Merge pull request #3503 from broadinstitute/fix-sv-location-filter-bug

Fix SV localtion interval filter bug.
broadinstitute · Jul 21, 2023 · 8a5f227 · 8a5f227
2 parents d41f2d3 + 929dde6
commit 8a5f227
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/seqr/utils/search/elasticsearch/es_search.py b/seqr/utils/search/elasticsearch/es_search.py
@@ -1413,7 +1413,9 @@ def _location_filter(genes, intervals, exclude_locations):
                     }
                 } for key in ['xpos', 'xstop']]
                 interval_q = _build_or_filter('range', range_filters)
-                interval_q |= Q('range', xpos={'lte': xstart}) & Q('range', xstop={'gte': xstop})
+                interval_q |= Q('range', xpos={'lte': xstart}) & Q('range', xstop={'gte': xstop}) & \
+                              Q('range', xpos={'gte': get_xpos(interval['chrom'], MIN_POS)}) & \
+                              Q('range', xstop={'lte': get_xpos(interval['chrom'], MAX_POS)})
 
             if q:
                 q |= interval_q

diff --git a/seqr/utils/search/elasticsearch/es_utils_tests.py b/seqr/utils/search/elasticsearch/es_utils_tests.py
@@ -1613,7 +1613,10 @@ def test_filtered_get_es_variants(self):
                         {'range': {'xstop': {'gte': 2000001234, 'lte': 2000005678}}},
                         {'bool': {'must': [
                             {'range': {'xpos': {'lte': 2000001234}}},
-                            {'range': {'xstop': {'gte': 2000005678}}}]}},
+                            {'range': {'xstop': {'gte': 2000005678}}},
+                            {'range': {'xpos': {'gte': 2000000001}}},
+                            {'range': {'xstop': {'lte': 2300000000}}},
+                        ]}},
                         {'terms': {'geneIds': ['ENSG00000223972']}},
                         {'bool': {'must': [
                             {'range': {'xpos': {'gte': 7000000001, 'lte': 7000001100}}},