Handle MT values as NaN to avoid string comparison

This change ensures that MT (Mitochondria) values are
treated as -1 to mean NaN (Not a Number),
improving the speed by eliminating string comparisons.

run/add_c_nc.py

@@ -28,6 +28,9 @@ def add_c_nc(score, ref):
     bl = clin_nc.new_start.values
     bc= clin_nc.new_chr.values
 
+    bc[bc=='MT'] = -1 # Treat MT chromosome as NaN values to avoid string comparison
+    bc = bc.astype(int)
+
     i, j = np.where((a[:, None] >= bl) & (a[:, None] <= bh) &(ac[:, None]==bc))
 
     cln=pd.concat([