From ce36a0ff217e018a5240d9b4a6e7956e8275e35c Mon Sep 17 00:00:00 2001
From: Nicholas Hathaway <nickjhathaway@gmail.com>
Date: Thu, 4 Jun 2026 16:45:20 -0700
Subject: [PATCH 01/12] update for deploy only on version tags;

---
 .github/workflows/docs.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 958b87e..9f7353e 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -4,7 +4,6 @@ on:
   push:
     tags:
       - 'v*.*.*'
-      - 'test*'
   workflow_dispatch:
 
 permissions:

From 1d22c1891f06e7e829fefac93e27419b5654e833 Mon Sep 17 00:00:00 2001
From: Nicholas Hathaway <nickjhathaway@gmail.com>
Date: Thu, 4 Jun 2026 18:03:39 -0700
Subject: [PATCH 02/12] default in the argparse was still mhap_id but we
 changed the default to be seq (it's changed to seq in the function itself)

---
 src/pmotools/scripts/pmo_to_tables/extract_allele_table.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pmotools/scripts/pmo_to_tables/extract_allele_table.py b/src/pmotools/scripts/pmo_to_tables/extract_allele_table.py
index bfd458b..93f8144 100755
--- a/src/pmotools/scripts/pmo_to_tables/extract_allele_table.py
+++ b/src/pmotools/scripts/pmo_to_tables/extract_allele_table.py
@@ -91,7 +91,7 @@ def get_parser() -> argparse.ArgumentParser:
         "--default_base_col_names",
         type=str,
         required=False,
-        default="library_sample_name,target_name,mhap_id",
+        default="library_sample_name,target_name,seq",
         help="default base column names, must be length 3",
     )
     return parser

From 374e14ee980deee4c0f9b5efe47e6ed729c95d81 Mon Sep 17 00:00:00 2001
From: Nicholas Hathaway <nickjhathaway@gmail.com>
Date: Mon, 29 Jun 2026 10:38:47 -0700
Subject: [PATCH 03/12] small fixes for mutation of input data for
 filter_pmo_by_target_ids;

---
 src/pmotools/pmo_engine/pmo_processor.py | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/pmotools/pmo_engine/pmo_processor.py b/src/pmotools/pmo_engine/pmo_processor.py
index cef95fb..651600a 100644
--- a/src/pmotools/pmo_engine/pmo_processor.py
+++ b/src/pmotools/pmo_engine/pmo_processor.py
@@ -646,8 +646,6 @@ def filter_pmo_by_library_sample_ids(pmodata, library_sample_ids: set[int]):
         if "targeted_genomes" in pmodata:
             pmo_out["targeted_genomes"] = copy.deepcopy(pmodata["targeted_genomes"])
 
-        if "read_counts_by_stage" in pmodata:
-            pmo_out["read_counts_by_stage"] = []
         # need to update read_counts_by_stage, library_sample_info, specimen_info, detected_microhaplotypes
 
         # specimen_info
@@ -703,6 +701,7 @@ def filter_pmo_by_library_sample_ids(pmodata, library_sample_ids: set[int]):
             pmo_out["detected_microhaplotypes"].append(new_detected_microhaplotypes)
         # read_counts_by_stage
         if "read_counts_by_stage" in pmodata:
+            pmo_out["read_counts_by_stage"] = []
             for read_count in pmodata["read_counts_by_stage"]:
                 new_read_count = {
                     "read_counts_by_library_sample_by_stage": [],
@@ -725,6 +724,7 @@ def filter_pmo_by_library_sample_ids(pmodata, library_sample_ids: set[int]):
                         ]["library_sample_id"] = library_id_index_key[
                             sample["library_sample_id"]
                         ]
+                pmo_out["read_counts_by_stage"].append(new_read_count)
         return pmo_out
 
     @staticmethod
@@ -884,11 +884,12 @@ def filter_pmo_by_target_ids(pmodata, target_ids: set[int]):
                     pmo_out["representative_microhaplotypes"]["targets"]
                 )
                 # update new target_id index
-                microhap_info["target_id"] = target_info_index_key[
+                microhap_info_copy = copy.deepcopy(microhap_info)
+                microhap_info_copy["target_id"] = target_info_index_key[
                     microhap_info["target_id"]
                 ]
                 pmo_out["representative_microhaplotypes"]["targets"].append(
-                    copy.deepcopy(microhap_info)
+                    microhap_info_copy
                 )
         # representative_microhaplotypes
         pmo_out["detected_microhaplotypes"] = []
@@ -908,10 +909,11 @@ def filter_pmo_by_target_ids(pmodata, target_ids: set[int]):
                 for target in sample["target_results"]:
                     if target["mhaps_target_id"] in mhaps_target_id_new_key:
                         # update with new mhaps_target_id id
-                        target["mhaps_target_id"] = mhaps_target_id_new_key[
+                        target_copy = copy.deepcopy(target)
+                        target_copy["mhaps_target_id"] = mhaps_target_id_new_key[
                             target["mhaps_target_id"]
                         ]
-                        new_sample["target_results"].append(copy.deepcopy(target))
+                        new_sample["target_results"].append(target_copy)
                 new_detected_microhaplotypes["library_samples"].append(new_sample)
             pmo_out["detected_microhaplotypes"].append(new_detected_microhaplotypes)
 
@@ -938,11 +940,12 @@ def filter_pmo_by_target_ids(pmodata, target_ids: set[int]):
                         for target in sample["read_counts_for_targets"]:
                             if target["target_id"] in target_ids:
                                 # update with new target_id index
-                                target["target_id"] = target_info_index_key[
+                                target_copy = copy.deepcopy(target)
+                                target_copy["target_id"] = target_info_index_key[
                                     target["target_id"]
                                 ]
                                 new_samples["read_counts_for_targets"].append(
-                                    copy.deepcopy(target)
+                                    target_copy
                                 )
                     new_read_counts_by_bioid[
                         "read_counts_by_library_sample_by_stage"

From 6ad954b3d6e5c6436f662f8f03f06829d9e41cd1 Mon Sep 17 00:00:00 2001
From: Nicholas Hathaway <nickjhathaway@gmail.com>
Date: Mon, 29 Jun 2026 11:08:18 -0700
Subject: [PATCH 04/12] update the hashes because now reads_by_stage is now
 properly exported so the old hashes were wrong;

---
 tests/test_pmo_engine/test_pmo_processor.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/test_pmo_engine/test_pmo_processor.py b/tests/test_pmo_engine/test_pmo_processor.py
index 2c4a41b..bce394b 100755
--- a/tests/test_pmo_engine/test_pmo_processor.py
+++ b/tests/test_pmo_engine/test_pmo_processor.py
@@ -358,7 +358,7 @@ def test_filter_pmo_by_library_sample_ids(self):
         )
         with open(output_fnp, "w") as f:
             json.dump(pmo_data_select_targets, f)
-        self.assertEqual("4a2c7b9d84322cc43adf2b9f0c518244", md5sum_of_fnp(output_fnp))
+        self.assertEqual("36d5cb8a79962707374fae86ba1a6f90", md5sum_of_fnp(output_fnp))
         # check pmo extracted against PMO schema
         checker = PMOChecker(self.pmo_jsonschema_data)
         checker.validate_pmo_json(pmo_data_select_targets)
@@ -374,7 +374,7 @@ def test_filter_pmo_by_library_sample_names(self):
         )
         with open(output_fnp, "w") as f:
             json.dump(pmo_data_select_library_sample_names, f)
-        self.assertEqual("ffdaeb6b57ed9a5c51e56cfaa4621796", md5sum_of_fnp(output_fnp))
+        self.assertEqual("6bd4e6367a62f1eb3c73f481a5ae9013", md5sum_of_fnp(output_fnp))
         # check pmo extracted against PMO schema
         checker = PMOChecker(self.pmo_jsonschema_data)
         checker.validate_pmo_json(pmo_data_select_library_sample_names)
@@ -388,7 +388,7 @@ def test_filter_pmo_by_specimen_ids(self):
         )
         with open(output_fnp, "w") as f:
             json.dump(pmo_data_select_targets, f)
-        self.assertEqual("f3dd2e0aee9afa82336ff48475a3c69c", md5sum_of_fnp(output_fnp))
+        self.assertEqual("664de0f14180de852f3f5d8942454004", md5sum_of_fnp(output_fnp))
         # check pmo extracted against PMO schema
         checker = PMOChecker(self.pmo_jsonschema_data)
         checker.validate_pmo_json(pmo_data_select_targets)
@@ -402,7 +402,7 @@ def test_filter_pmo_by_specimen_names(self):
         )
         with open(output_fnp, "w") as f:
             json.dump(pmo_data_select_targets, f)
-        self.assertEqual("f3dd2e0aee9afa82336ff48475a3c69c", md5sum_of_fnp(output_fnp))
+        self.assertEqual("664de0f14180de852f3f5d8942454004", md5sum_of_fnp(output_fnp))
         # check pmo extracted against PMO schema
         checker = PMOChecker(self.pmo_jsonschema_data)
         checker.validate_pmo_json(pmo_data_select_targets)
@@ -420,7 +420,7 @@ def test_extract_from_pmo_samples_with_meta_groupings(self):
         with open(output_fnp, "w") as f:
             json.dump(pmo_data_select_meta, f)
 
-        self.assertEqual("f0f67e399885824a7aa318ead8b3d09c", md5sum_of_fnp(output_fnp))
+        self.assertEqual("9deb0bccc0017593697190d45ae6c0a4", md5sum_of_fnp(output_fnp))
         # check pmo extracted against PMO schema
         checker = PMOChecker(self.pmo_jsonschema_data)
         checker.validate_pmo_json(pmo_data_select_meta)

From 5ea5a2e149b6404d4e4e86aac4e4d91368f11a95 Mon Sep 17 00:00:00 2001
From: Nicholas Hathaway <nickjhathaway@gmail.com>
Date: Mon, 29 Jun 2026 12:44:32 -0700
Subject: [PATCH 05/12] fix for when exporting a header for bed locations
 didn't add a newline; when asking for a sorted output would only return first
 panel, now will return all panels; added test

---
 src/pmotools/pmo_engine/pmo_exporter.py    | 14 +++----
 tests/test_pmo_engine/test_pmo_exporter.py | 48 ++++++++++++++++++++++
 2 files changed, 53 insertions(+), 9 deletions(-)

diff --git a/src/pmotools/pmo_engine/pmo_exporter.py b/src/pmotools/pmo_engine/pmo_exporter.py
index 361ebd7..646436a 100644
--- a/src/pmotools/pmo_engine/pmo_exporter.py
+++ b/src/pmotools/pmo_engine/pmo_exporter.py
@@ -451,6 +451,7 @@ def write_bed_locs(bed_locs: list[BedLoc], fnp, add_header: bool = False):
                         ]
                     )
                 )
+                f.write("\n")
             for bed_loc in bed_locs:
                 f.write(
                     "\t".join(
@@ -540,11 +541,10 @@ def extract_panels_insert_bed_loc(
         :param sort_output: whether to sort output by genomic location
         :return: a list of target inserts, with named tuples with fields: chrom, start, end, name, score, strand, ref_seq, extra_info
         """
-        bed_loc_out = {}
+        bed_loc_out = []
         if select_panel_ids is None:
             select_panel_ids = list(range(len(pmodata["panel_info"])))
         for panel_id in select_panel_ids:
-            bed_loc_out_per_panel = []
             for reaction_id in range(len(pmodata["panel_info"][panel_id]["reactions"])):
                 for target_id in pmodata["panel_info"][panel_id]["reactions"][
                     reaction_id
@@ -589,7 +589,7 @@ def extract_panels_insert_bed_loc(
                         if "ref_seq" not in tar["insert_location"]
                         else tar["insert_location"]["ref_seq"]
                     )
-                    bed_loc_out_per_panel.append(
+                    bed_loc_out.append(
                         BedLoc(
                             tar["insert_location"]["chrom"],
                             tar["insert_location"]["start"],
@@ -602,12 +602,8 @@ def extract_panels_insert_bed_loc(
                             extra_info,
                         )
                     )
-                if sort_output:
-                    return sorted(
-                        bed_loc_out_per_panel,
-                        key=lambda bed: (bed.chrom, bed.start, bed.end),
-                    )
-            bed_loc_out[panel_id] = bed_loc_out_per_panel
+        if sort_output:
+            return sorted(bed_loc_out, key=lambda bed: (bed.chrom, bed.start, bed.end))
         return bed_loc_out
 
     @staticmethod
diff --git a/tests/test_pmo_engine/test_pmo_exporter.py b/tests/test_pmo_engine/test_pmo_exporter.py
index 1984bfa..99c7045 100755
--- a/tests/test_pmo_engine/test_pmo_exporter.py
+++ b/tests/test_pmo_engine/test_pmo_exporter.py
@@ -105,6 +105,54 @@ def test_extract_panels_insert_bed_loc(self):
         PMOExporter.write_bed_locs(all_target_inserts, output_fnp)
         self.assertEqual("52b1f79a3a89f8265573fa54b5a7ce57", md5sum_of_fnp(output_fnp))
 
+    def test_extract_panels_insert_bed_loc_covers_all_reactions(self):
+        # regression: previously the function returned early inside the reaction
+        # loop, so only the first reaction of the first panel was returned.
+        import copy
+
+        pmo = copy.deepcopy(self.combined_pmo_data)
+        panel = pmo["panel_info"][0]
+        targets = panel["reactions"][0]["panel_targets"]
+        half = len(targets) // 2
+        panel["reactions"] = [
+            {"reaction_name": "pool1", "panel_targets": targets[:half]},
+            {"reaction_name": "pool2", "panel_targets": targets[half:]},
+        ]
+        bed_locs = PMOExporter.extract_panels_insert_bed_loc(pmo, sort_output=False)
+        # every target across BOTH reactions is present
+        self.assertEqual(len(bed_locs), len(targets))
+        self.assertEqual(
+            {b.name for b in bed_locs},
+            {pmo["target_info"][t]["target_name"] for t in targets},
+        )
+
+    def test_write_bed_locs_header_on_own_line(self):
+        # regression: header was written without a trailing newline, gluing the
+        # first data row onto it.
+        bed_locs = PMOExporter.extract_targets_insert_bed_loc(
+            self.combined_pmo_data, sort_output=True
+        )
+        out_fnp = os.path.join(self.test_dir.name, "with_header.bed")
+        PMOExporter.write_bed_locs(bed_locs, out_fnp, add_header=True)
+        with open(out_fnp) as f:
+            lines = f.read().splitlines()
+        self.assertEqual(
+            lines[0],
+            "\t".join(
+                [
+                    "#chrom",
+                    "start",
+                    "end",
+                    "name",
+                    "score",
+                    "strand",
+                    "ref_seq",
+                    "extra_info",
+                ]
+            ),
+        )
+        self.assertEqual(len(lines), len(bed_locs) + 1)
+
     def test_extract_alleles_per_sample_table(self):
         allele_data = PMOExporter.extract_alleles_per_sample_table(
             self.combined_pmo_data,

