fix tests

broadinstitute · Feb 14, 2024 · 4fc80a5 · 4fc80a5
1 parent 5eb3bb6
commit 4fc80a5
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/hail_search/queries/sv.py b/hail_search/queries/sv.py
@@ -80,7 +80,7 @@ def _filter_annotated_table(self, ht, *args, parsed_intervals=None, exclude_inte
         if padded_interval:
             padding = int((padded_interval['end'] - padded_interval['start']) * padded_interval['padding'])
             ht = ht.filter(hl.all([
-                ht.start_locus.contig == padded_interval['chrom'],
+                ht.start_locus.contig == f"chr{padded_interval['chrom']}",
                 self._locus_in_range(ht.start_locus, padded_interval['start'], padding),
                 self._locus_in_range(ht.end_locus, padded_interval['end'], padding)
             ]))

diff --git a/hail_search/test_search.py b/hail_search/test_search.py
@@ -612,17 +612,17 @@ async def test_location_search(self):
         )
 
         await self._assert_expected_search(
-            [GCNV_VARIANT4], padded_interval={'chrom': '17', 'start': 38724781, 'end': 38738703, 'padding': 0.2},
+            [GCNV_VARIANT4], padded_interval={'chrom': '17', 'start': 38720781, 'end': 38738703, 'padding': 0.2},
             omit_sample_type='SNV_INDEL',
         )
 
         await self._assert_expected_search(
-            [], padded_interval={'chrom': '17', 'start': 38722281, 'end': 38738703, 'padding': 0.1},
+            [], padded_interval={'chrom': '17', 'start': 38720781, 'end': 38738703, 'padding': 0.1},
             omit_sample_type='SNV_INDEL',
         )
 
         await self._assert_expected_search(
-            [SV_VARIANT1], padded_interval={'chrom': '14', 'start': 106692244, 'end': 106742587, 'padding': 0.1},
+            [SV_VARIANT4], padded_interval={'chrom': '14', 'start': 106692244, 'end': 106742587, 'padding': 0.1},
             sample_data=SV_WGS_SAMPLE_DATA,
         )
 

diff --git a/seqr/utils/search/hail_search_utils_tests.py b/seqr/utils/search/hail_search_utils_tests.py
@@ -249,7 +249,8 @@ def test_variant_lookup(self):
         })
         self._test_minimal_search_call(expected_search_body={
             'genome_version': 'GRCh38', 'data_type': 'SV_WES', 'annotations': {'structural': ['DEL', 'gCNV_DEL']},
-            'intervals': ['17:38718997-38738487'], 'sample_data': {'SV_WGS': SV_WGS_SAMPLE_DATA},
+            'padded_interval': {'chrom': '17', 'start': 38721781, 'end': 38735703, 'padding': 0.2},
+            'sample_data': {'SV_WGS': SV_WGS_SAMPLE_DATA},
         })
 
         # No second lookup call is made for non DELs/DUPs