use high confidence LoF

NBISweden · Apr 11, 2019 · c5ca6d2 · c5ca6d2
1 parent f39f3c8
commit c5ca6d2
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/backend/modules/browser/tests/test_utils.py b/backend/modules/browser/tests/test_utils.py
@@ -132,7 +132,7 @@ def test_get_flags_from_variant():
     fake_variant = {'vep_annotations':[{'LoF': 'LC', 'LoF_flags': 'something'},
                                        {'LoF': 'HC', 'LoF_flags': 'something'}]}
     flags = utils.get_flags_from_variant(fake_variant)
-    assert flags == ['LoF flag']
+    assert flags == ['LoF', 'LoF flag']
 
     fake_variant = {'mnps': 'no idea', 'vep_annotations':[]}
     flags = utils.get_flags_from_variant(fake_variant)

diff --git a/backend/modules/browser/utils.py b/backend/modules/browser/utils.py
@@ -239,6 +239,8 @@ def get_flags_from_variant(variant:dict):
     lof_annotations = [x for x in variant['vep_annotations'] if x['LoF'] != '']
     if not lof_annotations:
         return flags
+    if any([x['LoF'] == 'HC' for x in lof_annotations]):
+        flags.append('LoF')
     if all([x['LoF'] != 'HC' for x in lof_annotations]):
         flags.append('LC LoF')
     if all([x['LoF_flags'] != '' for x in lof_annotations]):