fix(amr): apply GTDB species matching on the SQLite index path

CHANGELOG.md

@@ -4,6 +4,16 @@ All notable changes to `atb-cli` are documented here. Format follows [Keep a Cha
 
 ## [Unreleased]
 
+### Fixed
+
+- `atb amr --species "Enterococcus faecium"` (an unsuffixed NCBI name) returned
+  0 results when a genus SQLite index was present. The AMR index path matched the
+  raw query with an exact `LOWER(species) IN (...)` clause and never applied the
+  GTDB-suffix stripping used everywhere else, so v0.22.0's GTDB matching reached
+  the parquet scan but not the SQLite index. The index path now resolves the
+  requested species against the stored names with the same GTDB-aware matcher
+  before querying. Explicit clade names still select a single clade.
+
 ## [v0.22.0](https://github.com/allthebacteria/atb-cli/releases/tag/v0.22.0) - 2026-09-02
 
 ### Changed

internal/amr/amr_gtdb_test.go

@@ -72,6 +72,57 @@ func TestQueryAMRSpeciesGTDBSuffix(t *testing.T) {
 	}
 }
 
+// TestQueryAMRSpeciesGTDBSuffixIndexed verifies that an NCBI-style --species
+// query matches GTDB-split rows through the SQLite index path (not just the
+// parquet scan). Building indexes makes Query route via QueryIndex/buildSQL.
+func TestQueryAMRSpeciesGTDBSuffixIndexed(t *testing.T) {
+	dir := t.TempDir()
+	writeAMRParquetAt(t, filepath.Join(dir, amr.PartitionDir, "Enterococcus_A.parquet"),
+		[]amrFixtureRow{{species: "Enterococcus_A faecium", genus: "Enterococcus_A", count: 2}})
+	writeAMRParquetAt(t, filepath.Join(dir, amr.PartitionDir, "Enterococcus_B.parquet"),
+		[]amrFixtureRow{{species: "Enterococcus_B faecium", genus: "Enterococcus_B", count: 3}})
+
+	if err := amr.BuildIndexes(dir, nil); err != nil {
+		t.Fatalf("BuildIndexes: %v", err)
+	}
+
+	results, err := amr.Query(dir, amr.Filters{
+		Genera:  []string{"Enterococcus"},
+		Species: []string{"Enterococcus faecium"},
+	})
+	if err != nil {
+		t.Fatalf("Query: %v", err)
+	}
+	if len(results) != 5 {
+		t.Fatalf("expected 5 GTDB-split rows via index, got %d", len(results))
+	}
+}
+
+// TestQueryAMRSpeciesCladeSelectIndexed verifies that an explicit clade name
+// through the SQLite index path selects only that clade.
+func TestQueryAMRSpeciesCladeSelectIndexed(t *testing.T) {
+	dir := t.TempDir()
+	writeAMRParquetAt(t, filepath.Join(dir, amr.PartitionDir, "Enterococcus_A.parquet"),
+		[]amrFixtureRow{{species: "Enterococcus_A faecium", genus: "Enterococcus_A", count: 2}})
+	writeAMRParquetAt(t, filepath.Join(dir, amr.PartitionDir, "Enterococcus_B.parquet"),
+		[]amrFixtureRow{{species: "Enterococcus_B faecium", genus: "Enterococcus_B", count: 3}})
+
+	if err := amr.BuildIndexes(dir, nil); err != nil {
+		t.Fatalf("BuildIndexes: %v", err)
+	}
+
+	results, err := amr.Query(dir, amr.Filters{
+		Genera:  []string{"Enterococcus"},
+		Species: []string{"Enterococcus_B faecium"},
+	})
+	if err != nil {
+		t.Fatalf("Query: %v", err)
+	}
+	if len(results) != 3 {
+		t.Fatalf("expected 3 rows for explicit _B clade, got %d", len(results))
+	}
+}
+
 // TestQueryAMRGenusGTDBPartitions verifies that an NCBI-style genus query reads
 // every on-disk GTDB clade partition, even when no monolithic file is present.
 func TestQueryAMRGenusGTDBPartitions(t *testing.T) {

internal/amr/indexer.go

@@ -300,6 +300,17 @@ func QueryIndex(dbPath string, filters Filters) ([]Result, error) {
 		}
 	}
 
+	if len(filters.Species) > 0 {
+		resolved, err := resolveIndexSpecies(db, filters.Species)
+		if err != nil {
+			return nil, wrapStaleIndexError(dbPath, err)
+		}
+		if len(resolved) == 0 {
+			return nil, nil
+		}
+		filters.Species = resolved
+	}
+
 	query, args := buildSQL(filters)
 	rows, err := db.Query(query, args...)
 	if err != nil {
@@ -329,6 +340,33 @@ func QueryIndex(dbPath string, filters Filters) ([]Result, error) {
 	return results, rows.Err()
 }
 
+// resolveIndexSpecies reads the distinct species stored in the index and returns
+// the concrete values that match any requested query under GTDB-aware matching.
+// SQLite cannot evaluate the GTDB suffix regex, so matching happens in Go and the
+// resolved names feed buildSQL's exact IN clause.
+func resolveIndexSpecies(db *sql.DB, queries []string) ([]string, error) {
+	rows, err := db.Query("SELECT DISTINCT species FROM amr")
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	var resolved []string
+	for rows.Next() {
+		var stored string
+		if err := rows.Scan(&stored); err != nil {
+			return nil, err
+		}
+		for _, q := range queries {
+			if match.SpeciesMatches(q, stored) {
+				resolved = append(resolved, stored)
+				break
+			}
+		}
+	}
+	return resolved, rows.Err()
+}
+
 func buildSQL(f Filters) (string, []any) {
 	var clauses []string
 	var args []any