From c71bbfde77612dbebd53e1cec6d17c7d9d99649e Mon Sep 17 00:00:00 2001
From: Nicholas Hathaway <nickjhathaway@gmail.com>
Date: Mon, 29 Jun 2026 13:28:27 -0700
Subject: [PATCH 06/12] update so pseudocigar is properly constructed during
 the building functions; updated unittests;

---
 src/pmotools/pmo_builder/mhap_table_to_pmo.py | 99 ++++++++++++++++++-
 .../test_mhap_table_to_pmo.py                 | 71 +++++++------
 .../test_schema_validation_integration.py     |  8 ++
 3 files changed, 140 insertions(+), 38 deletions(-)

diff --git a/src/pmotools/pmo_builder/mhap_table_to_pmo.py b/src/pmotools/pmo_builder/mhap_table_to_pmo.py
index be0ae34..70e4a57 100644
--- a/src/pmotools/pmo_builder/mhap_table_to_pmo.py
+++ b/src/pmotools/pmo_builder/mhap_table_to_pmo.py
@@ -26,6 +26,13 @@ def mhap_table_to_pmo(
     masking_delim: str = ",",
     microhaplotype_name_col: str | None = None,
     pseudocigar_col: str | None = None,
+    pseudocigar_chrom_col: str | None = None,
+    pseudocigar_start_col: str | None = None,
+    pseudocigar_end_col: str | None = None,
+    pseudocigar_ref_seq_col: str | None = None,
+    pseudocigar_strand_col: str | None = None,
+    pseudocigar_genome_id: int | None = None,
+    pseudocigar_generation_description_col: str | None = None,
     quality_col: str | None = None,
     additional_representative_mhap_cols: list | None = None,
     additional_mhap_detected_cols: list | None = None,
@@ -73,6 +80,20 @@ def mhap_table_to_pmo(
     :type microhaplotype_name_col: str, optional
     :param pseudocigar_col: the name of the column containing a pseudocigar for the microhaplotype
     :type pseudocigar_col: str, optional
+    :param pseudocigar_chrom_col: column for the pseudocigar ref_loc chromosome; defaults to chrom_col
+    :type pseudocigar_chrom_col: str, optional
+    :param pseudocigar_start_col: column for the pseudocigar ref_loc start (required if pseudocigar_col is set)
+    :type pseudocigar_start_col: str, optional
+    :param pseudocigar_end_col: column for the pseudocigar ref_loc end (required if pseudocigar_col is set)
+    :type pseudocigar_end_col: str, optional
+    :param pseudocigar_ref_seq_col: optional column for the pseudocigar ref_loc reference sequence
+    :type pseudocigar_ref_seq_col: str, optional
+    :param pseudocigar_strand_col: optional column for the pseudocigar ref_loc strand
+    :type pseudocigar_strand_col: str, optional
+    :param pseudocigar_genome_id: genome id for the pseudocigar ref_loc; defaults to genome_id
+    :type pseudocigar_genome_id: int, optional
+    :param pseudocigar_generation_description_col: optional column describing how the pseudocigar was generated
+    :type pseudocigar_generation_description_col: str, optional
     :param quality_col: the name of the column containing the ANSI FASTQ per-base quality score for this sequence
     :type quality_col: str, optional
     :param additional_representative_mhap_cols: additional columns to add to the representative microhaplotypes table
@@ -100,6 +121,13 @@ def mhap_table_to_pmo(
         masking_delim=masking_delim,
         microhaplotype_name_col=microhaplotype_name_col,
         pseudocigar_col=pseudocigar_col,
+        pseudocigar_chrom_col=pseudocigar_chrom_col,
+        pseudocigar_start_col=pseudocigar_start_col,
+        pseudocigar_end_col=pseudocigar_end_col,
+        pseudocigar_ref_seq_col=pseudocigar_ref_seq_col,
+        pseudocigar_strand_col=pseudocigar_strand_col,
+        pseudocigar_genome_id=pseudocigar_genome_id,
+        pseudocigar_generation_description_col=pseudocigar_generation_description_col,
         quality_col=quality_col,
         additional_representative_mhap_cols=additional_representative_mhap_cols,
     )
@@ -160,6 +188,13 @@ def create_representative_microhaplotype_dict(
     masking_delim: str = ",",
     microhaplotype_name_col: str | None = None,
     pseudocigar_col: str | None = None,
+    pseudocigar_chrom_col: str | None = None,
+    pseudocigar_start_col: str | None = None,
+    pseudocigar_end_col: str | None = None,
+    pseudocigar_ref_seq_col: str | None = None,
+    pseudocigar_strand_col: str | None = None,
+    pseudocigar_genome_id: int | None = None,
+    pseudocigar_generation_description_col: str | None = None,
     quality_col: str | None = None,
     additional_representative_mhap_cols: list[str] | None = None,
 ):
@@ -198,6 +233,20 @@ def create_representative_microhaplotype_dict(
     :type microhaplotype_name_col: str, optional
     :param pseudocigar_col: the name of the column containing a pseudocigar for the microhaplotype
     :type pseudocigar_col: str, optional
+    :param pseudocigar_chrom_col: column for the pseudocigar ref_loc chromosome; defaults to chrom_col
+    :type pseudocigar_chrom_col: str, optional
+    :param pseudocigar_start_col: column for the pseudocigar ref_loc start (required if pseudocigar_col is set)
+    :type pseudocigar_start_col: str, optional
+    :param pseudocigar_end_col: column for the pseudocigar ref_loc end (required if pseudocigar_col is set)
+    :type pseudocigar_end_col: str, optional
+    :param pseudocigar_ref_seq_col: optional column for the pseudocigar ref_loc reference sequence
+    :type pseudocigar_ref_seq_col: str, optional
+    :param pseudocigar_strand_col: optional column for the pseudocigar ref_loc strand
+    :type pseudocigar_strand_col: str, optional
+    :param pseudocigar_genome_id: genome id for the pseudocigar ref_loc; defaults to genome_id
+    :type pseudocigar_genome_id: int, optional
+    :param pseudocigar_generation_description_col: optional column describing how the pseudocigar was generated
+    :type pseudocigar_generation_description_col: str, optional
     :param quality_col: the name of the column containing the ANSI FASTQ per-base quality score for this sequence
     :type quality_col: str, optional
     :param additional_representative_mhap_cols: additional columns to add to the representative microhaplotypes table
@@ -211,6 +260,21 @@ def create_representative_microhaplotype_dict(
             microhaplotype_table, additional_representative_mhap_cols
         )
 
+    # the pseudocigar ref_loc shares the chromosome / genome with the
+    # microhaplotype location by default, but each may use its own column
+    ps_chrom_col = pseudocigar_chrom_col if pseudocigar_chrom_col else chrom_col
+    ps_genome_id = (
+        pseudocigar_genome_id if pseudocigar_genome_id is not None else genome_id
+    )
+    if pseudocigar_col and not (
+        ps_chrom_col and pseudocigar_start_col and pseudocigar_end_col
+    ):
+        raise ValueError(
+            "pseudocigar_col is set, so a Pseudocigar ref_loc must be "
+            "constructable: set a chromosome (pseudocigar_chrom_col or "
+            "chrom_col), pseudocigar_start_col, and pseudocigar_end_col."
+        )
+
     def get_if_present(row, col):
         return row[col] if col and pd.notna(row[col]) else None
 
@@ -263,6 +327,12 @@ def warn_if_duplicated_seqs(df, target_col, seq_col):
         alt_annotations_col,
         microhaplotype_name_col,
         pseudocigar_col,
+        ps_chrom_col,
+        pseudocigar_start_col,
+        pseudocigar_end_col,
+        pseudocigar_ref_seq_col,
+        pseudocigar_strand_col,
+        pseudocigar_generation_description_col,
         quality_col,
     ]
     masking_cols = [
@@ -319,7 +389,34 @@ def warn_if_duplicated_seqs(df, target_col, seq_col):
             if val := get_if_present(row, microhaplotype_name_col):
                 mhap["microhaplotype_name"] = val
             if val := get_if_present(row, pseudocigar_col):
-                mhap["pseudo_cigar"] = val
+                if not (
+                    pd.notna(row[ps_chrom_col])
+                    and pd.notna(row[pseudocigar_start_col])
+                    and pd.notna(row[pseudocigar_end_col])
+                ):
+                    raise ValueError(
+                        f"pseudocigar present for target {target}, seq "
+                        f"{row[seq_col]} but its ref_loc chrom/start/end "
+                        "is missing"
+                    )
+                ref_loc = {
+                    "genome_id": ps_genome_id,
+                    "chrom": row[ps_chrom_col],
+                    "start": row[pseudocigar_start_col],
+                    "end": row[pseudocigar_end_col],
+                }
+                if pseudocigar_ref_seq_col and pd.notna(row[pseudocigar_ref_seq_col]):
+                    ref_loc["ref_seq"] = row[pseudocigar_ref_seq_col]
+                if pseudocigar_strand_col and pd.notna(row[pseudocigar_strand_col]):
+                    ref_loc["strand"] = row[pseudocigar_strand_col]
+                pseudocigar = {"pseudocigar_seq": val, "ref_loc": ref_loc}
+                if pseudocigar_generation_description_col and pd.notna(
+                    row[pseudocigar_generation_description_col]
+                ):
+                    pseudocigar["pseudocigar_generation_description"] = row[
+                        pseudocigar_generation_description_col
+                    ]
+                mhap["pseudocigar"] = pseudocigar
             if val := get_if_present(row, quality_col):
                 mhap["quality"] = val
             if additional_representative_mhap_cols:
diff --git a/tests/test_pmo_builder/test_mhap_table_to_pmo.py b/tests/test_pmo_builder/test_mhap_table_to_pmo.py
index fad711b..b50903c 100644
--- a/tests/test_pmo_builder/test_mhap_table_to_pmo.py
+++ b/tests/test_pmo_builder/test_mhap_table_to_pmo.py
@@ -510,52 +510,49 @@ def test_create_representative_microhaplotype_dict_with_ad_cols(self):
         mhap_table_ad_cols = self.small_mhap_table.copy()
         mhap_table_ad_cols["adcol1"] = "this"
         mhap_table_ad_cols["adcol2"] = "that"
-        mhap_table_ad_cols["cig"] = "cigs"
 
         rep_dict_with_ad_cols = copy.deepcopy(self.small_representative_dict)
-        rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][0]["adcol1"] = "this"
-        rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][0]["adcol2"] = "that"
-        rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][0][
-            "pseudo_cigar"
-        ] = "cigs"
-        rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][1]["adcol1"] = "this"
-        rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][1]["adcol2"] = "that"
-        rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][1][
-            "pseudo_cigar"
-        ] = "cigs"
-        rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][2]["adcol1"] = "this"
-        rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][2]["adcol2"] = "that"
-        rep_dict_with_ad_cols["targets"][0]["microhaplotypes"][2][
-            "pseudo_cigar"
-        ] = "cigs"
-        rep_dict_with_ad_cols["targets"][1]["microhaplotypes"][0]["adcol1"] = "this"
-        rep_dict_with_ad_cols["targets"][1]["microhaplotypes"][0]["adcol2"] = "that"
-        rep_dict_with_ad_cols["targets"][1]["microhaplotypes"][0][
-            "pseudo_cigar"
-        ] = "cigs"
-        rep_dict_with_ad_cols["targets"][1]["microhaplotypes"][1]["adcol1"] = "this"
-        rep_dict_with_ad_cols["targets"][1]["microhaplotypes"][1]["adcol2"] = "that"
-        rep_dict_with_ad_cols["targets"][1]["microhaplotypes"][1][
-            "pseudo_cigar"
-        ] = "cigs"
-        rep_dict_with_ad_cols["targets"][2]["microhaplotypes"][0]["adcol1"] = "this"
-        rep_dict_with_ad_cols["targets"][2]["microhaplotypes"][0]["adcol2"] = "that"
-        rep_dict_with_ad_cols["targets"][2]["microhaplotypes"][0][
-            "pseudo_cigar"
-        ] = "cigs"
-        rep_dict_with_ad_cols["targets"][2]["microhaplotypes"][1]["adcol1"] = "this"
-        rep_dict_with_ad_cols["targets"][2]["microhaplotypes"][1]["adcol2"] = "that"
-        rep_dict_with_ad_cols["targets"][2]["microhaplotypes"][1][
-            "pseudo_cigar"
-        ] = "cigs"
+        for target in rep_dict_with_ad_cols["targets"]:
+            for mhap in target["microhaplotypes"]:
+                mhap["adcol1"] = "this"
+                mhap["adcol2"] = "that"
 
         actual = create_representative_microhaplotype_dict(
             mhap_table_ad_cols,
             additional_representative_mhap_cols=["adcol1", "adcol2"],
-            pseudocigar_col="cig",
         )
         self.assertEqual(actual, rep_dict_with_ad_cols)
 
+    def test_create_representative_microhaplotype_dict_with_pseudocigar(self):
+        tbl = self.small_mhap_table.copy()
+        tbl["chrom"] = "chr1"
+        tbl["start"] = 100
+        tbl["end"] = 150
+        tbl["cig"] = "8M"
+        actual = create_representative_microhaplotype_dict(
+            tbl,
+            chrom_col="chrom",
+            start_col="start",
+            end_col="end",
+            pseudocigar_col="cig",
+            pseudocigar_start_col="start",
+            pseudocigar_end_col="end",
+        )
+        first = actual["targets"][0]["microhaplotypes"][0]
+        # pseudocigar is a Pseudocigar object with a GenomicLocation ref_loc;
+        # the chromosome is reused from chrom_col and genome_id defaults to 0
+        self.assertEqual(first["pseudocigar"]["pseudocigar_seq"], "8M")
+        self.assertEqual(
+            first["pseudocigar"]["ref_loc"],
+            {"genome_id": 0, "chrom": "chr1", "start": 100, "end": 150},
+        )
+
+    def test_pseudocigar_without_ref_loc_columns_raises(self):
+        tbl = self.small_mhap_table.copy()
+        tbl["cig"] = "8M"
+        with self.assertRaises(ValueError):
+            create_representative_microhaplotype_dict(tbl, pseudocigar_col="cig")
+
     @patch(
         "pmotools.pmo_builder.mhap_table_to_pmo.create_representative_microhaplotype_dict"
     )
diff --git a/tests/test_pmo_builder/test_schema_validation_integration.py b/tests/test_pmo_builder/test_schema_validation_integration.py
index 766bca5..5f88b9b 100644
--- a/tests/test_pmo_builder/test_schema_validation_integration.py
+++ b/tests/test_pmo_builder/test_schema_validation_integration.py
@@ -191,6 +191,8 @@ def test_full_1_0_0_toy_pmo_validates_against_schema():
         umis_col="umis",
         microhaplotype_name_col="microhap_name",
         pseudocigar_col="pseudocigar",
+        pseudocigar_start_col="start",
+        pseudocigar_end_col="end",
         quality_col="quality",
         masking_seq_start_col="mask_start",
         masking_seq_segment_size_col="mask_segment",
@@ -467,6 +469,9 @@ def test_slimer_1_1_0_toy_pmo_validates_against_schema():
             "umis": [10],
             "microhap_name": ["mh1"],
             "pseudocigar": ["8M"],
+            "pseudocigar_chrom": ["chr1"],
+            "pseudocigar_start": [120],
+            "pseudocigar_end": [127],
             "quality": ["ABCD"],
             "mask_start": ["1"],
             "mask_segment": ["2"],
@@ -480,6 +485,9 @@ def test_slimer_1_1_0_toy_pmo_validates_against_schema():
         umis_col="umis",
         microhaplotype_name_col="microhap_name",
         pseudocigar_col="pseudocigar",
+        pseudocigar_chrom_col="pseudocigar_chrom",
+        pseudocigar_start_col="pseudocigar_start",
+        pseudocigar_end_col="pseudocigar_end",
         quality_col="quality",
         masking_seq_start_col="mask_start",
         masking_seq_segment_size_col="mask_segment",

From aa1c22f63b06f86473ab09cf47f249fb69915685 Mon Sep 17 00:00:00 2001
From: Nicholas Hathaway <nickjhathaway@gmail.com>
Date: Mon, 29 Jun 2026 13:38:15 -0700
Subject: [PATCH 07/12] start and end were flipped when setting location for
 forward primer location;

---
 .../pmo_builder/panel_information_to_pmo.py      |  4 ++--
 .../test_panel_information_to_pmo.py             | 16 ++++++++--------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/pmotools/pmo_builder/panel_information_to_pmo.py b/src/pmotools/pmo_builder/panel_information_to_pmo.py
index 949fd8c..563307f 100644
--- a/src/pmotools/pmo_builder/panel_information_to_pmo.py
+++ b/src/pmotools/pmo_builder/panel_information_to_pmo.py
@@ -332,8 +332,8 @@ def build_target_info_dict(
                 fwd_primer_dict["location"] = {
                     "genome_id": genome_id,
                     "chrom": row[chrom_col],
-                    "end": int(row[forward_primers_start_col]),
-                    "start": int(row[forward_primers_end_col]),
+                    "start": int(row[forward_primers_start_col]),
+                    "end": int(row[forward_primers_end_col]),
                 }
                 if strand_col and pd.notna(row[strand_col]):
                     fwd_primer_dict["location"]["strand"] = row[strand_col]
diff --git a/tests/test_pmo_builder/test_panel_information_to_pmo.py b/tests/test_pmo_builder/test_panel_information_to_pmo.py
index 29158a3..bf74cf3 100644
--- a/tests/test_pmo_builder/test_panel_information_to_pmo.py
+++ b/tests/test_pmo_builder/test_panel_information_to_pmo.py
@@ -416,8 +416,8 @@ def test_build_target_info_dict_full_info(
                     "location": {
                         "genome_id": 0,
                         "chrom": "chrom1",
-                        "end": 1,
-                        "start": 2,
+                        "start": 1,
+                        "end": 2,
                     },
                 },
                 "reverse_primer": {
@@ -443,8 +443,8 @@ def test_build_target_info_dict_full_info(
                     "location": {
                         "genome_id": 0,
                         "chrom": "chrom1",
-                        "end": 1,
-                        "start": 2,
+                        "start": 1,
+                        "end": 2,
                     },
                 },
                 "reverse_primer": {
@@ -470,8 +470,8 @@ def test_build_target_info_dict_full_info(
                     "location": {
                         "genome_id": 0,
                         "chrom": "chrom1",
-                        "end": 1,
-                        "start": 2,
+                        "start": 1,
+                        "end": 2,
                     },
                 },
                 "reverse_primer": {
@@ -526,8 +526,8 @@ def test_build_target_info_dict_missing_info(
                     "location": {
                         "genome_id": 0,
                         "chrom": "chrom1",
-                        "end": 1,
-                        "start": 2,
+                        "start": 1,
+                        "end": 2,
                     },
                 },
                 "reverse_primer": {"seq": "GTT"},

From fb800996dcd852f5d8004ef6f7a0b2b066f6eb24 Mon Sep 17 00:00:00 2001
From: Nicholas Hathaway <nickjhathaway@gmail.com>
Date: Mon, 29 Jun 2026 14:53:31 -0700
Subject: [PATCH 08/12] fix for the change in the schema to qpcr name in the
 schema which was never updated in the pmtools-python;

---
 src/pmotools/pmo_builder/metatable_to_pmo.py  | 12 +++---
 .../test_pmo_builder/test_metatable_to_pmo.py | 37 ++++++++++++++-----
 2 files changed, 33 insertions(+), 16 deletions(-)

diff --git a/src/pmotools/pmo_builder/metatable_to_pmo.py b/src/pmotools/pmo_builder/metatable_to_pmo.py
index 4162c22..6169646 100644
--- a/src/pmotools/pmo_builder/metatable_to_pmo.py
+++ b/src/pmotools/pmo_builder/metatable_to_pmo.py
@@ -157,7 +157,7 @@ def library_sample_info_table_to_pmo(
         library_prep_plate_position_col,
         meta_json,
         copy_contents,
-        "specimen_name",
+        "library_sample_name",
         "library_prep_plate_info",
     )
     meta_json = add_parasite_density_info(
@@ -166,7 +166,7 @@ def library_sample_info_table_to_pmo(
         meta_json,
         copy_contents,
         "library_sample_name",
-        entry_name="parasite_density_info",
+        entry_name="qpcr_parasite_density_info",
     )
     # listify columns that contain values that could be list, are delimited by the argument list_values_library_values_delimiter
     primitives = (int, float, str, bool, complex)
@@ -494,7 +494,7 @@ def add_plate_info(
     plate_position_col,
     meta_json,
     df,
-    specimen_name_col,
+    match_col,
     entry_name="plate_info",
 ):
     if all(
@@ -531,7 +531,7 @@ def add_plate_info(
                 ) from e
 
     for row in meta_json:
-        content_row = df[df[specimen_name_col] == row[specimen_name_col]]
+        content_row = df[df[match_col] == row[match_col]]
         plate_name_val = content_row[plate_name_col].iloc[0] if plate_name_col else None
         plate_row_val = (
             content_row[plate_row_col].iloc[0].upper() if plate_row_col else None
@@ -560,7 +560,7 @@ def add_parasite_density_info(
     parasite_density_method_col,
     meta_json,
     df,
-    specimen_name_col,
+    match_col,
     entry_name,
 ):
     density_method_pairs = []
@@ -608,7 +608,7 @@ def add_parasite_density_info(
 
     # Add parasite density info to meta_json
     for row in meta_json:
-        content_row = df[df[specimen_name_col] == row[specimen_name_col]]
+        content_row = df[df[match_col] == row[match_col]]
         density_infos = []
         for density_col, method_col in density_method_pairs:
             density_val = content_row[density_col].iloc[0] if density_col else None
diff --git a/tests/test_pmo_builder/test_metatable_to_pmo.py b/tests/test_pmo_builder/test_metatable_to_pmo.py
index 38d59bc..7223cca 100644
--- a/tests/test_pmo_builder/test_metatable_to_pmo.py
+++ b/tests/test_pmo_builder/test_metatable_to_pmo.py
@@ -1603,13 +1603,18 @@ def test_library_sample_info_table_to_pmo_with_parasite_density(self):
             parasite_density_method_col="parasite_density_method",
         )
 
-        self.assertEqual(result[0]["parasite_density_info"][0]["parasite_density"], 10)
         self.assertEqual(
-            result[0]["parasite_density_info"][0]["parasite_density_method"], "qPCR"
+            result[0]["qpcr_parasite_density_info"][0]["parasite_density"], 10
         )
-        self.assertEqual(result[1]["parasite_density_info"][0]["parasite_density"], 100)
         self.assertEqual(
-            result[1]["parasite_density_info"][0]["parasite_density_method"],
+            result[0]["qpcr_parasite_density_info"][0]["parasite_density_method"],
+            "qPCR",
+        )
+        self.assertEqual(
+            result[1]["qpcr_parasite_density_info"][0]["parasite_density"], 100
+        )
+        self.assertEqual(
+            result[1]["qpcr_parasite_density_info"][0]["parasite_density_method"],
             "microscopy",
         )
 
@@ -1638,10 +1643,18 @@ def test_library_sample_info_table_to_pmo_with_parasite_density_multiple(self):
             parasite_density_method_col=["method1", "method2"],
         )
 
-        self.assertEqual(result[0]["parasite_density_info"][0]["parasite_density"], 15)
-        self.assertEqual(result[0]["parasite_density_info"][1]["parasite_density"], 10)
-        self.assertEqual(result[1]["parasite_density_info"][0]["parasite_density"], 107)
-        self.assertEqual(result[1]["parasite_density_info"][1]["parasite_density"], 100)
+        self.assertEqual(
+            result[0]["qpcr_parasite_density_info"][0]["parasite_density"], 15
+        )
+        self.assertEqual(
+            result[0]["qpcr_parasite_density_info"][1]["parasite_density"], 10
+        )
+        self.assertEqual(
+            result[1]["qpcr_parasite_density_info"][0]["parasite_density"], 107
+        )
+        self.assertEqual(
+            result[1]["qpcr_parasite_density_info"][1]["parasite_density"], 100
+        )
 
     def test_library_sample_info_table_to_pmo_with_all_new_fields(self):
         """Test all new optional fields together"""
@@ -1685,7 +1698,9 @@ def test_library_sample_info_table_to_pmo_with_all_new_fields(self):
         self.assertEqual(result[0]["experiment_accession"], "EXP001")
         self.assertEqual(result[0]["fastqs_loc"], "/path/to/fastqs1")
         self.assertEqual(result[0]["run_accession"], "RUN001")
-        self.assertEqual(result[0]["parasite_density_info"][0]["parasite_density"], 10)
+        self.assertEqual(
+            result[0]["qpcr_parasite_density_info"][0]["parasite_density"], 10
+        )
         self.assertIn("library_prep_plate_info", result[0])
         self.assertEqual(result[0]["library_prep_plate_info"]["plate_col"], 1)
 
@@ -1693,7 +1708,9 @@ def test_library_sample_info_table_to_pmo_with_all_new_fields(self):
         self.assertEqual(result[1]["experiment_accession"], "EXP002")
         self.assertEqual(result[1]["fastqs_loc"], "/path/to/fastqs2")
         self.assertEqual(result[1]["run_accession"], "RUN002")
-        self.assertEqual(result[1]["parasite_density_info"][0]["parasite_density"], 100)
+        self.assertEqual(
+            result[1]["qpcr_parasite_density_info"][0]["parasite_density"], 100
+        )
         self.assertIn("library_prep_plate_info", result[1])
         self.assertEqual(result[1]["library_prep_plate_info"]["plate_col"], 2)
 

From e45234f48914ffb4a98e49643b4af7d695058ec9 Mon Sep 17 00:00:00 2001
From: Nicholas Hathaway <nickjhathaway@gmail.com>
Date: Mon, 29 Jun 2026 15:04:21 -0700
Subject: [PATCH 09/12] two bugs in combine_pmos fixed;

---
 src/pmotools/pmo_engine/pmo_reader.py    | 10 +++-
 tests/test_pmo_engine/test_pmo_reader.py | 67 ++++++++++++++++++++++++
 2 files changed, 75 insertions(+), 2 deletions(-)

diff --git a/src/pmotools/pmo_engine/pmo_reader.py b/src/pmotools/pmo_engine/pmo_reader.py
index 91a6e46..deb7930 100644
--- a/src/pmotools/pmo_engine/pmo_reader.py
+++ b/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
diff --git a/tests/test_pmo_engine/test_pmo_reader.py b/tests/test_pmo_engine/test_pmo_reader.py
index b612ae2..0075a48 100755
--- a/tests/test_pmo_engine/test_pmo_reader.py
+++ b/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(

From 8b32cda59ece4ed449c2bf32f6fd3c97014fd035 Mon Sep 17 00:00:00 2001
From: Nicholas Hathaway <nickjhathaway@gmail.com>
Date: Mon, 29 Jun 2026 15:48:33 -0700
Subject: [PATCH 10/12] fixed a left over old schema version where all fields
 were copies over, now checks for optionally ones;

---
 src/pmotools/pmo_engine/pmo_processor.py    | 24 +++++++++++-------
 tests/test_pmo_engine/test_pmo_processor.py | 28 ++++++++++++++++++++-
 2 files changed, 42 insertions(+), 10 deletions(-)

diff --git a/src/pmotools/pmo_engine/pmo_processor.py b/src/pmotools/pmo_engine/pmo_processor.py
index cef95fb..722cd7a 100644
--- a/src/pmotools/pmo_engine/pmo_processor.py
+++ b/src/pmotools/pmo_engine/pmo_processor.py
@@ -1073,23 +1073,29 @@ def extract_from_pmo_with_read_filter(pmodata, read_filter: float):
         pmo_out = {
             "pmo_header": copy.deepcopy(pmodata["pmo_header"]),
             "panel_info": copy.deepcopy(pmodata["panel_info"]),
-            "sequencing_info": copy.deepcopy(pmodata["sequencing_info"]),
             "target_info": copy.deepcopy(pmodata["target_info"]),
             "specimen_info": copy.deepcopy(pmodata["specimen_info"]),
             "library_sample_info": copy.deepcopy(pmodata["library_sample_info"]),
-            "project_info": copy.deepcopy(pmodata["project_info"]),
-            "targeted_genomes": copy.deepcopy(pmodata["targeted_genomes"]),
             "representative_microhaplotypes": copy.deepcopy(
                 pmodata["representative_microhaplotypes"]
             ),
-            "bioinformatics_methods_info": copy.deepcopy(
-                pmodata["bioinformatics_methods_info"]
-            ),
-            "bioinformatics_run_info": copy.deepcopy(
-                pmodata["bioinformatics_run_info"]
-            ),
             "detected_microhaplotypes": [],
         }
+        # only copy optional sections if they are present (no longer required by the schema)
+        if "sequencing_info" in pmodata:
+            pmo_out["sequencing_info"] = copy.deepcopy(pmodata["sequencing_info"])
+        if "project_info" in pmodata:
+            pmo_out["project_info"] = copy.deepcopy(pmodata["project_info"])
+        if "targeted_genomes" in pmodata:
+            pmo_out["targeted_genomes"] = copy.deepcopy(pmodata["targeted_genomes"])
+        if "bioinformatics_methods_info" in pmodata:
+            pmo_out["bioinformatics_methods_info"] = copy.deepcopy(
+                pmodata["bioinformatics_methods_info"]
+            )
+        if "bioinformatics_run_info" in pmodata:
+            pmo_out["bioinformatics_run_info"] = copy.deepcopy(
+                pmodata["bioinformatics_run_info"]
+            )
         # if has optional read_counts_by_stage then add as well
         # if does contain, @todo consider updating with new counts now that a filter has been applied
 
diff --git a/tests/test_pmo_engine/test_pmo_processor.py b/tests/test_pmo_engine/test_pmo_processor.py
index 2c4a41b..5ce6d31 100755
--- a/tests/test_pmo_engine/test_pmo_processor.py
+++ b/tests/test_pmo_engine/test_pmo_processor.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 
+import copy
 import os
 import tempfile
 import unittest
@@ -317,10 +318,35 @@ def test_extract_from_pmo_with_read_filter(self):
         )
         with open(output_fnp, "w") as f:
             json.dump(pmo_data_filtered, f)
-        self.assertEqual("879b1a0c62a77a8fcc910a21d8ec9de6", md5sum_of_fnp(output_fnp))
+        self.assertEqual("59e24e7efd4cd7822acde70828ad6119", md5sum_of_fnp(output_fnp))
         checker = PMOChecker(self.pmo_jsonschema_data)
         checker.validate_pmo_json(pmo_data_filtered)
 
