remove "ignore_missing_samples_when_subsetting" (#803)

* remove "ignore_when_subsetting"

* sample ids

Author: bpblanken

v03_pipeline/lib/misc/sample_ids.py

@@ -61,7 +61,6 @@ def remap_sample_ids(
 def subset_samples(
     mt: hl.MatrixTable,
     sample_subset_ht: hl.Table,
-    ignore_missing_samples_when_subsetting: bool,
 ) -> hl.MatrixTable:
     subset_count = sample_subset_ht.count()
     anti_join_ht = sample_subset_ht.anti_join(mt.cols())
@@ -78,12 +77,7 @@ def subset_samples(
             f"IDs that aren't in the callset: {missing_samples}\n"
             f'All callset sample IDs:{mt.s.collect()}'
         )
-        if (
-            subset_count > anti_join_ht_count
-        ) and ignore_missing_samples_when_subsetting:
-            logger.info(message)
-        else:
-            raise MatrixTableSampleSetError(message, missing_samples)
+        raise MatrixTableSampleSetError(message, missing_samples)
     logger.info(f'Subsetted to {subset_count} sample ids')
     mt = mt.semi_join_cols(sample_subset_ht)
     return mt.filter_rows(hl.agg.any(hl.is_defined(mt.GT)))

v03_pipeline/lib/misc/sample_ids_test.py

@@ -106,32 +106,6 @@ def test_remap_sample_ids_remap_has_missing_samples(self) -> None:
                 ignore_missing_samples_when_remapping=False,
             )
 
-    def test_subset_samples(self):
-        # subset 2 of 3 samples in callset
-        sample_subset_ht = hl.Table.parallelize(
-            [
-                {'s': 'HG00731'},
-                {'s': 'HG00732'},
-            ],
-            hl.tstruct(s=hl.tstr),
-            key='s',
-        )
-
-        subset_mt = subset_samples(
-            CALLSET_MT,
-            sample_subset_ht,
-            ignore_missing_samples_when_subsetting=True,
-        )
-
-        self.assertEqual(subset_mt.cols().count(), 2)
-        self.assertEqual(
-            subset_mt.cols().collect(),
-            [
-                hl.Struct(col_idx=0, s='HG00731'),
-                hl.Struct(col_idx=1, s='HG00732'),
-            ],
-        )
-
     def test_subset_samples_zero_samples(self):
         # subset 0 of 3 samples in callset
         sample_subset_ht = hl.Table.parallelize(
@@ -144,7 +118,6 @@ def test_subset_samples_zero_samples(self):
             subset_samples(
                 CALLSET_MT,
                 sample_subset_ht,
-                ignore_missing_samples_when_subsetting=True,
             )
 
     def test_subset_samples_missing_samples(self):
@@ -163,7 +136,6 @@ def test_subset_samples_missing_samples(self):
             subset_samples(
                 CALLSET_MT,
                 sample_subset_ht,
-                ignore_missing_samples_when_subsetting=False,
             )
 
     def test_subset_no_defined_gt(self):
@@ -187,6 +159,5 @@ def test_subset_no_defined_gt(self):
         mt = subset_samples(
             mt,
             sample_subset_ht,
-            False,
         )
         self.assertEqual(mt.count(), (1, 1))

v03_pipeline/lib/tasks/update_lookup_table.py

@@ -22,10 +22,6 @@ class UpdateLookupTableTask(BaseUpdateLookupTableTask):
     project_remap_paths = luigi.ListParameter()
     project_pedigree_paths = luigi.ListParameter()
     imputed_sex_paths = luigi.ListParameter(default=None)
-    ignore_missing_samples_when_subsetting = luigi.BoolParameter(
-        default=False,
-        parsing=luigi.BoolParameter.EXPLICIT_PARSING,
-    )
     ignore_missing_samples_when_remapping = luigi.BoolParameter(
         default=False,
         parsing=luigi.BoolParameter.EXPLICIT_PARSING,
@@ -84,7 +80,6 @@ def requires(self) -> list[luigi.Task]:
                 project_remap_path,
                 project_pedigree_path,
                 imputed_sex_path,
-                self.ignore_missing_samples_when_subsetting,
                 self.ignore_missing_samples_when_remapping,
                 self.validate,
                 False,

v03_pipeline/lib/tasks/update_project_table.py

@@ -20,10 +20,6 @@ class UpdateProjectTableTask(BaseUpdateProjectTableTask):
     project_remap_path = luigi.Parameter()
     project_pedigree_path = luigi.Parameter()
     imputed_sex_path = luigi.Parameter(default=None)
-    ignore_missing_samples_when_subsetting = luigi.BoolParameter(
-        default=False,
-        parsing=luigi.BoolParameter.EXPLICIT_PARSING,
-    )
     ignore_missing_samples_when_remapping = luigi.BoolParameter(
         default=False,
         parsing=luigi.BoolParameter.EXPLICIT_PARSING,
@@ -62,7 +58,6 @@ def requires(self) -> luigi.Task:
             self.project_remap_path,
             self.project_pedigree_path,
             self.imputed_sex_path,
-            self.ignore_missing_samples_when_subsetting,
             self.ignore_missing_samples_when_remapping,
             self.validate,
             False,

v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples.py

@@ -21,10 +21,6 @@ class UpdateVariantAnnotationsTableWithNewSamplesTask(
     project_remap_paths = luigi.ListParameter()
     project_pedigree_paths = luigi.ListParameter()
     imputed_sex_paths = luigi.ListParameter(default=None)
-    ignore_missing_samples_when_subsetting = luigi.BoolParameter(
-        default=False,
-        parsing=luigi.BoolParameter.EXPLICIT_PARSING,
-    )
     ignore_missing_samples_when_remapping = luigi.BoolParameter(
         default=False,
         parsing=luigi.BoolParameter.EXPLICIT_PARSING,
@@ -55,7 +51,6 @@ def requires(self) -> list[luigi.Task]:
                 self.project_remap_paths,
                 self.project_pedigree_paths,
                 self.imputed_sex_paths,
-                self.ignore_missing_samples_when_subsetting,
                 self.ignore_missing_samples_when_remapping,
                 self.validate,
                 self.force,

