do not drop columns

Author: jklugherz

v03_pipeline/lib/methods/sample_qc.py

@@ -1,7 +1,6 @@
 import hail as hl
 from gnomad.sample_qc.pipeline import filter_rows_for_qc
 
-from v03_pipeline.lib.misc.terra_data_repository import BIGQUERY_METRICS
 from v03_pipeline.lib.model import SampleType
 
 GNOMAD_FILTER_MIN_AF = 0.001
@@ -64,7 +63,4 @@ def annotate_filter_flags(
         filter_flags=hl.array(
             [hl.or_missing(filter_cond, name) for name, filter_cond in flags.items()],
         ).filter(hl.is_defined),
-    ).drop(
-        *BIGQUERY_METRICS[2:5],
-        'filtered_callrate',
     )

v03_pipeline/lib/tasks/write_sample_qc_json_test.py

@@ -47,17 +47,41 @@ def test_call_sample_qc(
 
         self.assertCountEqual(
             res['HG00731'],
-            {'filter_flags': ['contamination', 'coverage']},
+            {
+                'filtered_callrate': 1.0,
+                'contamination_rate': 5.099999904632568,
+                'percent_bases_at_20x': 93.69000244140625,
+                'mean_coverage': 29.309999465942383,
+                'filter_flags': ['contamination', 'coverage'],
+            },
         )
         self.assertCountEqual(
             res['HG00732'],
-            {'filter_flags': ['coverage']},
+            {
+                'filtered_callrate': 1.0,
+                'contamination_rate': 5.0,
+                'percent_bases_at_20x': 90.0,
+                'mean_coverage': 28.0,
+                'filter_flags': ['coverage'],
+            },
         )
         self.assertCountEqual(
             res['HG00733'],
-            {'filter_flags': ['contamination']},
+            {
+                'filtered_callrate': 1.0,
+                'contamination_rate': 6.0,
+                'percent_bases_at_20x': 85.0,
+                'mean_coverage': 36.400001525878906,
+                'filter_flags': ['contamination'],
+            },
         )
         self.assertCountEqual(
-            res['HG00732'],
-            {'filter_flags': []},
+            res['NA19675'],
+            {
+                'filtered_callrate': 1.0,
+                'contamination_rate': 0.0,
+                'percent_bases_at_20x': 80.0,
+                'mean_coverage': 30.0,
+                'filter_flags': [],
+            },
         )