fix(str): take the marker range from the majority value shape

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

@@ -1110,6 +1110,12 @@ pub struct MarkerStat {
     pub null_alleles: i64,
     /// Partial-repeat / footnoted values (`{type:complex}`), counted but unscored.
     pub complex_count: i64,
+    /// Observations reported in the *minority* shape for this marker — a single
+    /// repeat count where the marker is normally a copy vector, or vice versa.
+    /// DYS413 has 866 multi-copy calls and one bare `23`. The range is taken from
+    /// the majority shape, so these are excluded from it and surfaced here rather
+    /// than silently overriding it.
+    pub mixed_shape_count: i64,
     pub motif: Option<String>,
     pub period: Option<i16>,
     pub coordinates: Option<Value>,
@@ -1173,18 +1179,24 @@ const MARKER_STATS_AGGREGATION: &str = "WITH obs AS ( \
                     count(DISTINCT COALESCE(repeats::text, array_to_string(copies, '-'), raw)) \
                         AS distinct_values, \
                     count(*) FILTER (WHERE is_null_allele) AS null_alleles, \
-                    count(*) FILTER (WHERE vtype = 'complex') AS complex_count \
+                    count(*) FILTER (WHERE vtype = 'complex') AS complex_count, \
+                    count(*) FILTER (WHERE vtype = 'simple') AS simple_obs, \
+                    count(*) FILTER (WHERE vtype = 'multiCopy') AS multi_obs \
                FROM scored \
               GROUP BY marker \
          ) \
          SELECT a.marker AS marker_name, \
                 (a.observed_multi OR COALESCE(m.multi_copy, false)) AS multi_copy, \
                 a.observations, a.samples, \
-                a.min_value, a.modal_value, a.max_value, \
-                a.min_copies AS min_combination, \
-                array_to_string(a.modal_copies, '-') AS modal_combination, \
-                a.max_copies AS max_combination, \
+                CASE WHEN a.multi_obs <= a.simple_obs THEN a.min_value END AS min_value, \
+                CASE WHEN a.multi_obs <= a.simple_obs THEN a.modal_value END AS modal_value, \
+                CASE WHEN a.multi_obs <= a.simple_obs THEN a.max_value END AS max_value, \
+                CASE WHEN a.multi_obs > a.simple_obs THEN a.min_copies END AS min_combination, \
+                CASE WHEN a.multi_obs > a.simple_obs \
+                     THEN array_to_string(a.modal_copies, '-') END AS modal_combination, \
+                CASE WHEN a.multi_obs > a.simple_obs THEN a.max_copies END AS max_combination, \
                 a.distinct_values, a.null_alleles, a.complex_count, \
+                LEAST(a.simple_obs, a.multi_obs) AS mixed_shape_count, \
                 m.motif, m.period, NULLIF(m.coordinates, '{}'::jsonb) AS coordinates, \
                 r.mutation_rate::float8 AS mutation_rate, \
                 r.mutation_rate_lower::float8 AS rate_ci_low, \
@@ -1211,7 +1223,8 @@ const MARKER_STATS_AGGREGATION: &str = "WITH obs AS ( \
 /// Column list shared by the refresh insert and the read path, in table order.
 const MARKER_STAT_COLUMNS: &str = "marker_name, multi_copy, observations, samples, \
      min_value, modal_value, max_value, min_combination, modal_combination, max_combination, \
-     distinct_values, null_alleles, complex_count, motif, period, coordinates, \
+     distinct_values, null_alleles, complex_count, mixed_shape_count, \
+     motif, period, coordinates, \
      mutation_rate, rate_ci_low, rate_ci_high, rate_method, rate_source, age_model_status";
 
 /// Recompute `genomics.str_marker_stat` from every stored profile. Returns the

rust/crates/du-db/tests/str_marker_stats.rs

@@ -184,6 +184,51 @@ async fn marker_stats_reports_range_motif_and_rate_basis() {
     assert_eq!(dys442.modal_value, None);
 }
 
+/// A marker the vendor reports inconsistently — DYS413 in the real corpus has 866
+/// copy-vector calls and one bare `23`. The range must come from the majority
+/// shape: preferring the scalar let a single observation replace the whole range,
+/// which showed min=modal=max=23 for a marker with 25 distinct values.
+#[tokio::test]
+async fn minority_value_shape_does_not_hijack_the_range() {
+    let Some(url) = database_url() else {
+        eprintln!("DATABASE_URL unset — skipping mixed-shape test");
+        return;
+    };
+    let db = du_db::testing::ephemeral_db(&url).await.expect("ephemeral db");
+    let pool = db.pool().clone();
+
+    // Copy-vector calls plus one stray single count, on both marker shapes so the
+    // mirror case (mostly-simple with a stray vector) is covered too. 23-23 is
+    // repeated so it is a genuine mode rather than an arbitrary tie-break.
+    for (n, dys413, dys390) in [
+        (1, multi("DYS413", &[23, 23]), simple("DYS390", 24)),
+        (2, multi("DYS413", &[23, 23]), simple("DYS390", 24)),
+        (3, multi("DYS413", &[21, 23]), simple("DYS390", 25)),
+        (4, multi("DYS413", &[23, 25]), simple("DYS390", 24)),
+        (5, simple("DYS413", 23), multi("DYS390", &[9, 9])),
+    ] {
+        seed_profile(&pool, &format!("MIXED-{n}"), serde_json::json!([dys413, dys390])).await;
+    }
+
+    let stats = ystr::marker_stats(&pool).await.expect("marker_stats");
+
+    // Majority multi-copy ⇒ the copy vectors win and the lone scalar is set aside.
+    let m = find(&stats, "DYS413");
+    assert_eq!(m.min_combination.as_deref(), Some("21-23"));
+    assert_eq!(m.modal_combination.as_deref(), Some("23-23"));
+    assert_eq!(m.max_combination.as_deref(), Some("23-25"));
+    assert_eq!(m.min_value, None, "the stray single count must not be shown as the range");
+    assert_eq!(m.max_value, None);
+    assert_eq!(m.mixed_shape_count, 1, "the odd observation is surfaced, not discarded");
+    assert_eq!(m.observations, 5, "it still counts as an observation");
+
+    // Mirror case: majority simple ⇒ scalars win over the stray vector.
+    let s = find(&stats, "DYS390");
+    assert_eq!((s.min_value, s.modal_value, s.max_value), (Some(24), Some(24), Some(25)));
+    assert_eq!(s.min_combination, None);
+    assert_eq!(s.mixed_shape_count, 1);
+}
+
 #[tokio::test]
 async fn load_marker_models_honors_the_active_rate() {
     let Some(url) = database_url() else {

rust/crates/du-web/src/api/dto.rs

@@ -694,6 +694,10 @@ pub struct StrMarkerStatDto {
     pub null_alleles: i64,
     /// Partial-repeat / footnoted values, preserved but unscored.
     pub complex_count: i64,
+    /// Observations in this marker's minority value shape (a bare repeat count
+    /// where it is normally a copy vector, or vice versa). Excluded from the
+    /// reported range, which follows the majority shape.
+    pub mixed_shape_count: i64,
     /// Repeat unit, where known — we hold one for a minority of markers.
     pub motif: Option<String>,
     pub period: Option<i16>,
@@ -726,6 +730,7 @@ impl From<du_db::ystr::MarkerStat> for StrMarkerStatDto {
             distinct_values: m.distinct_values,
             null_alleles: m.null_alleles,
             complex_count: m.complex_count,
+            mixed_shape_count: m.mixed_shape_count,
             motif: m.motif,
             period: m.period,
             coordinates: m.coordinates,

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

@@ -129,14 +129,18 @@ fn range_cell(value: Option<i32>, combination: &Option<String>) -> String {
 
