delete bin/ scripts and fn (#688)

Author: jklugherz

v03_pipeline/bin/write_combined_interval_reference_ht.py

@@ -205,25 +205,3 @@ def join_hts(
         joined_ht = joined_ht.join(dataset_ht, 'outer')
         joined_ht = annotate_dataset_globals(joined_ht, dataset, dataset_ht)
     return joined_ht
-
-
-def update_existing_joined_hts(
-    destination_path: str,
-    dataset: str,
-    reference_genome: ReferenceGenome,
-    dataset_type: DatasetType,
-    reference_dataset_collection: ReferenceDatasetCollection,
-):
-    joined_ht = hl.read_table(destination_path)
-    dataset_ht = get_dataset_ht(dataset, reference_genome)
-    joined_ht = joined_ht.drop(dataset)
-    joined_ht = joined_ht.join(dataset_ht, 'outer')
-    joined_ht = joined_ht.filter(
-        hl.any(
-            [
-                ~hl.is_missing(joined_ht[dataset])
-                for dataset in reference_dataset_collection.datasets(dataset_type)
-            ],
-        ),
-    )
-    return annotate_dataset_globals(joined_ht, dataset, dataset_ht)

v03_pipeline/bin/write_combined_reference_ht.py

@@ -17,7 +17,6 @@
 from v03_pipeline.lib.reference_data.dataset_table_operations import (
     get_dataset_ht,
     get_enum_select_fields,
-    update_existing_joined_hts,
     update_or_create_joined_ht,
 )
 
@@ -473,35 +472,6 @@ def test_parse_version(self, mock_read_table):
         )
         self.assertRaises(Exception, ht.globals.collect)
 
-    @mock.patch.dict(f'{PATH_TO_FILE_UNDER_TEST}.CONFIG', MOCK_CONFIG)
-    @mock.patch(f'{PATH_TO_FILE_UNDER_TEST}.hl.read_table')
-    @mock.patch(f'{PATH_TO_FILE_UNDER_TEST}.get_dataset_ht')
-    @mock.patch(f'{PATH_TO_FILE_UNDER_TEST}.datetime', wraps=datetime)
-    @mock.patch.object(ReferenceDatasetCollection, 'datasets')
-    def test_update_existing_joined_hts(
-        self,
-        mock_reference_dataset_collection_datasets,
-        mock_datetime,
-        mock_get_dataset_ht,
-        mock_read_table,
-    ):
-        mock_reference_dataset_collection_datasets.return_value = ['a', 'b']
-        mock_datetime.now.return_value = MOCK_DATETIME
-        mock_read_table.return_value = MOCK_JOINED_REFERENCE_DATA_HT
-        mock_get_dataset_ht.return_value = MOCK_B_DATASET_HT
-        ht = update_existing_joined_hts(
-            'destination',
-            'b',
-            ReferenceGenome.GRCh38,
-            DatasetType.SNV_INDEL,
-            ReferenceDatasetCollection.INTERVAL,
-        )
-        self.assertCountEqual(
-            ht.collect(),
-            EXPECTED_JOINED_DATA,
-        )
-        self.assertCountEqual(ht.globals.collect(), EXPECTED_GLOBALS)
-
     @mock.patch(f'{PATH_TO_FILE_UNDER_TEST}.get_dataset_ht')
     @mock.patch(f'{PATH_TO_FILE_UNDER_TEST}.datetime', wraps=datetime)
     @mock.patch.object(ReferenceDatasetCollection, 'datasets')