Fix #5896 - managed variants start to end interval search

Author: dnil

CHANGELOG.md

@@ -20,6 +20,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Tests for cli command to update VCF files not running (#5888)
 - Gene in panels search results broken layout - overflow when a panel has many panel versions containing the gene (#5899)
 - ACMG evaluation PDF export, both style and colors (#5879)
+- Start to end interval search for managed variants (#5917)
 
 ## [4.106]
 ### Added

scout/adapter/mongo/managed_variant.py

@@ -183,13 +183,22 @@ def add_options(self, query, query_options):
                     "$options": "i",
                 }
 
+            start = max(int(query_options.get("position", 1)), 1)
+            end = max(int(query_options.get("end", 1)), 1)
+
             if "position" in query_options:
-                position = max(int(query_options["position"]), 1)
-                query["end"] = {"$gte": position}
+                query["position"] = {"$gte": start}
+                if "end" in query_options:
+                    query["position"]["$lte"] = end
 
             if "end" in query_options:
-                end = max(int(query_options["end"]), 1)
-                query["position"] = {"$lte": end}
+                query.setdefault("$or", []).extend(
+                    [
+                        {"end": {"$gte": start, "$lte": end}},
+                        {"end": {"$exists": False}},
+                        {"end": {"$in": [None, ""]}},
+                    ]
+                )
 
             if "sub_category" in query_options:
                 query["sub_category"] = {"$in": query_options["sub_category"]}

tests/adapter/mongo/test_query.py

@@ -173,7 +173,7 @@ def test_genotype_query_other(adapter, case_obj):
 
 
 def test_gene_symbol_gene_panel_query(adapter, case_obj):
-    """Test variants query using a gene panel cointaining a certain gene and a hgnc symbol of another gene"""
+    """Test variants query using a gene panel containing a certain gene and a hgnc symbol of another gene"""
 
     # GIVEN a database containing a minimal gene panel
     test_gene = "POT1"
@@ -199,7 +199,7 @@ def test_gene_symbol_gene_panel_query(adapter, case_obj):
     query = {"hgnc_symbols": ["ATM"], "gene_panels": ["POT panel"]}
     mongo_query = adapter.build_query(case_obj["_id"], query=query)
 
-    # THEN the query should countain both genes in the hgnc_symbols list
+    # THEN the query should contain both genes in the hgnc_symbols list
     mongo_query_gene_list = mongo_query["hgnc_ids"]["$in"]
     for gene in [test_gene_hgnc_id, other_gene_hgnc_id]:
         assert gene in mongo_query_gene_list