
}
}

// determine the number of sites that are mutated in the node but missing in seq.
// determine the number of sites that are mutated in the node but missing or deleted in seq.
// for these we can't tell whether the node agrees with seq
let mut undetermined_sites = 0_i64;
for pos in node.tmp.substitutions.keys() {
if !is_nuc_sequenced(*pos, &masked_qry_missing, aln_range) {
if !is_nuc_sequenced(*pos, &masked_qry_missing, aln_range)
|| qry_deletions.iter().any(|del| del.range().contains(*pos))
{
undetermined_sites += 1;
}
}
Comment on lines 117 to 127
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@ivan-aksamentov ivan-aksamentov Apr 28, 2026 •
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Dels are new passed to distance metric calculation and counted same as unknowns or unsequenced. But I imagine it can also be treat differently if needed.

Expand Down Expand Up @@ -234,7 +246,15 @@ mod tests {
let aln_range = NucRefGlobalRange::from_usize(0, 100);
let masked_ranges = vec![];

let result = tree_calculate_node_distance(&node, &qry_nuc_subs, &qry_missing, &aln_range, &masked_ranges);
let qry_deletions: Vec<NucDelRange> = vec![];
let result = tree_calculate_node_distance(
&node,
&qry_nuc_subs,
&qry_missing,
&qry_deletions,
&aln_range,
&masked_ranges,
);

assert_eq!(result, 0);

Expand All @@ -249,7 +269,15 @@ mod tests {
let aln_range = NucRefGlobalRange::from_usize(0, 100);
let masked_ranges = vec![];

let result = tree_calculate_node_distance(&node, &qry_nuc_subs, &qry_missing, &aln_range, &masked_ranges);
let qry_deletions: Vec<NucDelRange> = vec![];
let result = tree_calculate_node_distance(
&node,
&qry_nuc_subs,
&qry_missing,
&qry_deletions,
&aln_range,
&masked_ranges,
);

assert_eq!(result, 3);

Expand All @@ -264,7 +292,15 @@ mod tests {
let aln_range = NucRefGlobalRange::from_usize(0, 100);
let masked_ranges = vec![];

let result = tree_calculate_node_distance(&node, &qry_nuc_subs, &qry_missing, &aln_range, &masked_ranges);
let qry_deletions: Vec<NucDelRange> = vec![];
let result = tree_calculate_node_distance(
&node,
&qry_nuc_subs,
&qry_missing,
&qry_deletions,
&aln_range,
&masked_ranges,
);

assert_eq!(result, 5);

Expand All @@ -279,7 +315,15 @@ mod tests {
let aln_range = NucRefGlobalRange::from_usize(0, 100);
let masked_ranges = vec![];

let result = tree_calculate_node_distance(&node, &qry_nuc_subs, &qry_missing, &aln_range, &masked_ranges);
let qry_deletions: Vec<NucDelRange> = vec![];
let result = tree_calculate_node_distance(
&node,
&qry_nuc_subs,
&qry_missing,
&qry_deletions,
&aln_range,
&masked_ranges,
);

assert_eq!(result, 5);

Expand All @@ -294,7 +338,15 @@ mod tests {
let aln_range = NucRefGlobalRange::from_usize(0, 100);
let masked_ranges = vec![];

let result = tree_calculate_node_distance(&node, &qry_nuc_subs, &qry_missing, &aln_range, &masked_ranges);
let qry_deletions: Vec<NucDelRange> = vec![];
let result = tree_calculate_node_distance(
&node,
&qry_nuc_subs,
&qry_missing,
&qry_deletions,
&aln_range,
&masked_ranges,
);

assert_eq!(result, 4);

Expand All @@ -309,7 +361,15 @@ mod tests {
let aln_range = NucRefGlobalRange::from_usize(0, 20);
let masked_ranges = vec![];

let result = tree_calculate_node_distance(&node, &qry_nuc_subs, &qry_missing, &aln_range, &masked_ranges);
let qry_deletions: Vec<NucDelRange> = vec![];
let result = tree_calculate_node_distance(
&node,
&qry_nuc_subs,
&qry_missing,
&qry_deletions,
&aln_range,
&masked_ranges,
);

assert_eq!(result, 3);

Expand All @@ -324,7 +384,15 @@ mod tests {
let aln_range = NucRefGlobalRange::from_usize(0, 100);
let masked_ranges = vec![NucRefGlobalRange::from_usize(0, 100)];

let result = tree_calculate_node_distance(&node, &qry_nuc_subs, &qry_missing, &aln_range, &masked_ranges);
let qry_deletions: Vec<NucDelRange> = vec![];
let result = tree_calculate_node_distance(
&node,
&qry_nuc_subs,
&qry_missing,
&qry_deletions,
&aln_range,
&masked_ranges,
);

assert_eq!(result, 0);

Expand All @@ -343,7 +411,15 @@ mod tests {
NucRefGlobalRange::from_usize(30, 50),
];

let result = tree_calculate_node_distance(&node, &qry_nuc_subs, &qry_missing, &aln_range, &masked_ranges);
let qry_deletions: Vec<NucDelRange> = vec![];
let result = tree_calculate_node_distance(
&node,
&qry_nuc_subs,
&qry_missing,
&qry_deletions,
&aln_range,
&masked_ranges,
);

assert_eq!(result, 3);

Expand All @@ -358,10 +434,51 @@ mod tests {
let aln_range = NucRefGlobalRange::from_usize(0, 30);
let masked_ranges = vec![NucRefGlobalRange::from_usize(12, 13)];

let result = tree_calculate_node_distance(&node, &qry_nuc_subs, &qry_missing, &aln_range, &masked_ranges);
let qry_deletions: Vec<NucDelRange> = vec![];
let result = tree_calculate_node_distance(
&node,
&qry_nuc_subs,
&qry_missing,
&qry_deletions,
&aln_range,
&masked_ranges,
);

assert_eq!(result, 3);

Ok(())
}

#[rstest]
fn deletion_covering_node_mutations_reduces_distance() -> Result<(), Report> {
let node = node_with_simple_nuc_subs();
let qry_nuc_subs: Vec<NucSub> = vec![];
let qry_missing: Vec<NucRange> = vec![];
let aln_range = NucRefGlobalRange::from_usize(0, 100);
let masked_ranges = vec![];

let no_deletions: Vec<NucDelRange> = vec![];
let distance_without_del = tree_calculate_node_distance(
&node,
&qry_nuc_subs,
&qry_missing,
&no_deletions,
&aln_range,
&masked_ranges,
);
assert_eq!(distance_without_del, 5);

let qry_deletions = vec![NucDelRange::from_usize(10, 25)];
let distance_with_del = tree_calculate_node_distance(
&node,
&qry_nuc_subs,
&qry_missing,
&qry_deletions,
&aln_range,
&masked_ranges,
);
assert_eq!(distance_with_del, 2);

Ok(())
}
}
Comment on lines +451 to 484
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@ivan-aksamentov ivan-aksamentov Apr 28, 2026

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Tests that adding a del reduces distance metric

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