+    def test_extract_from_pmo_with_read_filter_missing_optional_sections(self):
+        # the v1.1.0 schema relaxed the required fields, so a PMO may omit these
+        # optional sections; the extracted PMO must not copy them in as null/empty keys
+        optional_sections = [
+            "sequencing_info",
+            "project_info",
+            "targeted_genomes",
+            "bioinformatics_methods_info",
+            "bioinformatics_run_info",
+            "read_counts_by_stage",
+        ]
+        stripped_pmo_data = copy.deepcopy(self.combined_pmo_data)
+        for section in optional_sections:
+            stripped_pmo_data.pop(section, None)
+        pmo_data_filtered = PMOProcessor.extract_from_pmo_with_read_filter(
+            stripped_pmo_data, 1000
+        )
+        for section in optional_sections:
+            self.assertNotIn(section, pmo_data_filtered)
+        # the relaxed required fields are a v1.1.0 change, so validate against v1.1.0
+        checker = PMOChecker(
+            load_schema("portable_microhaplotype_object_v1.1.0.schema.json")
+        )
+        checker.validate_pmo_json(pmo_data_filtered)
+
     def test_filter_pmo_by_target_ids(self):
         pmo_data_select_targets = PMOProcessor.filter_pmo_by_target_ids(
             self.combined_pmo_data, {1, 10, 11, 55}

From 6bb05646d7cf24f5420321730a70d6996bf61ef9 Mon Sep 17 00:00:00 2001
From: Nicholas Hathaway <nickjhathaway@gmail.com>
Date: Mon, 29 Jun 2026 16:45:40 -0700
Subject: [PATCH 11/12] small fixes for handling minimum format; added more
 robust unittests for the v1.1.0 files;

---
 src/pmotools/pmo_engine/pmo_exporter.py      |  12 +++++--
 src/pmotools/pmo_engine/pmo_processor.py     |   4 +++
 tests/data/minimum_Furstenau2025_PMO.json.gz | Bin 0 -> 18894 bytes
 tests/test_pmo_engine/test_pmo_exporter.py   |  32 +++++++++++++++++++
 tests/test_pmo_engine/test_pmo_processor.py  |  28 ++++++++++++++++
 5 files changed, 74 insertions(+), 2 deletions(-)
 create mode 100644 tests/data/minimum_Furstenau2025_PMO.json.gz

