added better variant type search

GC-HBOC · Jul 22, 2024 · 69ef6be · 69ef6be
1 parent 1dacb33
commit 69ef6be
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Showing 3 changed files with 14 additions and 6 deletions.
diff --git a/src/common/db_IO.py b/src/common/db_IO.py
@@ -766,13 +766,20 @@ def get_variants_page_merged(self, page, page_size, sort_by, include_hidden, use
             new_constraints = functions.enbrace(new_constraints)
             postfix = self.add_constraints_to_command(postfix, new_constraints)
         if variant_types is not None and len(variant_types) > 0:
+            new_constraints = []
             for variant_type in variant_types:
-                if 'small' in variant_type:
-                    actual_information += ('small', )
+                if 'insert' in variant_type:
+                    new_constraints.append("(LENGTH(ref) = 1 AND LENGTH(alt) > 1 AND variant_type = 'small')")
+                elif 'delet' in variant_type:
+                    new_constraints.append("(LENGTH(ref) > 1 AND LENGTH(alt) = 1 AND variant_type = 'small')")
+                elif 'delins' in variant_type:
+                    new_constraints.append("(LENGTH(ref) > 1 AND LENGTH(alt) > 1 AND variant_type = 'small')")
+                elif 'small' in variant_type:
+                    new_constraints.append("(LENGTH(ref) = 1 AND LENGTH(alt) = 1 AND variant_type = 'small')")
                 elif 'struct' in variant_type:
-                    actual_information += ('sv',)
-            placeholders = self.get_placeholders(len(variant_types))
-            postfix = self.add_constraints_to_command(postfix, "variant_type IN " + placeholders)
+                    new_constraints.append("(variant_type = 'sv')")
+            new_constraints = ' OR '.join(new_constraints)
+            postfix = self.add_constraints_to_command(postfix, new_constraints)
         if cdna_ranges is not None and len(cdna_ranges) > 0:
             new_constraints = []
             for cdna_range in cdna_ranges:

diff --git a/src/frontend_celery/webapp/templates/index.html b/src/frontend_celery/webapp/templates/index.html
@@ -100,6 +100,7 @@ <h4>Changelog</h4>
         <ul>
             <li>Added retry import button for single failed HerediCaRe VIDs</li>
             <li>Improved HerediCaRe VID information page</li>
+            <li>Added more fine grained variant type search: added insertion, deletion and delins. Small variants are now single nucleotide variants.</li>
         </ul>
         Bugfixes:
         <ul>

diff --git a/src/frontend_celery/webapp/utils/search_utils.py b/src/frontend_celery/webapp/utils/search_utils.py
@@ -475,7 +475,7 @@ def get_static_search_information(user_id, conn: Connection):
     allowed_user_classes = functions.order_classes(conn.get_enumtypes('user_classification', 'classification'))
     allowed_consensus_classes = functions.order_classes(conn.get_enumtypes('consensus_classification', 'classification'))
     allowed_automatic_classes = functions.order_classes(conn.get_enumtypes('automatic_classification', 'classification_splicing'))
-    allowed_variant_types = ['small_variants', 'structural_variant']
+    allowed_variant_types = ['small_variants', 'insertions', 'deletions', 'delins', 'structural_variant']
     annotation_types = conn.get_annotation_types(exclude_groups = ['ID'])
     annotation_types = preprocess_annotation_types_for_search(annotation_types)
     lists = conn.get_lists_for_user(user_id)