modified calls to pass in threshold to generate script and use argume…

…nt parser default

src/dialect/__main__.py

@@ -24,7 +24,12 @@ def main():
 
     if args.command == "generate":
         os.makedirs(args.out, exist_ok=True)
-        generate_bmr_and_counts(maf=args.maf, out=args.out, reference=args.reference)
+        generate_bmr_and_counts(
+            maf=args.maf,
+            out=args.out,
+            reference=args.reference,
+            threshold=args.threshold,
+        )
 
     elif args.command == "identify":
         os.makedirs(args.out, exist_ok=True)
@@ -80,7 +85,9 @@ def main():
                     out=args.out,
                 )
             else:  # args.type == "pair"
-                logging.info("Evaluating methods on simulated data for a pair of genes")
+                logging.info(
+                    "Evaluating methods on simulated data for a pair of genes"
+                )
                 raise NotImplementedError
             # TODO: add method for matrix
 

src/dialect/utils/generate.py

@@ -43,7 +43,7 @@ def convert_maf_to_CBaSE_input_file(maf, out):
     return out_fn
 
 
-def generate_bmr_using_CBaSE(maf, out, reference, threshold="1e-100"):
+def generate_bmr_using_CBaSE(maf, out, reference, threshold):
     """
     Generates background mutation rate (BMR) distributions and count matrix using the CBaSE method.
 
@@ -184,7 +184,12 @@ def generate_bmr_files_from_CBaSE_output(out):
 # ---------------------------------------------------------------------------- #
 
 
-def generate_bmr_and_counts(maf, out, reference):
+def generate_bmr_and_counts(
+    maf,
+    out,
+    reference,
+    threshold,
+):
     """
     Main function to generate background mutation rate (BMR) distributions and a count matrix.
 
@@ -195,7 +200,7 @@ def generate_bmr_and_counts(maf, out, reference):
     """
     logging.info(f"Generating BMR and count matrix for MAF file: {maf}")
     check_file_exists(maf)
-    generate_bmr_using_CBaSE(maf, out, reference)
+    generate_bmr_using_CBaSE(maf, out, reference, threshold)
     generate_bmr_files_from_CBaSE_output(out)
     generate_counts_from_CBaSE_output(out)
     logging.info("BMR and count matrix generation completed successfully.")