diff --git a/src/pmotools/pmo_engine/pmo_exporter.py b/src/pmotools/pmo_engine/pmo_exporter.py
index 361ebd7..66238c7 100644
--- a/src/pmotools/pmo_engine/pmo_exporter.py
+++ b/src/pmotools/pmo_engine/pmo_exporter.py
@@ -121,10 +121,14 @@ def export_specimen_meta_table(pmodata, separator: str = ",") -> pd.DataFrame:
         for specimen in pmodata["specimen_info"]:
             export_row = {}
             for key, value in specimen.items():
-                if "project_id" == key:
+                if "project_id" == key and "project_info" in pmodata:
                     export_row["project_name"] = pmodata["project_info"][value][
                         "project_name"
                     ]
+                elif "project_id" == key:
+                    # project_info is optional as of schema v1.1.0; keep the raw id
+                    # rather than failing to resolve a name that isn't available
+                    export_row[key] = value
                 elif PMOExporter._is_primitive(value):
                     export_row[key] = value
                 elif PMOExporter._is_primitive_list(value):
@@ -145,10 +149,14 @@ def export_library_sample_meta_table(pmodata, separator: str = ",") -> pd.DataFr
         for library_sample in pmodata["library_sample_info"]:
             export_row = {}
             for key, value in library_sample.items():
-                if "sequencing_info_id" == key:
+                if "sequencing_info_id" == key and "sequencing_info" in pmodata:
                     export_row["sequencing_info_name"] = pmodata["sequencing_info"][
                         value
                     ]["sequencing_info_name"]
+                elif "sequencing_info_id" == key:
+                    # sequencing_info is optional as of schema v1.1.0; keep the raw id
+                    # rather than failing to resolve a name that isn't available
+                    export_row[key] = value
                 elif "specimen_id" == key:
                     export_row["specimen_name"] = pmodata["specimen_info"][value][
                         "specimen_name"
diff --git a/src/pmotools/pmo_engine/pmo_processor.py b/src/pmotools/pmo_engine/pmo_processor.py
index 722cd7a..c452916 100644
--- a/src/pmotools/pmo_engine/pmo_processor.py
+++ b/src/pmotools/pmo_engine/pmo_processor.py
@@ -20,6 +20,10 @@ def get_index_key_of_bioinformatics_run_names(pmodata):
         :return: a dictionary of indexes keyed by bioinformatics_run_name
         """
         ret = {}
+        # bioinformatics_run_info is optional as of schema v1.1.0; a PMO without it
+        # simply has no run-name to index mapping
+        if "bioinformatics_run_info" not in pmodata:
+            return ret
         for idx, bioinformatics_run in enumerate(pmodata["bioinformatics_run_info"]):
             ret[bioinformatics_run["bioinformatics_run_name"]] = idx
         return ret
diff --git a/tests/data/minimum_Furstenau2025_PMO.json.gz b/tests/data/minimum_Furstenau2025_PMO.json.gz
new file mode 100644
index 0000000000000000000000000000000000000000..b87e2e68517c4deb2c2bc9584534191f3c60dde5
GIT binary patch
literal 18894
zcmagE1yCHp_b$4)%i`_<LVzp~U~xhgcUZ`VV2cL{?!j#r2pZf;(4Yw(d~t$11h?P>
zcOJk0|JJK_Z{2rq)i+)Jo$s8}Gd(?B(>=o+g^N4bf@6#R=<wm=2M2ct69sn{S2xR#
zaCbqFps<OSx+cG^tK&z&ewK+NqgcY`@~tl6?wpV*=Ht=(HS~<5pVxKVG)w$LZfNI@
z4wt-iAvcHLGk(8N{h>oqnWnh*LDZ*kkl$$0La?9kVXX`K_%PUZH%Jn2cXNB&w)p94
zXKS70aoyzM_QJ8Q?Y1%_Hpl<rzJ8(Y?)AgaUB>mQ(Y0s5z1QjL=|P*<<3z-W=yt$&
z1ymc|W98aQnUfsRryRU8XM022ZTAloi;mKdhp}ys+r1=ht&az&%DrC4w!PD%w#Snl
zlgF#xgV=|<`xsxDtEsRund9w)$H&vVpE7qRr;pcHtLrjL0XN5c%x!;~AFt~lukJ6b
zA1`loJ(q9(M(~?Fv_0G}mn-j@zcOjPnqU?UxWAssSYCSk)arD)87zJ0aXNUBvPrij
z?2p{{L%Q9OE#8tHTs`wRQnl}W>FjH=Chm`1z9n1!r`oxc5*lMdcG=3|ahFhY`K)9;
zWuxU~|9vaRL50^&!^Xrz!coK4#9?|$OqBEizt2v??!;kfO3dIB@!e@SoH%Ssi6M|V
z;QzGKa58Z?kP@T%MErIdE=~{UXJYJRjw<{Pp2)*(>-zl2FFO;7iu>kY7q$O4a$A0H
z;W5)H%-Ck>dGLPcitm@*vTd*99La^lQ)zTN?S7ZMSnKHbUqr<1zliyNlmAvED*T?@
zD%R&y7Hf~h|5qZj<7s&N<JW~zZ|%#c%<lhNQu(Ajxi$T|@awJp-;&ttr_75+|GBoA
zr)Hko{GZ6LUl(tBYaKmj{Qovw930M*FwV3-IpnR+*Z;DUaWlO2@H~i!v0FYAdiYOS
zaX;#Ou&`Lmd{gGv&l+(*Vb}L``IpKuh3obE(*4@v{)2~!47LA7#yswl@7<F2o;pU;
z<?KIhd{l4R9Oq<OdS?H<_gFToUY}onA~ALWk7w!P757isb{j4(N0LhZBfKsAk6@Vg
zAHmh~{~|R0SH#wTM?BrXr-;M<O7(vh{%!szqKm6=eQjCh1i902b2;+KOq~Dm{!LD*
z|K4NTrv#dre|8sP9EHoo$7%}7YJabUZv_R(CH#k4I|skTn4JDT`OVm7^{7lf@#L5D
zYNwt+5_KnEvp%yw^4aYV)>&HPP6NSyTdutLA^OFCkp^pp31@1j5gUDpL-fNm#oTrN
zm7K92k3U#<57Q-#o@i|W6E#n^%ga{>4FsY0I0jFC@W-I(m|wD9TgrP+HtXz~Co($&
zmw9pX>;6%u!d=Wn`piOpc(KjDlxn;Gh5r`$_#K|ZL+BIi9zq=-AT|#W`v-{a1LWg9
z#5VhMQgXY*dsz20vuI09bI3J2eOpp^#QVR6M(<(Q)6DHHv5_YsV_Q;m#QS6R=^x4M
z{|I}TIa4#`IdNN>Hm6+nr(A}oT%S(4<W9NFPPueWxze`{|If(SHvIp`ACZwphiumc
z$?ZDtVTaSqg)OoAA=i%?+kfhQU(3f&-QX?U;mzFPE#DzW?~t>1$ctYY?`6i$wwjAQ
z4P?e7x5xhnLdGTk2j(S1{wFls)_M>Bzxe;OVLd7`lIxKDdO<Q|$g$R9US>@Esf&s<
zh9ul=mpm7SnNu=9>~W<Z>7Du~rC%mYHb3=Vsrr!Jab~;SJ>*n(EnV?2qjxnU2eRz1
zH#DMW)A}p#`Y?RUm+~pbNk&qo!2Vq_*D3ervXOs((FpUy)xs@Fz@yjcrRLG&_Ogus
z&8O3ah_>&IInz(Z)k<sEI!({E{fC#Ij@doiE@d7b248x%tu9^qKOFy)ag>(1Q{R3}
z^(1-VCV4C-d9-1E7?ZmD8gSKnd>s34m3aasv!$5w@9GDWQHo>}$lJ~G<nQ>#SZ)8;
zs6@rLT(SI`Oh!4<P11g!mj6e^&F|*#&8t7R>#?4XciSe1k3%WF6>5jWuJ!kWzluD4
zUh4nxd)5_j_weu0@9JveRz`YBdYk#k8<3szkn!mIFxi}`F(LVK;!}FEw?Q&<9rN|+
z(u9u)pxOJdp0~cu%AoMH(%@sjl%#rnfV8@2+g|_qW!HJcis8cfvj2qOqW|8(W7hDS
zM#ioWtsWHH-(|7_Mh+asvpxnm?*X7E7!!Hagt>-i2lwK9r`O}#J56>bj#u8;$?i;r
zjpy^_)#-GV_ZI})=P{a_tm2Ee^U2>$m|M<8`7F`jzg&8^Cuig9^6}-BTdUo6l#ER4
zjMS^`ZGXSBkr_XO0NvAWi6gm%ESaJ0@7W)z=e_5$6`ePmjAlj*vo9CWYK(nAtFMJS
zR6R0J33Dp%E(#Zoue`gBy|*15FTH=gtIzgc1Pr(RbjPg+W~cVB{+`&38qt+ba&T<?
zxS7qIu`uQPaCG1&mc^X6<u_5>Fews#J|^Snu6up4kZ0I<o;iK~vqd`jl*;3wcF3GG
zV43tpo@D%0O0BPW!1+1JxHsnrx!1h$`-2((U(P)}2iEsZr|iB<;U6Ph{DYY#Th(=|
zc(>oKTx%N+AE8b^W#^P`1^r<nI``k~i83}#xpx(dHC@Eid|Mex7FG80d||uz{+>QD
zwQetG(CB^r;i<oYvDIJ_{cg>n{2sP;aOrpb&imjH>I22S3Evo&;m2QUGpz%K2iUyZ
z^=7_j=H-|(UY8>oqu1d%ZSG=5jEz}!n{Eas9}Zp$*1nee(lgu0ySRCmb6)PTIHhUX
zQL%S%(UTJ}a;?ETL&#?7K;L!qU}C;?YN|1j#Li7n->ft(At2>NXd(`v{$aCVw{qvc
zw`g#Abb9K$`NqvZC(|T&&)4!p?CYtF6^Fe=6BFa2b2QlY{d~mVnu^DX8y%BafrFHn
za|Lyuw`<CmbjAKTBswj!LoXgq0|pmi^PT~fJFkg0RXKAF&*>T+D}!E)m@K%u#*_??
zXq|TBFh8@~n{$3ga=hsvlmz-aVCwUH;g|}${Bcw|{7aVWXPhf<0_mCD0^Z;kZ+0vt
zD6>R=Ha16U&iw8YOPOoJE7$I7ZuQ%WKy#YFoj&yy!>=6N?P&4Z0ho>BF#URIfKyb$
zAg2N{j1hes?!5i%la=5g)T8z~oz-imnQl1t$opAYQJkG7#wMh>MP0*^Vo&UsAK|qm
zqG#L2FJa4_#nZX_(`G{Uw0Vb*>Q-=CVP$rq#Prp_t=L%6oR9vucdMr(kM5@rGdYhp
z|1R77uGUkQWggdKGc-*M5<d}T9{HWm<TPm(Jl>)av`~BSZ;nsb_g@Fh{QRRctgx_L
zu^n|D{>95q%At(p9h_z_%V0Xqz$9Q(@&|>a*TdMaAen~v&nbE_VlyVwHAd4-QbVfs
zgXzl~mMv~%nq2!FtwYv(ztxvk7JXhJ9oIGVxQ@%EV81-=q#D%*@4xeWuR2{c=vnyL
zx--^vyUpBYxNIctP}}5vr*YpiGh2h5jkQtE+DDa;^L0$lYC3@5y4l@u^JPkB$BZ*o
zbTeAXc|Q!FcwyFJ-LKMUeCNPue8zL<%pnEpN8IJ%PpZOZ!{6B8F1h_!L9%xZ6CT;j
zTO78tBiro^(A=H^RRSy-?fTWry{AswGPZkuEq;1FVP`yWqJKE>=R<Jmi1Fe5-|`Q4
z352lAp`9Po`e3NYV1n;^mDap(!*z^jgvJ9hNm=gm7b`m-zZ(5C+KZ8LkP#`rvygDf
z8ps)DP8%di5<R}*+f#2=6gClmzn7}<l4j!MEH!x`HJLj0!;P)lX{mdIi`u!jxRHeB
zpy=<3JHFEzLmH(=>m$8hw^5&TpV*RzCZVj$O!rr(C7|!#sM&?cm%p|Pp|CBNgH8FL
zTl5;wR=`PlU$`qQz7>%HE7H2%KU4;^-X%m?6bj$KD&6Vs42s@VoS$tPq}02VpSsR8
zowZKC9BDt9tkqb|3EDL{XobFQg7Mq?rBrTTZ$f*T?UgqUMjOUY$!>V}{?4o~8y;`a
zHCOieOC=_~ujV8gfNck>6%7I%-ia8QB9~`;MJpf09B^9M0KY!n`cNM!|1cJ>e@k+F
zrj8*gCDXn`MCkNf_94THR3_~7GUALL2i#^6I1%!X&wf3_SlaLWs^l_T(xk%57~bPk
zKP+mahtBVMok1B)0d^605U&+J<L!*l^A<1>eLu0d=(TwiQ1DNt>GAY^<D+ZrQKigq
zOV0Mh&JQxpXWL-vcio>99gEn!mxEElAOn76n8QqtXp>7`$KD?bf5YG&;pv+nBW0qN
zN&7kc&NGXSJhuZSj0ViF;;yG~1Y7!POJqvtZ?zY{`0gd-M1FL5f%YzCwlq$<vPpQ$
zMA79TBkJr|bH4uPcEbm+`Lio5V*4-}`UYba4p<FkhRv~?L6}uoS-Cx2>RCBmaY10u
z3ARzC^HK~n<<s!ZrRwzrG-hS*dc!#8vHLo$hrW99W7paKXPB`Ey9SA4*QZ9{#PDY@
zqZfPfk*HY<aAFgg`gZHS$Fb{V#Dl$Jk-ap-@v`MIGbAmAO=3Zz+J2`wfr|Iv%nzcS
zlX>3C!leFTyDJm3TOGw3{t4lv*0n4b+1W31n}jYUI?uUc4}{+?#V(|+xryyLXyqyu
zM@rwe@>~^+jMT@t8uyA##JbY@WU4NJQ#!I2EJx4Z#XdJWBHZ_J<VR);UoC!nQIxR$
ze5U2gH;Z`R<o9p!y<W~03g<QNz^A)*N~4T>7h;;*R`Zi1sB8C)Cr^B+-5)iE95*%2
zvsyR#j3-w|ChJWm|9EJhrbxKoxM&w`^Ov@EUmf1$7bxuyUNk75Og}C{_$HDyv!gi8
z66-VTF!fFwCC--FU$*B#MCo->@mcu`Y$kTH$&TGF{f(BH5564mj~efs7zTE4z9_mi
zd3SYLQWbq)S+-m|dtXt`>*xD3n?JZ=qQKB;P^jGO@nj&o=-^M&ba$r8Mw`6`@I@?a
z?_;62t%>!r7vBVZQ}X?-V131x$t<nK#I!FVt8UuqWwvGKcv942N%!`uF)3bUqb-)V
zE1MQxw$cF4*3j!FRoK$F5zN>J&vpCPs5x7qaY|M5^v~mRPq_aU*=|&Gn~m#dJ$<yZ
z^r^JBT)Da>*g18jeMtp5Bf15$9{el;JVEMWNJ^r)Zl$76HKF2r+8=a(@>Bl`S8ow_
zv@RdQ{Dx~jKqToPtU2`lWKi+dLA1@a59Bn1W-Rip#L$>4dwLGz*ra>RmSfIW%i^L#
zg!`+O>!L#}*H;+ZHdga{g{|!A%Y6)ttuY$Q(u(JQ!o=3N>+lm)G>Sld<*-kDi~KaF
zWg7EVcHiL{$r5_K9^Z@{X109W93%=15g$6zpY7E=+`9~27cX>cEW1>nr|p(2%<*8n
zd}da_P-8Q$f_;>)3ag87cl{wwDG}<e`m4M+K<drMwI8Yu{?Fg>RQ45k7qndM8sDC1
zINoe!*@`;)Oo%$t2H0xyy?wikRpa~NP|ze)^K?hY+VJG8+tqz>CV59^=jV^!#^&Gw
z91ZHqA#Zx?yv~I&mpNm<Q~jM!t7&_KH~9Vf-X$@gIwm%QMNclmUwYl_5;OaB3?@-G
zOQBA6W4i>XC1qSA_M&E)v`hk;RKv1FfbeP)BM~BXfuXdQJ3lN>yLp?kgh67I@{60Y
z!Vaus$!*5^o7dR!qB3&{A;z`B@*cnJ(~u<)^*zEbY8@`=l_e1`+fD|H3;n<HSf3Rs
zxX;s0olF*Q5r0iLafRw`YY*Z4o_ZknLYE3U&G153guQjNtA|x-u6+94WI(*gm;Ck*
zU!k@~)Xn>QKnt`VpYnqoYt}>|tHfe|Yn|Gmhj}vJFt2IJtTRP$^&eotIUWz~!zp4r
zfufaytBmdT*ZwG_PiAF>H`8&tiC0bvT4m$4bk5S6U$(JF4%gMGWI*GV_ZML>vv1Cx
zZ_$xSTaEF*nrl}3<h+SOuZ((z%kB)*pRfh|>5<=sxOw~q4Mo8RQMvmy1K$SJ`F6h#