 /// Null-allele and partial-repeat counts folded into one cell, so two columns
 /// that are empty for nearly every marker don't widen the table.
-fn notes(null_alleles: i64, complex: i64, t: &T) -> String {
+fn notes(null_alleles: i64, complex: i64, mixed_shape: i64, t: &T) -> String {
     let mut parts = Vec::new();
     if null_alleles > 0 {
         parts.push(format!("{null_alleles} {}", t.get("str.markers.note.null")));
     }
     if complex > 0 {
         parts.push(format!("{complex} {}", t.get("str.markers.note.partial")));
     }
+    // Explains why `distinct` can exceed what the shown range accounts for.
+    if mixed_shape > 0 {
+        parts.push(format!("{mixed_shape} {}", t.get("str.markers.note.mixedShape")));
+    }
     parts.join(" · ")
 }
 
@@ -168,7 +172,7 @@ fn to_row(m: du_db::ystr::MarkerStat, t: &T) -> MarkerRow {
         observations: fmt_count(m.observations),
         samples: fmt_count(m.samples),
         distinct_values: fmt_count(m.distinct_values),
-        notes: notes(m.null_alleles, m.complex_count, t),
+        notes: notes(m.null_alleles, m.complex_count, m.mixed_shape_count, t),
         rate: fmt_rate(m.mutation_rate),
         rate_ci: ci,
         rate_source: m.rate_source.unwrap_or_default(),

rust/locales/en.txt

@@ -800,6 +800,7 @@ str.markers.multiCopy=multi-copy
 str.markers.multiCopy.help=Palindromic or duplicated locus, reported as a copy vector (e.g. 11-15) and not used for age estimation.
 str.markers.note.null=null
 str.markers.note.partial=partial
+str.markers.note.mixedShape=other shape
 str.markers.status.measured=Measured rate
 str.markers.status.default=Default rate
 str.markers.status.excluded=Not scored

rust/locales/es.txt

@@ -794,6 +794,7 @@ str.markers.multiCopy=multicopia
 str.markers.multiCopy.help=Locus palindrómico o duplicado, notificado como vector de copias (p. ej. 11-15) y no utilizado para estimar la edad.
 str.markers.note.null=nulo
 str.markers.note.partial=parcial
+str.markers.note.mixedShape=otra forma
 str.markers.status.measured=Tasa medida
 str.markers.status.default=Tasa por defecto
 str.markers.status.excluded=No puntuado

rust/locales/fr.txt

@@ -794,6 +794,7 @@ str.markers.multiCopy=multicopie
 str.markers.multiCopy.help=Locus palindromique ou dupliqué, rapporté sous forme de vecteur de copies (p. ex. 11-15) et non utilisé pour l'estimation de l'âge.
 str.markers.note.null=nul
 str.markers.note.partial=partiel
+str.markers.note.mixedShape=autre forme
 str.markers.status.measured=Taux mesuré
 str.markers.status.default=Taux par défaut
 str.markers.status.excluded=Non évalué

rust/migrations/0072_str_marker_stat_mixed_shape.sql

@@ -0,0 +1,23 @@
+-- Record observations reported in a marker's minority value shape.
+--
+-- Some markers are reported inconsistently by the vendor export: DYS413 has 866
+-- multi-copy calls (23-23, 21-23, …) and exactly one bare `23`. The report picked
+-- whichever shape was non-null with the scalar winning ties, so that single
+-- observation replaced the whole copy-vector range — the page showed
+-- min=modal=max=23 for a marker with 25 distinct observed values, presenting one
+-- sample's value as the corpus range.
+--
+-- The range is now taken from whichever shape the majority of observations use
+-- (which also fixes the mirror case: a mostly-simple marker with a stray vector),
+-- and the minority count is kept here so the discrepancy is visible in the report
+-- rather than silently discarded — the same reasoning as null_alleles and
+-- complex_count.
+
+ALTER TABLE genomics.str_marker_stat
+    ADD COLUMN mixed_shape_count BIGINT NOT NULL DEFAULT 0;
+
+COMMENT ON COLUMN genomics.str_marker_stat.mixed_shape_count IS
+    'Observations in the marker''s minority value shape (single count vs copy vector); excluded from the reported range';
+
+-- Existing rows carry the old shape-precedence result; the next
+-- `du-jobs run-once str-marker-stats` recomputes them.