fixup: pr comments -- keep mane select version in globals

Author: rileyhgrant

data-pipeline/src/data_pipeline/data_types/gene.py

@@ -226,8 +226,11 @@ def import_hgnc(path):
     return ds
 
 
-def prepare_table_for_release(genes_path):
+def prepare_table_for_release(genes_path, keep_mane_version_global_annotation):
     ds = hl.import_table(genes_path)
+    if keep_mane_version_global_annotation:
+        globals_dict = ds.index_globals()
+        ds = ds.select_globals(mane_select_version=globals_dict["annotations"]["mane_select_transcript"]["version"])
     ds = ds.select_globals()
     return ds
 

data-pipeline/src/data_pipeline/pipelines/genes.py

@@ -328,6 +328,7 @@ def annotate_with_preferred_transcript(table_path):
     f"/{genes_subdir}/genes_grch37_public_release.ht",
     {
         "genes_path": pipeline.get_task("annotate_grch37_genes_step_5"),
+        "keep_mane_version_global_annotation": False,
     },
 )
 
@@ -401,6 +402,7 @@ def annotate_with_constraint(genes_path, constraint_path):
     f"/{genes_subdir}/genes_grch38_public_release.ht",
     {
         "genes_path": pipeline.get_task("remove_constraint_for_release"),
+        "keep_mane_version_global_annotation": True,
     },
 )