z8QRU)ly1{kEoDrhTQ9i@cYn1kk7&prU#nI4=@ettD3flvcV2DFTS+r?w{KJE$TYOG
zH}=~^;in|s(0yY^jFnHwS8rd<dFQ<?`ka~)cj|_+jJ++ZOroZTn_WH({wxd)dc+?>
zz~IV2{NJ?&rxH#6u)~FZ>(hf@cXywhe;KdG3(GfNkk1n9Wu#1h_?eK&@A+Xc;-mMW
zd(y{e+<TfS%XOt!6=~N+*!2t|4V&{F>b=At`T3>`*H#1$R|=1W-ZK8tF>)<J!x3ea
zcAZ+BVOpK9uWt4hLK@$KsmM>tOP1ztZ2SnaBGHSLobmN-vCVEx8Vy@dFmDGY+)dtP
zan1N;*JX3N#>0|&UA`MUw;nIq*jAZ)bh#WIDR|hq>&sFZ^%3i!iVd8A&i5Ght$k{O
z*&Ay#6!^{gh^m-ZZH`-RnIS!^dw8Y3&u3j_GcEiPtSfN0FRB-<+nK9Ye>1W$X}4tT
zX}?^vv?VH1_o2r6N7KQDg5CS)Yg@WC_FR?ay>t4p&_BCvclSF{%KvKIYv%#$HAGEa
zc-?Z%UKk^uQy-`+mp{uTOD_0W8=Ptk?woP*`!#Nj=lt3mTxdOe+ps6EcXsj8uXVTL
z?OVUc&J7(76AP_Dt6BFCK0n^+8M^7D{P=n8hNNj@z#15_A6iK!GyZt#GAL(nTkgSk
zi6W4^|7o&<`K$dp>2L+TrF}O&ie$d`{wl>mOXkk)^m?l@$I;)Xt^W8>eDnT)+1-;g
zNV`1h-?Woi`gC*qGKaZxrT6lvdBd^oeBu@dd;Tc<F0ImkO1JIsu(!TtYf<;{VSOkf
zXSi+n!_BVA<Mm%h|4+x;GRw8Z3O7VOk`golT<y{yLGzBFn|;&#9u$tbwvajMUx;&Y
z2PELmeCw7-A$u9%0{#R-6BaTnm-zGwSeMnfUc}i^$jK;^8cnALAXE_V0o2vm?*Bsp
z|0G()1k52i!xM#AAU}&QKXaf-+E>A3g8@t;uves#rY=safnH+%V4$#=028yPO0WYa
z835H^1*SVD*2BnPSpWSG)e(fY9?ML`%Z5Ow`7G~DTn#)f7MtZfhzZ!_=4C>p$1<zS
ze&$TuQo32n@o#?o#oVzH;XuOtCrrD)>O3AvNY5n5P(~IHm;Hk&LBvV#)mJ4d2MM3D
zcrr(CvZB%jNoZp@1>)hzPDpr50UOE~gPit402IF(8W;-}WFRD`6_EzUuYL)AN+r8S
zuNV&e@QHzTIFJLAlrRbu1jj5#1;MfQ$7DhFQsgum*|>z;7xr(-X{dNWWyv^%5`lDB
z*x^R`=%^SRLYx<n1o$8aEmgaXQvy5#$$<*IdMSi#3^JW%>3R<a*?+Z0M@?%5!Ba{&
zQ2OXVnu|a%5l*-e3thYODybxpdKlO0(FpWu@ehq+Xjqmu8!rPuj){ees_QE@s<T5I
z4u?oTTTw_P>F&H?Bxuv)CB)4Pgn^Gu;aJe9_LyLPGBIVF3rQH507zK}h0>4?S^e?t
z0cx*eB7VnfrK<9k^?+W(RX5q=Nymh$+z`sV48Tx{wJlCEfz^$)Z=DEIy53N7xqr9>
zIJ|O(1X0+Akq|X7`<;}j(rmX{XlMwSjbneo{iV9ntRO2Ki&yo}LoCQ6h;>yqH1yev
zcpVzk=1pg-*m$Mq_J9pwPw3P$CQd@I$Z8xY7;`nQN*$sEW{3O%v+>5LaPs2*2usAH
z4;-Q<#*^s!N#*1&q9zEBJ-$!^Pf;bR!O$E`os_^l)MQpaC_QkE_@2Bh<vL^V@P7Ta
zU|MyRq`;E^kcBVu;&~TOI2`o7o&sA}wTdOR<FP8B`m@pIaDrNfAz^<(sry<*T<@O;
zGVV64^00Nhf-2qKd@r<CvU{-@P5e1sQjcwsY)XF)@<mCp7~Ki!7I@sZYCz1D4Qaxn
z__lsF*+I5Bmbl*k6{81z@ay{=<jG%PhkBs58+_nvhE2)I-zBZhF>>7q<BZh(I=1$E
z%oIgWD3K4V`XSugEp&&8KbDEq+6D&Bg?hZ#NLBgH7Wi@f<nOdlql35XzZam`C1a~a
zNGJv+P`~$0DC=iqE&4)qL7VpRQYA<z8s~Ducxk3LqKYIQfs4VgOI9U?4J5;!)L)CM
z8VSe6Q*5UtjR^f}eKH>jAi!ZDjfp9_50*!Wz=Hw@JG(-FWKbFs55#YbiVFNVt?qxO
zDTL%Cg{9wrAQYHEO#4E*mspTQWd@SE?0(z9G;_*MV0#Gsy%o#&B)Urm*u><GMIfe4
zB-&Ru07gx8;)FmgRe_GU94{%QC>?93K_m#jV~2q}F+?&qu?658t;kl2<>k7To9tD{
zpNYUBiU?{Z)n<|XK|C8m&MF!5I+p=K69+J;T%j4IY%$KD(V|l&hpltMIn+%pwR`dq
z`cvspMKUb?Y#|wn-0#f;`HTZj_ui;P!s0o+hSNquECxIJbY^8L*u-u|{PBk{u!;+$
z(9ISj5u`=ld8gn^YaQ5t_E&Ygg<Y^vm))E)>Ne7xCTT2Nj*beFDv_nYxh*S<AcQFB
z&30#|Ws>TuyvbXQRDIU@onbb8L7pu~rPd4)&C{J$4RE#u>$`Ky8LG<Hhzi=tb*13}
z-^7H2aM5scOt(7$RXlYKbXV<f5Pm9>fwP}2IShb!pQqw}vU%cgYny(8`K_#?mSAj>
zyk@DGb!%VQJ5dQ7<g2R-e>3q&tTT{*owN$a|3z!LqGqdb`b+}VEddYGV8MNWCS4pM
zJw39oN=U5~?ihwkNDxf0(q2Wa*cHYo_mKqE+1jE~fW%)ObOM>eRlhOl2M*F}@l$wL
zfz|{<;Hv;xLs?#X@2V=?+;i$^g7>n&LtoTm;xd{Vf?=F<PQ=ibGGSj%UV9-*D*Y}L
zHZO}X1U9Sfo~p8jta1V{;5flxgzeh+ePO_SC=InnpaTFA7S^vbNuXzPyI}emmms2@
zgZcuAN1!N1LqI@Ir5|_#3=d;<1f-t5OPlO`ergKGDXs{F!#~F>@ez{ZuN8w>E~9k`
zFxJ|lB|cbi@<bnhA<G4FQBx|curN^8*&>Ral(Lcd>}AxZP%!qh{7&Mr8B&F?uYz+*
zu)s4~oUk|gY~1$1uzL{qKItDIPS|JbaeRsPLhMO=3^{rhijVbbA456^u)?I`^=Vck
zyCxrqiYQ|sT3`S#FI<Zz{u42{wE#jzrltcYis_S+OUngyeFZ$F`3cp6J<WD;<IXhX
z8fpE;v)+aL4g%WG!=xz5FQ9U8*-@l<r*>LqSeCU}Cll*hT|;4RXJ{yUqF<;Y42FuU
z8pL6TtA>T5g}nr4Rq3&1fpnL}(9X2NSmAq;@ftLv6S(1_=A3e!_{H?Sjfx;vxO%)Y
zSF~0>dOS#PL`)mA7^6wif>U>uH0=+&q+AQ0c_-Rx7@B$K^mB6Z;m&X5*pt$LG*FUv
z=nbTR+)6OEFHnl8H`GB5qBd)5`h((Q3bIB3uGk%l<}nW9v`<pz%tQy0dms^b8GWcw
zzQh72C&&^IKMos>F^n(XGgSF$5=S?vW@%vu3`@&$^2Q8k&$95`IIDrV*f^v6+%eLe
zEKXvo04?k>csPMeSiPZBg5HW={G5b+^Jr-xxp?BU7+J9MdM+q;kCzmmeVjy=J2N({
zlL-(O#Bjcsab9txfz1tU7faST&%%i_`14N;#F#xL<h~Asi#xDkDm8?^OfESFuGVvc
z-%{se1kQ)(o(J*h#ga;(<kV1;_tc}DBr{vAq)CoqPlK<8-Q_G2AY@^BYEmjf62z^i
zIkm+qUU*WzUs77%#mP1sN2)Ike)AG8coxhN;*9j^YU&X7&Q+Q8#gy%)bfo312ur0m
z&1YH(1gK47e1n2DsM+=Y>6;0j{YWeE8mxVLTmxKHk`DzwEsq*QHd#CIxqW(pa8+pY
zCLuWxyXL+N2oGcxkHLMP&qR_?f~aC=>y#Ec_fj(CV~Q3$zYp{36*HVN&*fPZgg|Cr
zBxa?!s?EzDm8jH{uE{b0Jyi6Xx*?%_!H(}U#}x9}I>V8;uC-n^)|n0v@Mrl@bNNuR
za5B8N7izM)VzUG+sd<pjq(l0^iNuh!1eUUC$;0Ds>;kI;lUIKggFBO^!vfQHF~2Kd
zGKdJOG2?pu_K{mvxi?n$!hz}p2&+s{vu;((+HR&2k4gDXdb6vrv6Zj^zG5L8R#^yV
zoV@jpdJ<-OR74eM@eB2Nqe5o$Y)UI@lxU+0_0uB>3oFazF$I&`FRouf<n}R`rW@sY
zJ4@<3S)ueALs0M(ppSH)fsz5Jac*9#SUeTW#g=IcxR-&0DV<@xj5rv%Z}9hDr2^2z
z35&!Ny`4%C?rM_4Y?vP!sPN`=&MA~|Eh5%StU#8f(>|}PIdgaO&CyG-1H<BEDFq}z
zxpWC|^in3Lfey4OTu|Rr8ET5r5Z8|3Q?wdrJDi4FjL+8I0o04<j$oVeW$eX^vqi*5
z6pM!n;K#^%vE}bFl4z?3s?gAAxhLZl<F_9YdC;8!enK;)rxclT>CnvHvuMiGr~tfq
z@*_mziVS46d1HzqU7yYnfKG3^z#toz0@#z_C0C=YRojIE=&(DX=3%&n;-OqzgoW67
zIz=jx5Rfn@r@JkbGubDsxRR&<pIqfUNGa1680pVIO~v%3^qsesEhe<5Q>*kdgj*P+
znHkRYIt7D7neq2Sty$`BXyiBi#K-T&d8KEf0y^=N?a-Ygpclc#P3YC!no_AVghTjU
zp<n>PES3|Ca4G9rG1cfcX|Fcpic;WuG2UuB099;E1XLgjEF_hUo;R+T4%bdniKqM0
zFF18#3Z+N#>Qd(VhQguSVK`rT+V6m##F(i^E1*)Y(&H4_P;FMa*DMN~JjbHRs&Tt%
z_;*5U?=W<rg(nY~#X)2%dlN$1llG|_#W5vyGPL}WbgA4toiXGyVS*r}wu4#ezT&H|
z-P)6>chwYA=-fQRhHl)~h2@QGpSu`egpB2FWL!*11Y@O^tFrAnd<*<5i6SFG1RICo
zTPKy$#}NV0xcIxDLB9>pRx245xYkeQDH#<@+CsBFo6$v1>J0~p>u-8lz7nJ=QKj_j
z)5<-(hOsPE%NiBKWHRz(7x!M$8%AB>RvGQ!?eaMEnbY7;>UCupN1(e?TIzutZ2t%Z
ziT_KBz<I{TV8N&DNEJv(sSpB12NIp6DeqdK5jV@yZKMvEe2s#DaP!D|I#`C(x+`BJ
zV56q_d~e0_B-nh&qPf<H)}(-rP93EGu>1bBdxgx(cF|YRsM9+hLz~f9iNgM2vw5&7
zq^>A)1aoy_XaWuro%g%MIX%$DFwp0atY%zjuXjxMIariPW3pJ(cAeztEQ7iF1$Jxz
z=x_!}=jT9WO*sp;*Fi{3)=d34jy}P7mIAid2iWos9Nf|J!91FR`KQ?SyAxVekHXR!
z3Tp;Q5I%sI7jzU8k!Jd<K<G^pLN8nJ9KwwY%!pb`m*HZgu*mTmU2^vqik&*1sP`Q7
zpLzG^WBA&;Y8PX(A5L<!`{x_)lID#<Yw+|{HhWJbOMxsB6eFdUA-xGAddZ*9->|Yg
z?)tU*u;mUUVuOk>shDdeSnFAH!O1f|rC)RaY_2eMmfQpt=OrU#gmt%4*Uv6ALUSn%
zIdw?QBw+qX9`=Gm_UlY&q~I%HhXOG07;4JJ#heOtBi5!VY}jaokB^B3F5?k9>?Z2t
z9QmY(l2#94I^hC-sAr_E6v6_(<HvnuOMlsEJWlou_-}|K9N}mcSilwIi2qH61{chj
z*pgtV-7ymmCMRE`sFXxZVBlw)D$+v|$)ZjR-6au1g31>R?M}?~*IawvxJ5Ya)(oqd
zZpI<N;bOHwUBblmRt|^&PmB}Y3utJfa`SUmfmKBWmT|kc7&p)_I<3E82}Aq`#_CrE
z*5FvC6`H`1ShPIf;1(I6{@<7nny8>j8b)$OVV5dL!@{*<KzrDFv3YH88HEhmr?0%j
zU=44uEqWI%IA&K6sCb?aVVDwnE{`_gNuzj<c*D0(gP<WK{%Yk|0^*UqCGIK){F5O4
zY847(BL0fryck47S?y#>BkWy>@4n4TsXzp!nWE>3E>)wMB85+4_K~iGY~^qp;aoeT
zht2a4?ITJ;pw{GXsG}qDj-4?#pB!5|sb6LsV^<7LI+fmzq3z0MRy+)03b)PLgcrZY
zAb(@YQ%7x=8hOyoYH++lQwo2g@_meOLSY!^b6YvL{xAV33FzvLAe1vhQ=kVZ09A4j
zjLy61+Bl`f(4}oAfzDR9kTnrW48Ufq>pt|vH<%Bt+7+{1MNY}&CXcN7s17RqsUF{E
z-Fi~6rik<~OvLOO@>Et{sP_DdS2D7+)-ZQZ@s~EmN8(MfcFGuf?$Ee#YrW-@|M4ci
z$$)01M@K^cOD*mJ=l(&76>qKiGl$sGkDQr1kFY=5#u5`#<P!Rk`-U`;;^|ADT}+b1
z)8A??UP3?W+draV3rf-27F?P$MCIuliz4*58a!zE83(nJBJ=QpZy3Knv`qI(p0G@=
zc;S{}u;9#2ACZ&47KUI_lD=HUwfzmj6gDUf{ud_%e0?4wY+31rWT#;y&YibG0!je`
z+JWi;30&yKRIGox&?Zfh0G@o7xs};EGPKDu$Q?A1^q(%o6l0?(9GPQa=|ZX}RR>J0
zRlB1w^$Q-%K_iTFx`XnP$ea(LG@to0ZT%G{7f|e%{H;wY+>HHptFwzi7{<1RaB6E8
zP(%>0?OS4uWv{-<Fzg!>_#mPeiYvx;<G0Ffq{W)=hOo6@D8TSaT;b08oQ)V~6|rF`
zAn!^H|LS(on<1jI-KyJEue|fgtW+UJl9wB_GXh9LfGECT0P%uT8_{%$)i`j+)bN#p
zLy?$bmZeMbHK_I=mM$A7mOcYE(r-xRiX_scj{_S&g3Y<m09wxb9J<1k$szC%W&)9o
zfnQ>=5PBXYK-Q7OP!ld2OP9&^iUcb-n^_Gz(^l&DJag6c`o+V_x)SXB4-5d^TDzI6
zg#PE^a!fVz#{DTB>%at0mO@p3-kg^7u0=t2%H(2yZk@Nj>i`~4%xQ)fNNY3qr&Sef
z+t!cTjoZNb#ZU8I9!et0qOeyKpUNcdY<pZ5zGu3SB`z2%ec(<uc=~A!CRZ~s*ZwUp
z)TTC3gDH~8&h!0-2$%ujMDsQo7ewNswq^vg*ehF)cVvagf%|p8@%Up<oT5i9f9ZF6
zAr4QFe1_VnFHq}t45R>RoN&aKm;?!_)jBRo<j>c)cQHUx&)(~&GL&M*>2yrBmVn%q
zlP+AAMAk@45FxBQG>PpNOrc=BPK_P>QGE=}9YkR)RK@wvb16unZc~7*s_)D%&ai$g
z9PJcrUVk&eC8|&jLPd0R-G7Nzg;oKGj+IHAG(1dha$G?1au5?3w=`%SaFAQ~8G{3W
z)6SR`)@LWr7cYbNEs-z=16Ox5giWv$T;I~yg~p-}ZnyU{8<@t3(fChAkejw_BTokt
zS@pR+YYdIar9r4k6k>hWH>sh*K0zxbbUn$|PBkjFwZiUW^`k@{8opxNL$vZ26RHh>
z{H5y6V2tPNLU*HJ!WG5<7DWx8K&KGOaE{wll^yI{QR28faUR5OnN~^3C)3X2=K{5N
zKd`mig1)PqCr5shyBS<%Ll;&9>6L+|q)X6n%Y5njpf9j^$r(jDp}&(7%}cj}Up;mL
z*V^?)Ecue+UJzQb=`PIvseWd3Ic|%YIg6()^Ai`W+5vJVL`IPL1{zQ(A}L2PN$VbQ
ziX`J;a{5e4nShEHV1?h4I9kyl%0H1L&~gBIz7l0GLfve9ercFEaaNyF%O%XbYYtT6
zAP;Z|3PQlph7-UL-nX-r&2R_<S~-hTDD0I0<@HV9Hx`W;WjS7|IN=_&wT)s(7qb6&
z4_|szAp%P_BB=AdW*3VPNiYOg%xTLqaFLm7|BGyBBk2VUG(brjBM0>r8rA2wV(Ur*
zWRrnADM^XAowFT9w9)u^E<I(_UJ^TEStI}IgCI_WXbDSFbNXeNA`lx@pvVVM&8B)`
zg0$dsW?_1sRdeZN`yE)5qW66}-d{`2&=7`|RN}Hz%hG5{PKJ#%4ozHYRTd&SxA0zJ
zTBmFT_B)7}SjEjVOCCB7C|0%FVX#K3IKXQi0l=5Fj(s&m0_l4V{6>7ygw~Y_UW>c0
zZtu`Ri})s~Ll?*kfDNU1&mythtOBdaWzp<=l1>EPMOv1&5+XRA1|~DG{&IyEdv+v6
zvTk8VXaK^Mz-|e}WnH9MEY5zk0RK$cZ9Z9fw$W02_yHy_M2E8$J6}G>dVa!b|C`aq
zWRJ!l*gl6$EIsMsfis+3&I5CQ0I0ZTU{K=zian@&VDL9apMLMb@{}QU#7RjhB`d)2
zH@g!#O=;Tea)=jqzkc^zKaqYXm#}jKTrSqRD!WR@Zbmv;Td!OcgC&u_LCt5h`pf%P
z{TDsZzM?pvC0v4;PfXvxR8B*1NLSCwHVJA29e4%Ozn3vW9I=DS8AGGV5r`1l?-@ap
zBD-J;j=I`8yf@lw>4|*#mCAtvnX?r?9Wc7Hzn7AXJ*S$P!iIC;_<k|s)RB#}82lOp
z#p0L=bT~|Smf*(2@~LwQC9XJmIgKHS<vi6wJ61))sZ*Pty1!I*swSv66jahRLyH;R
zHFd>_*@D8t)J{#Ov-u|Irz`LF47*gXB%Kc74)t^VSqljpTx)Dz?t-z2Rby|bs#IfX
zw?_XANK~7;nwIzF<spU^!@i!xnMHtxAPyP)3QSt|81W;ynvm34v<9Bx>wa$S%{C0~
z8F(D5`B>KMD3zv~TXqo59uIwICYYS~T_6T-)loTtnsi*fW2S5u!Y>kn0AqmhV@Q2b
z7MOT=Q%-@ic)I3syg|4m?8G@>@qIMo7THR?kT`kNiW4d4PbA`4tDDxn?((B8J1Rbk
z5QE9m5c#}a0z)C3FA-U4kRRUFLB}S@3psETloiFrK#7o*M97!4gA!5YG^K~KW@Jgd
z<*(zQ1a6oF5K}O_4g|~}&3zYvg#jFc5%h*JCJs4ZyTN+k@F+kDh&L0!A0f*dEqhUA
z(=JwcsNV0Qy($X{lgbt1i^1=`z;71e$!sWl1_&E$z+hcd4!0ct!6ldspg?u}XA65L
z3=J2{gP2gwuQRkitb>j-$N>_^XP88kdxxf|oh8nOpac4oRZ&}Gax^&;Qg+Y>UJwK}
zOU31(m+A%*CJp$qTCs)Fp^?yyda-hGhTeP;UjMZ;&&Q@hPm0N?@F9znO=XWQ(PL(y
