feat(variants): show tree branch(es) a SNP is assigned to on the deta…

rust/crates/du-db/src/variant.rs

@@ -233,6 +233,62 @@ pub async fn set_coordinates_batch(
     Ok(affected)
 }
 
+/// One tree branch a variant is assigned to (defines). Surfaced on the Variant Browser detail.
+#[derive(Debug, Clone)]
+pub struct BranchAssignment {
+    /// Haplogroup (branch) name, e.g. `R-M269`.
+    pub haplogroup_name: String,
+    /// `"Y_DNA"` or `"MT_DNA"` — selects the tree page for the link.
+    pub dna_type: String,
+    /// The link is marked provisional/low-confidence.
+    pub low_confidence: bool,
+    /// The defining variant's canonical name. Differs from the viewed variant when the tree
+    /// placement lives on a same-site sibling row (the de-novo coordinate-named variant vs a
+    /// separately-named catalog row).
+    pub via_name: String,
+}
+
+/// The tree branch(es) a variant is assigned to (defines) in the *current* tree.
+///
+/// Matched by genomic **site**, not just the row's own links: the de-novo tree places a
+/// coordinate-named variant (`chrY:<pos><ref>>>...`) while the same physical SNP may also exist
+/// as a separately-named catalog row (e.g. a YBrowse name like `V3739`) carrying no direct
+/// link. `site` is a `{"hs1":{"contig":…,"position":…}}` containment blob built from the
+/// viewed variant's hs1 coordinate (the tree is hs1-native) — GIN-indexed on `coordinates` —
+/// or `None` when it has no hs1 coordinate (then only the variant's own direct links match).
+pub async fn tree_branches(
+    pool: &PgPool,
+    variant_id: VariantId,
+    site: Option<serde_json::Value>,
+) -> Result<Vec<BranchAssignment>, DbError> {
+    let rows: Vec<(String, String, bool, String)> = sqlx::query_as(
+        "WITH cand AS ( \
+             SELECT $1::bigint AS id \
+             UNION \
+             SELECT id FROM core.variant WHERE $2::jsonb IS NOT NULL AND coordinates @> $2::jsonb \
+         ) \
+         SELECT DISTINCT h.name, h.haplogroup_type::text, hv.low_confidence, def.canonical_name \
+         FROM cand \
+         JOIN tree.haplogroup_variant hv ON hv.variant_id = cand.id AND hv.valid_until IS NULL \
+         JOIN core.variant def ON def.id = cand.id \
+         JOIN tree.haplogroup h ON h.id = hv.haplogroup_id \
+         ORDER BY h.name",
+    )
+    .bind(variant_id.0)
+    .bind(site)
+    .fetch_all(pool)
+    .await?;
+    Ok(rows
+        .into_iter()
+        .map(|(haplogroup_name, dna_type, low_confidence, via_name)| BranchAssignment {
+            haplogroup_name,
+            dna_type,
+            low_confidence,
+            via_name,
+        })
+        .collect())
+}
+
 /// Region types whose sequence is structurally unreliable for Y-SNP placement
 /// (multi-copy / repeat-rich), so a variant landing inside one should not be
 /// trusted as branch-defining without scrutiny. AZF intervals are deliberately

rust/crates/du-web/src/routes/variants.rs

@@ -100,6 +100,17 @@ struct CoordView {
     change: Option<String>,
 }
 
+/// A tree branch this variant defines, flattened for the template.
+struct BranchView {
+    name: String,
+    /// Link to the branch on the relevant tree page.
+    tree_url: String,
+    low_confidence: bool,
+    /// The defining variant's name, shown only when it differs from the viewed variant
+    /// (the placement is carried by a same-site sibling row).
+    via: Option<String>,
+}
+
 #[derive(askama::Template)]
 #[template(path = "variants/detail.html")]
 struct DetailTemplate {
@@ -110,6 +121,7 @@ struct DetailTemplate {
     common_names: Vec<String>,
     rs_ids: Vec<String>,
     coords: Vec<CoordView>,
+    branches: Vec<BranchView>,
 }
 
 async fn browser(
@@ -156,6 +168,28 @@ async fn detail(
         .collect();
     coords.sort_by(|a, b| a.build.cmp(&b.build));
 
