add missing param

rxu17 · rxu17 · commit 042dca8b0d90 · 2025-01-24T13:25:47.000-08:00
diff --git a/genie/database_to_staging.py b/genie/database_to_staging.py
@@ -756,7 +756,7 @@ def store_sv_files(
                 )
 
     sv_df = sv_df[sv_df["SAMPLE_ID"].isin(keep_for_merged_consortium_samples)]
-    sv_df = filter_out_germline_variants(input_data=sv_df)
+    sv_df = filter_out_germline_variants(input_data=sv_df, status_col_str = "SV_STATUS")
     sv_df.rename(columns=transform._col_name_to_titlecase, inplace=True)
     sv_text = process_functions.removePandasDfFloat(sv_df)
     sv_path = os.path.join(GENIE_RELEASE_DIR, "data_sv.txt")

Original file line number	Diff line number	Diff line change
`@@ -756,7 +756,7 @@ def store_sv_files(`
`756`	`756`	`)`
`757`	`757`
`758`	`758`	`sv_df = sv_df[sv_df["SAMPLE_ID"].isin(keep_for_merged_consortium_samples)]`
`759`		`- sv_df = filter_out_germline_variants(input_data=sv_df)`
	`759`	`+ sv_df = filter_out_germline_variants(input_data=sv_df, status_col_str = "SV_STATUS")`
`760`	`760`	`sv_df.rename(columns=transform._col_name_to_titlecase, inplace=True)`
`761`	`761`	`sv_text = process_functions.removePandasDfFloat(sv_df)`
`762`	`762`	`sv_path = os.path.join(GENIE_RELEASE_DIR, "data_sv.txt")`