z1G}A8_5+-&#?-5dlVua}f(o-3<rGuKdD<=%*o^hp)Han+jW02v1YNKL>=8bT?zGPf
z=Dg3tXa)x@6=aw28}aHIiOaQ<yyBO4(+FDSjIh}xMyVr9S-*H1a^^s|mA)ufarFT6
zSmMpGd@u2_B1reA#0gnW7OJF#q?4TfM*jsm;J_!2I6i;FFXO%6Kv)FP0VeTgTtEt<
zWPfUs8faPOg2&Y5p^=^VJ-SRPe__ZBVF@;aJ+`Ez;@Hk_?q?k_Qy)tO8OVEokWCFZ
z0j&RK_tlNZ7&0a<jbV48sI=*8cTFej*uLX`;1$(=EA}_EdR|@6imT@pMR<iaE-e9M
zrs=yPr*{6&0jNX;?p{(hZ<EWCvROp%m~i-nvHOg|*D$04fgFg~m&8Ig#6347m6Azk
z9}UMS*PcRaYTLQHsuP8r0sw%~<XoI;`}xPFW&+3o*elw?NH0CeoG|}~Oj18rC*pNZ
z0l3+D3?6wDT5)3FxG^G<Asi_WShR9Vh3WJ`Qo$r!{08fBf&N8cl}rFz00YM`?i-Cv
zgE<;_!V7}H#TA-r8hRv6HQ3kw-%ZPs0%kOrKEG8Lw}a^EeGxz$0+O>&i^dX^CBwt$
zGDd`UtuX*uhy$sG2ua_wjsq0~llbCD-ayB|()NP7>(9f^ntQ!JD~2W&pal2>dC__!
z$lH^M5D|K5(5^Y%F?iJMjHw&A*gPMlk%S<|L2<AW2i}Rs5UV2M5yVBQh!rRN7zEMn
zg$Iv=&8%SFDh0Bc7kvdmAVH=Om<A*y`el#oLYX1DP_N0!>0`o?L|kklgif~M)vK6*
zMI{l2;u;h-+#&J>`v8Jp5iG($%E}c-M33qU4~rzCALL*hMv#$k&{J`WWF{er?96nC
zBl^0+TNF4&_W2TjK~&VX$oehWL^9VqrpaPdM52rLJ6g~Lf%F<`Kj5-0Z794ZauPZZ
zF|s`PQ4%f@LA*T-ZTb`V72#hpd<g1w<7m}SsLiZ%e|Vx`9(<b(NEfs8R6(ox+?xkS
zyn9JXM9+By$8k!R%ZCT{phtu=<_j`$(JPE9GSGPh3egi2DMHxQXy}Fklnlf~y%%fe
zBCqy)<xtnx>Ju69qfXs(RR5$=b7#cQo|e)hds;DMNj@ha3ObLZ-rupI;RRdRQeSLg
z#zvz=dyEx<g+a6)N+jkb;V-`TU<@ca+rUUm>4Lh^Yyph!fi__FzwD#Npy*BR)yFg_
zDw6b%B29ft_58RVSpro&`z{Sx=-Zj7GYE=u+xdlg-s%7=&T4iv`RBQ6C@M*`7z=Yk
zYOKod+}5#sib8@GpJ?Vs{DtY9Q|^y1$B-XzlH;207PL&kcPbogs(9;C@rzDoKfY+m
zwzzaTph52c^0wnMS&P~??1ux5Vgm2`(fk;Kn&1#LASto0>`$uPk6>*0I1vVMh>|KE
zWI-#lAXMj_3T|gKmi2RZG4C_Xjs_<SfL2}P1W_-CS`!?LVik?=8DNpZscDr)D*hvw
z!QnZuWEPYg!gWXlC}u&q=aXM%5w$6cME4b~jDlFcVdbxOSv*JM4gq-N6F_XhVw|sd
zkt(A5q`Z1T7tI5q;lLrecpI9PUK|Jtm)`x`LKV9l3Qv0}=nbkz$UXnGUnmcbvV6Xp
z#`{c?r6?GJ3c@4m?b{GxkRqpR?W|}cBI4qFMfic1$QJ`}leIbu%GJaec9<n|&nI|?
z_!G{aXbS^K00@bEQ5zy<5E~l!1sVi}{kkd0W){r(D%xosBOe~+w5!lWBqW?qklgP8
z_T?00XoR48p1!x@IQ{O7UnT5QK<{wU;si02yh3pb1;HUlP7E}}xH#v>;d)gLreL9<
z)fGY#8hzO^GzrosrEj!#foaZa{S-7bbx+T)mJngpYG=@@>^EAfz(Q=C@XwFL;miCq
z7tnM#K~<gNyfRB>ZczHF4YIweJ{*tmJ*OxhBAXsNT&VLDr#B2JzX9gYOl#)gMR)9I
zs1kxo{VmHQBa9Msh9{OZbHq>*E=!b=bcETJ_q%SOq43~bp>`Gf2oBVkpcs*_ta$hO
zzP%;KtGl~FH9pz5<jzx7fsGy4%HQ(J!tID+zVvI!VWDX|JvW2sVBtheeP<0u*`g^Q
zWjkG6Kj_jKG2jyy&8tQzi}2#UAI|n_2-i7*mH)N<`PGA4*6`mg;2Vrm5l6>Lhq(7u
zvP(k`4q%EA3@Pj3V1w{Rf>Qo9baJ<UDB|L%IG_Ff08`;r`vS(|?0x$1!$iyvEQvt7
z=m+=0&AmyhF+yw6-V$$n<5m+uTK;0jMTerT;TG>>L`E>mx{y$i_==$5JpY^q<hmld
zF(x&^(hQPG-!XI3&|`=d_tI9X++%Qw7gnAsY~dL8^4m|-8zIymMJyl&63JxOebKZ*
zPEJeZTjdW+>vOW&m5%_gt$lh1h&crbmZ@2Q0SUVxLHqKPIJma#$QuSaY?$j>OmJWz
zRd~2m`wSf-{7tSL3bDnhgo4XbE9Sb*;wHM$jNem4gtNC>;(q||BS)R8((s8e2JW40
zXvQ8X5aBIA&feA3)KO3;3iB^-5U3uzF8}A#`1fIzL%p3;u8)TgLc%ffyGUjZ5q+>u
zbe;-R3z}8Y-Bg!RCfJ7R(-?wOkfo;)MxZGY(a?C9H4;W7;Sth@zIn+@*oT{=ooPYy
zuc^a%l|m3m75)mZON<cxj?5W0%bMVcEMX#344V?d3s1BZOdRd|MtzZh$aVVWLSKig
zNlQb10jT6<ASXWXHJ~T=0B}bCw862_p-le4IOvl{^`R>sWNT^V#{K5~Td_j&TJfLe
zb94GC@(l4DQ)qwceG(K+PBrSG8v+82bCGCJS(dS{GkK%tmhW{#oso+1(8@G~ln;cU
z7uW6$&T$_ZOfn8lz)kZa)!5_&odB0i?k!ib)KGZ!thpt1Ts3A%(%J(>gjp=5!FKNt
zp5jq)(PXCDe9GyNxv$n{v1{xkzEDT+*{?K;T}<j0X0hQBQuw*7V*6#Q7$iQB8Z1;^
zZ}eZ0kV#2=pm#K4Y^B{CfZG_fB0y(}9=k*ur06b($poY|WAIX&CJR!83_dqx8>fGU
z9-A%%^m4OBwwt3fOb4!vd9xk=6(aYVyjc4pa!k|16FQQF9+k(dW5<^sZkzoq$>K(f
zsw7D~8%!Zzj(cUqR6^RiMvu--PXunml0APPS}+P2D97~W+s->HPBIg~loF`YTNl)O
z)?ELQo5wIMYrjNgH8DJ|s%nx@x~H@AVakr&83rR&!DOH&4xvQN_=rR@;}b@_C7Jd~
zShXcMspcr5OvdM?YfnOL_d&wtfrp(Sq#maIxYU?aHy62+t*#*srTJa8Jy@_BK9r3h
zD(XXpXNfb3*sE{AQB1k3ozJk}aG0UcVXr_U`@#a%t4}(6yBuy`cvuwCdu26yFbz+C
z6_JHKSg0BfIRI4nCDU>CgK~wriHY7AWOVdZ4Q3+<*{6v}3F&!qpzXv&m?*Y*T*8Q4
zi0Q0^B4+p-=~RNE>W1Sz)kaLNN+1(IFA{e)teOt3|GUJ?m15FR=hfdQ<cY?l@V2lw
za)@F)#Zbw7J`7%2PZy^GJ*F47rQgJ)v<s5Z$2A8i(APfAgcjR$=}f(|fMf<mr8kqx
zt21ed<Ewq6?fs(U8q^;$RWGz%SoNHabJhZQgE4DL`cKAQ4_$n#qqC6E20fA>1B&b{
zq)6-JB!LMxR6W-^SLw%fPDPbxKq!R6E{NwHv=c${>KdWABJc8x@y61qsf7hPIH^<f
z3mJ&CCqw@Z;fJat&YqKs&=xWnISpWD>{p956|0Gf%Y*IP*@zUs+3NsC!^70^Ob?<6
zGB%JM&3lFoFV!Sf(|nw`0hw$Qf#KYOs{KM(R&vj>2Ucg>e+yz+K_v$bM#xj&$x6`-
zvv+p&k*8f3Lp3lBA%nU=K27-=4#EDS{HH_imY|5w$pu>LqpAFQ$$e>HZ504u5yi3H
zKK-YgfE-=c_32-_96Z6S)@%Z}wVD7_eKK!nb;Z;EO|yf@L@RnD%VtAfB<_x|3ATba
zk95D(ToSJr>ulh1fmo1I4@B%eLSst+FD_=@xHI#tsERmv+up%7O9XRtkL@z7<b34t
zSnQuTg>PjV`|LXN+6wZjRXWLi?|w^%Q?KkYP?TDhWa88dD%SYz3$aNuS#e~){2FX(
zqp&6Y*vOF<sN3BX=9cZ+Fzjj+(^rdLS$!g&B%ByyBGhO^w&0<Fuhz&uRusJH*-}5S
zo~W4CS26B`RYjd|teh{+^hiNoG9ipctjq(U<@g6+;m_~g+n3T#ACUe)KY1&L{i+g^
z2^9=?Dbg|rG;nbgy26~oxpfPc=GGH$0Y_ldg)kZbaBB>wy3dU?3Lqa#5O^$yECuHS
zEI#!gGj!!MXp%Fmz=8(#y#wy5*$A}xT%3BD&-pqHD0{C2SCWy~g$dTxoo*_@EZw+q
zK!Bz)dKCwT2#@-|E8T>v-_W+K4X>#NQJjoR4*t_@0B#?0HxA&WhRmeT`BLmg!jHVE
zFIdm1gnW^A2^1HF=wS^j;W?pLf|!QOo(nM=W{PFEYcsz8p>zHEUF@ift{y96KyPQq
zkb|JESucHlC~j8{kw~iSB)JyD%Aa&oW2bAc5AJnp(aSiT@j7y9#5&n3dOJ)+l(aLy
zq2bviAM+E74M^C?s2cwMCVeNzN@oMGWa>GASWh#U^c3)Ghgl;$J~tc_2K{zgP4m*E
z%r0oB%oaEYfB9-Trd&++fX!kgq}Kga8e?FRS9@TY`Q=GJ<Uw2mi{&{mJF^Yzs#Csj
zOPRPT?44z2!8AzNW*oQpuUi`TMl5tutXw%zlyD*s9UkD^9r;0`Udx@9k{K~f5nr5^
zw9&V*E(e|CO2fPMd9z8Ekjkc}iuK9JN-%qdqJ-_Id2Ir+6swpsfBpr5()Fr`+8c|e
z6|{f6#4qu6m-B2&=mHH2v2%x?9?a(~yPurH1P8i)+Dq0s`?x^M@Q%eXwkp$Lx-7e5
zI{+o}8B(3pn?hguRG!rGf&nYRYEH-0e9rAOm4M3Ql8;g8#Z4FnuAkoGi$ck&rdx1E
z5gH1S_qNuL>rotcTC0|uk`=w4dyrRB%HXfmvIOG7Z^HVMekAc*37%+LaBh&QAHd)L
zNL;T^{XO}dEv@=@D32qJY@0ONr1#p*`MZF-@U*kpH>$ZRan^;HVzRX{s&N=Pe&F|-
ziW`j|$dgz(SqcDZaocL4KCJQ&?JKeUn_OCHcMTWc<law0rrxXm{^wUI89(@S<2Q79
z=u3!ZP_Kg0#?^$S>8{6~nVHI|uD9fTYVr7;T+&v(+FGAmRR_CXFN<@pbw8=kGs7H^
zW#m1Ap;an(Ovh&`;bdu-zOa+VI*pKnHDAeezt`gEz}zD89?*K#*O?k(-lmqsH`PUv
z3Vbal42eO!CeyB)6qHwI^)4*NtIk2=!%D?BCu=8vnhCu}CVLke%?FV`;gRV-p8Y_@
z1frtXu*tphIbYW-hlHumrJ}r(L7Re8fXEi7ym!%R8ZX&I$hxg;$r9gW7Yl9*ksKis
zO2qRyWKCWfdRZa<7_%jgt9_1ztfme1Mp&ouNdAQ0hXTd;EKuTb{1JOWwbggO)rfn{
zI;+KcpEj5}UTAw+2|XPlWMe|-kSt~fy=@%eU}#;iV6A^&jB?S-IBAcDQRUz~{H*<I
z%k()xu@f=+wEdIf=6$l*vCLG+2Ksg<EHAPAdPo4yWi1)+XF$Q(kqrI}*|IV-V{>6r
zJ!nywXX8?&6r&v^7ZVFa0f$}4SiW`1Yar+_4L81oJ$DIi9uCY1G>^=bTZzm>*W36a
zsl7ol)M3k0%1^rVLUV({Yzvu5`T@sqW24tLTkqYg5O=I%h{nV7`<-7)B!I+OBSLK_
zPDBMu`(OJSl`exSF__HNJc^1K`+X3;J?odCDqe#V$n)2%yHd|~rGT?8hNh~i3`eZx
z2F|8~x+NveBal4Zy3Q{^`+6CBf=trnOSHGga+CEhg&fileAxBeX))=z+wW(8hlY3#
zLXxmXf4lyU2Bd%tsaSBw1caha7=&0UXzH+()YN)^V{&_7u=#9DB{6>%g*Yd&`53?W
zQMkKOnxz)@H;sZ~i8gz-|Ap=pF?uFvrVf`tw?@zaFQ*shK?%*9XVOI4X&XcWLfS=k
zWq288Tmm89d~ch)ec9?$U)a_yRlHZjwqbC#@_!fZ5>-NTAT?+A(^XR@u$yN%zNZxK
z@(t)bV6jcjr~3$c0Ua`*iulb!f-}E_`2q(g2pTiI%b-choyLs|4TQ0S&O1A6p9{rv
zOA{cGIVI-1VXK6?PE_(pGa<*+%w&h#g+c-Qd>4Z{Tyi(qw|KJn3Bg=>JYIVhl}Q}b
zyFw;2y!c{N5)Kdf<cUI>+hJPCFS}QA6e5i%-I$AC)Av)Ig+~UL^>iYBGfi!a4LeV!
zCpbVfmTM0mCk;FW4u8$wf5z5a?ml!B@w(yn2>8`8;aPqA-*DfKIWoJfTj>`<E(+6g
zW+fhT>~jF0?W3;<pq}j)yJ?IGoEML7AjmvKKs%Xox#ME;|4#t(2MqYfl(3Vdbxwgv
z=j2S{37Zg2*m2TO$J9~YWulJq!3CnYNi0Af2yE`<m;$FHj>-c$F-1;dEK}%|+N;tV
zL#N1;t`nw?@`0#(1OU+>Te=)R7#O0r@%R<vVS}+l^(cA%7#Q>MAz*}|GjDkE+W>f;
zaZ6^bT)kGBtx(m~B8m`z4WyW4j?punni8VHr^l@uz>^kmLN~yZh6@A`y<KpPaRFyE
z$w2A$@h46k3qX_#;bH*+$WL&wfHg$AFb}BXQWz0%2GCR<7YhIcm5Pf6+Ka3kaWGYz
zCsEIXgVRtxYZXUVK&>c_2RkAj>;Pvc57TR;%u^$jED;a3&hqeJ0o0)2fUsd|CLR&E
z0jHx;rpCA~jnzxMB0SNMh)TCo9E%9o{O}zS5l$*Y5#h?*Amnr~9coHpC?Z^`;0t*u
zB3!9Pib6z$EkIJCz+hl3B3$7c#^s@qaHSjx;83KvU;t5Eg{yvb>0l&G)xB1&BSOMT
zgoFX<T3kycKn@M(;vrUfm~eDVrkk1_4-`gNdL<^oM#fdwXCf$k8`3cO$a_T56VBJq
z2PP_Psi?46pNO!qL%=#*Fkqr3;=)OpxUfJ<Q}Y|{!SIH`uo%fiWH=%!hZSeVFHB?@
zVZDbV!#OgMVV{`DaBSBlwvpj`Ju(Q~N^Mpm+bu+n1J}fk$aX8oz~j0FX<>(JFBrM7
z5L0`>keS*GW=Txd<A8n-ILocjeo$`=n}jN%K9*Z)E!7!`GU_q&WYjef6<KAMh!W}m
z{Vp(}4$!^h66%0}7FT5js7%Bq)YVfZ)T!)>1AsW=66(QHCDa|lMhuuxM|iy90J<?;
z3H3yjP!EnOp>7;grIn3Ll~x%LMdR}6J~4T3g^-x?=@wwV0L-ULX3D1{Y~FDBbUC;e
z!#z`^<G`>2o4<}k>}s8#0ukhbD8>zNI7IM4Tp~(zibvQ90UKH)+Oq;X=Te;rohLGt
z6$>!0!v#-b^k_ArWlF09tV(ct^r4(fE2-O|j7uxqzw!j=2=eSvPy^BZGvKstmM5dG
zArfWO0SN(|Z)r$GXWEdN&a~EgqJ+9dl-c6W83y20gFB&TL<cxnAfR5Da08%NuxC2G
z5~LwO9SoiXL_fO>TQ@pZHoel-GLO~Cs**|p6bvY=E=fHTbWEP9la&W39~B1$l&LuV
zit5Bh9PF5i)13%UaXP|-754&&j;J^t(3cAq(z?J@oQ{xG0*MepC=S~Lyo+2!h^e=E
za7t92?%VlRW8CD&ikobuHLoSAPDga+g$)MK&lI*Q5xfbPO3!hmRC<j8_>sbMef{D`
zTn|tHI>Y7C0lhdfP8c*+F5Oj9f=nkTuZBt=j!33EToX{hHqbNuY+v0)5?9Wh5u<^n
zpB<pXT+j4#tzljm%O1V5a1h-LVTWjhFJ{mDb7kQG4xYGbZUo>!7QFzXo1O{i=O49z
z*amRb+<-buTmm|^2cC@}HH-yPD~Bk@V~hz1HGqm89$QRjiEJ^|D^CrN_nD}M2T+m@
z<BotL;f(9eY=}%ToiKS~A{Gs<ga<MjoF>3Kq6!{}O(84{5QGQ~76%~O{^1NUHD{s<
z9w&y#4^t2>g}B~gfMc2hV*w_DiV$$){4gEBpaf@!iI9lk0IDMDkpj*V@n|J#91Ec8
zt2>9_DtMd_Rq%}E?OE%ZZiy;*0M<dk_L3@0KnT#s6j;F{Oscw+JW~OWIHCd`myh<r
zOiVtQ_tWS{O+E~5Y8tAtqSEvWQ1cRC$r?b-OT;xXG$SPiE6UKoloYgvDFzh4euhg5
zN)VzL(B-j`f)xuaL?<?n64Qw=)m2zP)9ju}!Ae+z@N$6FRY2Z18MkhP$kq=*gmFnh
zi8@qLP+wiP0Za-4tV(f7L5-fs)=%tMRTUM&ad?-P%#;+Qvh_o_yu%U#h(a`A^Q9Ph
zvVuM``TB`)8T)xEV?R%2>?eqvEi4X<2$OeUGp>WX3*Y<wLqtx#f}V*A9~IE;&*PE;
zj>mD$1B$qCc|lK9_~;Ff-<tR^R76{0&e>BHJ}Om?GcpxEBKp|ld{+m{aq8>$u@6+o
zT9|j70E&cgg^xCjmE-iUt_{Fh$04)<xYlK=RE3Ww6IsW3<CqE`#W3YKeIm+nS~)n!
zd9O~0K*8_qP=$}R-p@l7KGxcDCmxG3F)8xUEjL&<`&y|8qQ^LF6L5y9oqYuK6anTq
zokk)vEHMBm1ne*D4mRCYr3#%4QTH;3a4Lrl#yg_WNdPXQxX>vJQ|JVFp8+=k#}qn+
zz!f?Ls?Z5xx(Az`*j~xi7&=*|(8&Yr*I~P6h(wKFg9f6|$pfT2iK@3CE_CuwxzxSu
z{QwX}XHg83)=3PNdOwL}3eOyX*8@A3NjMs9IV!XTXpM%;3MNmK6$ETExcE$&nv6Tg
zg|-kcG+bkD8<@}*K(d2uGY)8AhKrrD6{e)1x`QJp4~U##uQY_`9xM#ZOnW9`kHM`<
zro(1ZqWv-)y<G+-iycL@lY<qCX3Jx-qdxOk?1bcb9CoaUL=HP4F^NyrF&XSQK-CT|
zW{RRr^~fd?`RiDJaJw?4YFB1Gku#yDMC42eFsKH$D<d){bN~ZPV7oFzS8-g5PL;`*
z5MfG#LrvK-*%BHd3Y)Iz_}&;c-D_9&m;1l({HGuP^5_2t009600|1@Se^LYv2>`@R
BqwoL#