v03_pipeline/lib/tasks/write_family_table.py

@@ -15,9 +15,6 @@ class WriteFamilyTableTask(BaseWriteTask):
     project_remap_path = luigi.Parameter()
     project_pedigree_path = luigi.Parameter()
     imputed_sex_path = luigi.Parameter(default=None)
-    ignore_missing_samples_when_subsetting = luigi.BoolParameter(
-        parsing=luigi.BoolParameter.EXPLICIT_PARSING,
-    )
     ignore_missing_samples_when_remapping = luigi.BoolParameter(
         parsing=luigi.BoolParameter.EXPLICIT_PARSING,
     )
@@ -61,7 +58,6 @@ def requires(self) -> luigi.Task:
             self.project_remap_path,
             self.project_pedigree_path,
             self.imputed_sex_path,
-            self.ignore_missing_samples_when_subsetting,
             self.ignore_missing_samples_when_remapping,
             self.validate,
             False,

v03_pipeline/lib/tasks/write_metadata_for_run.py

@@ -18,10 +18,6 @@ class WriteMetadataForRunTask(BaseHailTableTask):
     project_remap_paths = luigi.ListParameter()
     project_pedigree_paths = luigi.ListParameter()
     imputed_sex_paths = luigi.ListParameter(default=None)
-    ignore_missing_samples_when_subsetting = luigi.BoolParameter(
-        default=False,
-        parsing=luigi.BoolParameter.EXPLICIT_PARSING,
-    )
     ignore_missing_samples_when_remapping = luigi.BoolParameter(
         default=False,
         parsing=luigi.BoolParameter.EXPLICIT_PARSING,
@@ -63,7 +59,6 @@ def requires(self) -> list[luigi.Task]:
                 project_remap_path,
                 project_pedigree_path,
                 imputed_sex_path,
-                self.ignore_missing_samples_when_subsetting,
                 self.ignore_missing_samples_when_remapping,
                 self.validate,
                 self.force,

v03_pipeline/lib/tasks/write_new_variants_table.py

@@ -42,10 +42,6 @@ class WriteNewVariantsTableTask(BaseWriteTask):
     project_remap_paths = luigi.ListParameter()
     project_pedigree_paths = luigi.ListParameter()
     imputed_sex_paths = luigi.ListParameter(default=None)
-    ignore_missing_samples_when_subsetting = luigi.BoolParameter(
-        default=False,
-        parsing=luigi.BoolParameter.EXPLICIT_PARSING,
-    )
     ignore_missing_samples_when_remapping = luigi.BoolParameter(
         default=False,
         parsing=luigi.BoolParameter.EXPLICIT_PARSING,
@@ -112,7 +108,6 @@ def requires(self) -> list[luigi.Task]:
                         self.project_remap_paths,
                         self.project_pedigree_paths,
                         self.imputed_sex_paths,
-                        self.ignore_missing_samples_when_subsetting,
                         self.ignore_missing_samples_when_remapping,
                         self.validate,
                         self.force,
@@ -131,7 +126,6 @@ def requires(self) -> list[luigi.Task]:
                         project_remap_path,
                         project_pedigree_path,
                         imputed_sex_path,
-                        self.ignore_missing_samples_when_subsetting,
                         self.ignore_missing_samples_when_remapping,
                         self.validate,
                         False,

v03_pipeline/lib/tasks/write_project_family_tables.py

@@ -12,10 +12,6 @@ class WriteProjectFamilyTablesTask(BaseHailTableTask):
     project_remap_path = luigi.Parameter()
     project_pedigree_path = luigi.Parameter()
     imputed_sex_path = luigi.Parameter(default=None)
-    ignore_missing_samples_when_subsetting = luigi.BoolParameter(
-        default=False,
-        parsing=luigi.BoolParameter.EXPLICIT_PARSING,
-    )
     ignore_missing_samples_when_remapping = luigi.BoolParameter(
         default=False,
         parsing=luigi.BoolParameter.EXPLICIT_PARSING,
@@ -58,7 +54,6 @@ def run(self):
             self.project_remap_path,
             self.project_pedigree_path,
             self.imputed_sex_path,
-            self.ignore_missing_samples_when_subsetting,
             self.ignore_missing_samples_when_remapping,
             self.validate,
             False,

v03_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py

@@ -32,10 +32,6 @@ class WriteRemappedAndSubsettedCallsetTask(BaseWriteTask):
     project_remap_path = luigi.Parameter()
     project_pedigree_path = luigi.Parameter()
     imputed_sex_path = luigi.Parameter(default=None)
-    ignore_missing_samples_when_subsetting = luigi.BoolParameter(
-        default=False,
-        parsing=luigi.BoolParameter.EXPLICIT_PARSING,
-    )
     ignore_missing_samples_when_remapping = luigi.BoolParameter(
         default=False,
         parsing=luigi.BoolParameter.EXPLICIT_PARSING,
@@ -178,7 +174,6 @@ def create_table(self) -> hl.MatrixTable:
                 hl.tstruct(s=hl.dtype('str')),
                 key='s',
             ),
-            self.ignore_missing_samples_when_subsetting,
         )
         # Drop additional fields imported onto the intermediate callsets but
         # not used when creating the downstream optimized tables.