+    // Which tree branch(es) this SNP is assigned to. Match by hs1 site (the tree is
+    // hs1-native), so a catalog-named SNP still surfaces the placement its de-novo
+    // coordinate-named sibling carries.
+    let site = v
+        .coordinates
+        .get(du_domain::enums::ReferenceBuild::Hs1)
+        .map(|c| serde_json::json!({ "hs1": { "contig": c.contig, "position": c.position } }));
+    let variant_name = v.canonical_name.clone();
+    let branches = du_db::variant::tree_branches(&st.pool, VariantId(id), site)
+        .await?
+        .into_iter()
+        .map(|b| {
+            let base = if b.dna_type == "MT_DNA" { "/mtree" } else { "/ytree" };
+            BranchView {
+                tree_url: format!("{base}?root={}", b.haplogroup_name),
+                via: (b.via_name != variant_name).then_some(b.via_name),
+                name: b.haplogroup_name,
+                low_confidence: b.low_confidence,
+            }
+        })
+        .collect();
+
     Ok(html(&DetailTemplate {
         t: locale.t,
         name: v.canonical_name,
@@ -164,5 +198,6 @@ async fn detail(
         common_names: v.aliases.common_names,
         rs_ids: v.aliases.rs_ids,
         coords,
+        branches,
     }))
 }

rust/crates/du-web/templates/variants/detail.html

@@ -41,5 +41,20 @@ <h6 class="mt-3">{{ t.get("variants.detail.coordinates") }}</h6>
       </tbody>
     </table>
     {% endif %}
+
+    <h6 class="mt-3">{{ t.get("variants.detail.branches") }}</h6>
+    {% if branches.is_empty() %}
+    <p class="detail-empty">{{ t.get("variants.detail.nobranches") }}</p>
+    {% else %}
+    <ul class="list-unstyled mb-0">
+      {% for b in branches %}
+      <li class="mb-1">
+        <a href="{{ b.tree_url }}"><code>{{ b.name }}</code></a>
+        {% if b.low_confidence %}<span class="badge text-bg-warning">{{ t.get("variants.detail.lowconf") }}</span>{% endif %}
+        {% if let Some(via) = b.via %}<small class="text-muted">{{ t.get("variants.detail.via") }} <code>{{ via }}</code></small>{% endif %}
+      </li>
+      {% endfor %}
+    </ul>
+    {% endif %}
   </div>
 </div>

rust/locales/en.txt

@@ -106,6 +106,10 @@ variants.detail.aka=Also known as:
 variants.detail.rsids=rs IDs:
 variants.detail.coordinates=Coordinates
 variants.detail.nocoords=No mapped coordinates.
+variants.detail.branches=Tree branch(es)
+variants.detail.nobranches=Not assigned to a tree branch.
+variants.detail.via=via
+variants.detail.lowconf=provisional
 variants.col.build=Build
 variants.col.contig=Contig
 variants.col.position=Position

rust/locales/es.txt

@@ -58,6 +58,10 @@ variants.detail.aka=También conocido como:
 variants.detail.rsids=Identificadores rs:
 variants.detail.coordinates=Coordenadas
 variants.detail.nocoords=Sin coordenadas asignadas.
+variants.detail.branches=Rama(s) del árbol
+variants.detail.nobranches=No asignado a ninguna rama del árbol.
+variants.detail.via=vía
+variants.detail.lowconf=provisional
 variants.col.build=Ensamblaje
 variants.col.contig=Contig
 variants.col.position=Posición

rust/locales/fr.txt

@@ -58,6 +58,10 @@ variants.detail.aka=Aussi connu sous le nom de :
 variants.detail.rsids=Identifiants rs :
 variants.detail.coordinates=Coordonnées
 variants.detail.nocoords=Aucune coordonnée cartographiée.
+variants.detail.branches=Branche(s) de l'arbre
+variants.detail.nobranches=Non assigné à une branche de l'arbre.
+variants.detail.via=via
+variants.detail.lowconf=provisoire
 variants.col.build=Assemblage
 variants.col.contig=Contig
 variants.col.position=Position

rust/migrations/0055_haplogroup_variant_variant_idx.sql

@@ -0,0 +1,9 @@
+-- Index tree.haplogroup_variant by variant_id for the *current* (valid_until IS NULL) links.
+--
+-- The existing haplogroup_variant_current_key is UNIQUE (haplogroup_id, variant_id) — it leads
+-- with haplogroup_id, so the reverse lookup "which branch(es) is this variant assigned to?" has
+-- no supporting index and seq-scans the whole table. That lookup backs the Variant Browser's
+-- tree-branch panel (site-matched, so it runs per variant-detail view), plus any future
+-- variant->branch surfacing. Partial (valid_until IS NULL) to match the current-links workload.
+CREATE INDEX IF NOT EXISTS haplogroup_variant_variant_idx
+    ON tree.haplogroup_variant (variant_id) WHERE valid_until IS NULL;