Update combine_pmos

src/pmotools/pmo_engine/pmo_reader.py

@@ -394,10 +394,11 @@ def combine_multiple_pmos(pmos: list[dict]):
                 pmo["bioinformatics_run_info"]
             ):
                 bioinformatics_run_info_copy = copy.deepcopy(bioinformatics_run_info)
+                # remap using the run's own methods id, not its position index
                 bioinformatics_run_info_copy[
                     "bioinformatics_methods_id"
                 ] = bioinformatics_methods_info_old_index_key[pmo_index][
-                    bioinformatics_run_info_index
+                    bioinformatics_run_info_copy["bioinformatics_methods_id"]
                 ]
                 if "bioinformatics_run_info" not in pmo_out:
                     pmo_out["bioinformatics_run_info"] = []
@@ -501,8 +502,13 @@ def combine_multiple_pmos(pmos: list[dict]):
                     new_mhaps_target_index = len(
                         pmo_out["representative_microhaplotypes"]["targets"]
                     )
+                    new_rep_target = copy.deepcopy(representative_microhaplotypes)
+                    # remap the new target's target_id to the combined target_info
+                    new_rep_target["target_id"] = target_info_old_index_key[pmo_index][
+                        new_rep_target["target_id"]
+                    ]
                     pmo_out["representative_microhaplotypes"]["targets"].append(
-                        copy.deepcopy(representative_microhaplotypes)
+                        new_rep_target
                     )
                     representative_microhaplotypes_old_index_key[pmo_index][
                         representative_microhaplotypes_index

tests/test_pmo_engine/test_pmo_reader.py

@@ -165,6 +165,73 @@ def test_combine_multiple_pmos_fail_dup_library_sample_names(self):
         )
         self.assertRaises(Exception, PMOReader.combine_multiple_pmos, pmo_data_list_2)
 
+    def test_combine_multiple_pmos_remaps_new_rep_target_id(self):
+        # a representative-microhaplotype target newly added from a
+        # non-first PMO must have its target_id remapped to the combined
+        # target_info (previously it kept its local target_id), this test
+        # ensures this is tested as it was previously untested (2026-06-29)
+        import pandas as pd
+        from pmotools.pmo_builder.mhap_table_to_pmo import mhap_table_to_pmo
+        from pmotools.pmo_builder.panel_information_to_pmo import (
+            panel_info_table_to_pmo,
+        )
+        from pmotools.pmo_builder.merge_to_pmo import merge_to_pmo
+
+        def build(libs, targets, seqs, panel_name, panel_targets):
+            mhap_info = mhap_table_to_pmo(
+                pd.DataFrame(
+                    {
+                        "library_sample_name": libs,
+                        "target_name": targets,
+                        "seq": seqs,
+                        "reads": [10] * len(libs),
+                    }
+                )
+            )
+            panel_info = panel_info_table_to_pmo(
+                pd.DataFrame(
+                    {
+                        "target_name": panel_targets,
+                        "fwd_primer": [
+                            "A" * (i + 4) for i in range(len(panel_targets))
+                        ],
+                        "rev_primer": [
+                            "C" * (i + 4) for i in range(len(panel_targets))
+                        ],
+                    }
+                ),
+                panel_name,
+            )
+            return merge_to_pmo(mhap_info=mhap_info, panel_target_info=panel_info)
+
+        pmo_a = build(
+            ["S1", "S2"], ["t1", "t2"], ["AAA", "GGG"], "panelA", ["t1", "t2"]
+        )
+        # pmo_b introduces a brand-new target t3
+        pmo_b = build(
+            ["S3", "S4"], ["t1", "t3"], ["AAA", "CCC"], "panelB", ["t1", "t3"]
+        )
+
+        combined = PMOReader.combine_multiple_pmos([pmo_a, pmo_b])
+        self.assertEqual(
+            [t["target_name"] for t in combined["target_info"]],
+            ["t1", "t2", "t3"],
+        )
+        # every rep target's target_id resolves to the right combined target
+        for rep in combined["representative_microhaplotypes"]["targets"]:
+            self.assertLess(rep["target_id"], len(combined["target_info"]))
+        t3_reps = [
+            rep
+            for rep in combined["representative_microhaplotypes"]["targets"]
+            if combined["target_info"][rep["target_id"]]["target_name"] == "t3"
+        ]
+        self.assertEqual(len(t3_reps), 1)
+        # validate against schema (minimal builder PMO targets v1.1.0)
+        checker = PMOChecker(
+            load_schema("portable_microhaplotype_object_v1.1.0.schema.json")
+        )
+        checker.validate_pmo_json(combined)
+
     def test_combine_multiple_pmos_fail_for_combine_only_one_file(self):
         # will fail for only having 1 PMO
         pmo_data_list_2 = PMOReader.read_in_pmos(