literal 0
HcmV?d00001

diff --git a/tests/test_pmo_engine/test_pmo_exporter.py b/tests/test_pmo_engine/test_pmo_exporter.py
index 1984bfa..89c8dfa 100755
--- a/tests/test_pmo_engine/test_pmo_exporter.py
+++ b/tests/test_pmo_engine/test_pmo_exporter.py
@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+import copy
 import gzip
 import hashlib
 import os
@@ -38,6 +39,15 @@ def setUp(self):
             "rt",
         ) as f:
             self.minimum_fields_v1_1_0_pmo_data = json.load(f)
+        # a real, schema-valid v1.1.0 PMO with only the required top-level sections
+        with gzip.open(
+            os.path.join(
+                os.path.dirname(self.working_dir),
+                "data/minimum_Furstenau2025_PMO.json.gz",
+            ),
+            "rt",
+        ) as f:
+            self.minimum_v1_1_0_pmo_data = json.load(f)
 
     def tearDown(self):
         self.test_dir.cleanup()
@@ -245,6 +255,28 @@ def test_export_library_sample_meta_table(self):
             md5sum_of_fnp(os.path.join(self.test_dir.name, "library_sample_table.csv")),
         )
 
+    def test_export_meta_tables_without_optional_cross_ref_sections(self):
+        # project_info and sequencing_info are optional as of v1.1.0; the specimen and
+        # library_sample meta-table exporters must not raise a raw KeyError when a
+        # referencing id is present but the referenced optional section is absent
+        self.assertNotIn("project_info", self.minimum_v1_1_0_pmo_data)
+        self.assertNotIn("sequencing_info", self.minimum_v1_1_0_pmo_data)
+        # a clean minimal PMO (no dangling ids) should export fine
+        PMOExporter.export_specimen_meta_table(self.minimum_v1_1_0_pmo_data)
+        PMOExporter.export_library_sample_meta_table(self.minimum_v1_1_0_pmo_data)
+
+        # inject the referencing ids without the optional sections (referential dangling)
+        # the raw id is kept rather than resolving an unavailable name
+        dangling = copy.deepcopy(self.minimum_v1_1_0_pmo_data)
+        dangling["specimen_info"][0]["project_id"] = 0
+        dangling["library_sample_info"][0]["sequencing_info_id"] = 0
+        spec_table = PMOExporter.export_specimen_meta_table(dangling)
+        self.assertIn("project_id", spec_table.columns)
+        self.assertNotIn("project_name", spec_table.columns)
+        library_table = PMOExporter.export_library_sample_meta_table(dangling)
+        self.assertIn("sequencing_info_id", library_table.columns)
+        self.assertNotIn("sequencing_info_name", library_table.columns)
+
     def test_export_sequencing_info_meta_table(self):
         sequencing_info_table = PMOExporter.export_sequencing_info_meta_table(
             self.small_example_pmo_data
diff --git a/tests/test_pmo_engine/test_pmo_processor.py b/tests/test_pmo_engine/test_pmo_processor.py
index 5ce6d31..2a48ba8 100755
--- a/tests/test_pmo_engine/test_pmo_processor.py
+++ b/tests/test_pmo_engine/test_pmo_processor.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 
 import copy
+import gzip
 import os
 import tempfile
 import unittest
@@ -37,6 +38,16 @@ def setUp(self):
             )
         ) as f:
             self.minimum_pmo_data = json.load(f)
+        # a real, schema-valid v1.1.0 PMO that contains only the required top-level
+        # sections (no sequencing_info/project_info/targeted_genomes/bioinformatics_*/
+        # read_counts_by_stage) to guard against unguarded optional-section access
+        with gzip.open(
+            os.path.join(
+                os.path.dirname(self.working_dir),
+                "data/minimum_Furstenau2025_PMO.json.gz",
+            )
+        ) as f:
+            self.minimum_v1_1_0_pmo_data = json.load(f)
 
     def tearDown(self):
         self.test_dir.cleanup()
@@ -347,6 +358,23 @@ def test_extract_from_pmo_with_read_filter_missing_optional_sections(self):
         )
         checker.validate_pmo_json(pmo_data_filtered)
 
+    def test_bioinformatics_run_name_lookups_without_run_info(self):
+        # bioinformatics_run_info is optional as of v1.1.0; the run-name lookups
+        # must not raise a raw KeyError on a valid PMO that omits it
+        self.assertNotIn("bioinformatics_run_info", self.minimum_v1_1_0_pmo_data)
+        self.assertEqual(
+            {},
+            PMOProcessor.get_index_key_of_bioinformatics_run_names(
+                self.minimum_v1_1_0_pmo_data
+            ),
+        )
+        self.assertEqual(
+            [],
+            PMOProcessor.get_sorted_bioinformatics_run_names(
+                self.minimum_v1_1_0_pmo_data
+            ),
+        )
+
     def test_filter_pmo_by_target_ids(self):
         pmo_data_select_targets = PMOProcessor.filter_pmo_by_target_ids(
             self.combined_pmo_data, {1, 10, 11, 55}

From 336184665e02a6f32463d091aade272e643c7192 Mon Sep 17 00:00:00 2001
From: Nicholas Hathaway <nickjhathaway@gmail.com>
Date: Tue, 21 Jul 2026 14:11:00 -0700
Subject: [PATCH 12/12] change ps_chrom_col to pseduocigar_chrom_col

---
 src/pmotools/pmo_builder/mhap_table_to_pmo.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/pmotools/pmo_builder/mhap_table_to_pmo.py b/src/pmotools/pmo_builder/mhap_table_to_pmo.py
index 70e4a57..fb00da7 100644
--- a/src/pmotools/pmo_builder/mhap_table_to_pmo.py
+++ b/src/pmotools/pmo_builder/mhap_table_to_pmo.py
@@ -262,12 +262,14 @@ def create_representative_microhaplotype_dict(
 
     # the pseudocigar ref_loc shares the chromosome / genome with the
     # microhaplotype location by default, but each may use its own column
-    ps_chrom_col = pseudocigar_chrom_col if pseudocigar_chrom_col else chrom_col
+    pseudocigar_chrom_col = (
+        pseudocigar_chrom_col if pseudocigar_chrom_col else chrom_col
+    )
     ps_genome_id = (
         pseudocigar_genome_id if pseudocigar_genome_id is not None else genome_id
     )
     if pseudocigar_col and not (
-        ps_chrom_col and pseudocigar_start_col and pseudocigar_end_col
+        pseudocigar_chrom_col and pseudocigar_start_col and pseudocigar_end_col
     ):
         raise ValueError(
             "pseudocigar_col is set, so a Pseudocigar ref_loc must be "
@@ -327,7 +329,7 @@ def warn_if_duplicated_seqs(df, target_col, seq_col):
         alt_annotations_col,
         microhaplotype_name_col,
         pseudocigar_col,
-        ps_chrom_col,
+        pseudocigar_chrom_col,
         pseudocigar_start_col,
         pseudocigar_end_col,
         pseudocigar_ref_seq_col,
@@ -390,7 +392,7 @@ def warn_if_duplicated_seqs(df, target_col, seq_col):
                 mhap["microhaplotype_name"] = val
             if val := get_if_present(row, pseudocigar_col):
                 if not (
-                    pd.notna(row[ps_chrom_col])
+                    pd.notna(row[pseudocigar_chrom_col])
                     and pd.notna(row[pseudocigar_start_col])
                     and pd.notna(row[pseudocigar_end_col])
                 ):
@@ -401,7 +403,7 @@ def warn_if_duplicated_seqs(df, target_col, seq_col):
                     )
                 ref_loc = {
                     "genome_id": ps_genome_id,
-                    "chrom": row[ps_chrom_col],
+                    "chrom": row[pseudocigar_chrom_col],
                     "start": row[pseudocigar_start_col],
                     "end": row[pseudocigar_end_col],
                 }