edit tests

broadinstitute · Feb 6, 2025 · 388e2b7 · 388e2b7
1 parent c74eaf1
commit 388e2b7
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Showing 2 changed files with 19 additions and 2 deletions.
diff --git a/gnomad/assessment/validity_checks.py b/gnomad/assessment/validity_checks.py
@@ -635,6 +635,21 @@ def check_raw_and_adj_callstats(
                 ),
             }
 
+        # Check that nhomalt <= AC / 2.
+        check_field_nhomalt = f"{nhomalt_metric}{delimiter}{group}"
+        check_field_AC = f"AC{delimiter}{group}"
+
+        field_check_expr[f"{check_field_nhomalt} <= {check_field_AC} / 2"] = {
+            "expr": t.info[check_field_nhomalt] > (t.info[check_field_AC] / 2),
+            "agg_func": hl.agg.count_where,
+            "display_fields": hl.struct(
+                **{
+                    check_field_nhomalt: t.info[check_field_nhomalt],
+                    check_field_AC: t.info[check_field_AC],
+                }
+            ),
+        }
+
         # Check AF missing if AN is missing and defined if AN is defined and > 0.
         check_field = f"AF{delimiter}{group}"
         an_field = f"AN{delimiter}{group}"
@@ -682,7 +697,7 @@ def check_raw_and_adj_callstats(
             ),
         }
 
-    # Check overall gnomad's raw subfields >= adj
+    # Check overall gnomad's raw subfields >= adj.
     for subfield in ["AC", "AN", nhomalt_metric]:
         check_field_left = f"{subfield}{delimiter}raw"
         check_field_right = f"{subfield}{delimiter}adj"

diff --git a/tests/assessment/test_validity_checks.py b/tests/assessment/test_validity_checks.py
@@ -541,7 +541,7 @@ def ht_for_check_raw_and_adj_callstats() -> hl.Table:
                 "AF_adj": -0.01,
                 "AN_raw": 1000,
                 "AN_adj": 1100,
-                "nhomalt_raw": 1,
+                "nhomalt_raw": -3,
                 "nhomalt_adj": 2,
             },
             "filters": {"LowQual"},
@@ -615,6 +615,7 @@ def test_check_raw_and_adj_callstats(
         "PASSED AC_adj defined when AN defined and missing when AN missing check",
         "PASSED AF_adj defined when AN defined (and > 0) and missing when AN missing check",
         "PASSED AC_raw >= AC_adj check",
+        "PASSED nhomalt_raw <= AC_raw / 2 check",
         # Expected FAILURES.
         "Found 1 sites that fail nhomalt_raw defined when AN defined and missing when AN missing check:",
         "Found 1 sites that fail AF_raw defined when AN defined (and > 0) and missing when AN missing check:",
@@ -627,6 +628,7 @@ def test_check_raw_and_adj_callstats(
         "Found 1 sites that fail AF_adj >= 0 check:",
         "Found 1 sites that fail AN_raw >= AN_adj check:",
         "Found 1 sites that fail nhomalt_raw >= nhomalt_adj check:",
+        "Found 1 sites that fail nhomalt_adj <= AC_adj / 2 check:",
     ]
 
     for msg in expected_logs: