move missing AF/DP tags earlier in arg check

Author: sigven

pcgr/arg_checker.py

@@ -49,6 +49,23 @@ def verify_args(arg_dict):
             err_msg = f"Tumor ploidy value ('--tumor_ploidy' = {arg_dict['tumor_ploidy']}) must be > 0"
             error_message(err_msg, logger)
 
+    ## check that allelic support tags are set correctly when minimum/maximum depth/allelic fractions are set
+    if arg_dict['tumor_dp_tag'] == "_NA_" and arg_dict['tumor_dp_min'] is not None:
+        err_msg = f"Minimum sequencing depth tumor ('tumor_dp_min' = {arg_dict['tumor_dp_min']}) requires '--tumor_dp_tag' to be set"
+        error_message(err_msg, logger)
+    
+    if arg_dict['tumor_af_tag'] == "_NA_" and (arg_dict['tumor_af_min'] is not None or arg_dict['tumor_ad_min'] is not None):
+        err_msg = f"Minimum AF/AD tumor ('tumor_af_min' = {arg_dict['tumor_af_min']}, 'tumor_ad_min' = {arg_dict['tumor_ad_min']}) requires '--tumor_af_tag' to be set"
+        error_message(err_msg, logger)
+    
+    if arg_dict['control_dp_tag'] == "_NA_" and arg_dict['control_dp_min'] is not None:
+        err_msg = f"Minimum sequencing depth control ('control_dp_min' = {arg_dict['control_dp_min']}) requires '--control_dp_tag' to be set"
+        error_message(err_msg, logger)
+    
+    if arg_dict['control_af_tag'] == "_NA_" and (arg_dict['control_af_max'] is not None or arg_dict['control_ad_max'] is not None):
+        err_msg = f"Maximum AF/AD control ('control_af_max' = {arg_dict['control_af_max']}, 'control_ad_max' = {arg_dict['control_ad_max']}) requires '--control_af_tag' to be set"
+        error_message(err_msg, logger)
+
     # check that minimum/maximum depth/allelic fractions are set correctly
     dp_tumor_set = False
     if arg_dict['tumor_dp_min'] is not None:
@@ -135,22 +152,6 @@ def verify_args(arg_dict):
                 err_msg = f"Minimum AF (tumor) for TMB calculation ('tmb_af_min' = {str(arg_dict['tmb_af_min'])}) must be "
                 err_msg += f"greater or equal to minimum AF tumor ({str(arg_dict['tumor_af_min'])}, i.e. global filter for variant inclusion in report)"
                 error_message(err_msg, logger)
-    
-    if arg_dict['tumor_dp_tag'] == "_NA_" and arg_dict['tumor_dp_min'] is not None:
-        err_msg = f"Minimum sequencing depth tumor ('tumor_dp_min' = {arg_dict['tumor_dp_min']}) requires '--tumor_dp_tag' to be set"
-        error_message(err_msg, logger)
-    
-    if arg_dict['tumor_af_tag'] == "_NA_" and (arg_dict['tumor_af_min'] is not None or arg_dict['tumor_ad_min'] is not None):
-        err_msg = f"Minimum AF/AD tumor ('tumor_af_min' = {arg_dict['tumor_af_min']}, 'tumor_ad_min' = {arg_dict['tumor_ad_min']}) requires '--tumor_af_tag' to be set"
-        error_message(err_msg, logger)
-    
-    if arg_dict['control_dp_tag'] == "_NA_" and arg_dict['control_dp_min'] is not None:
-        err_msg = f"Minimum sequencing depth control ('control_dp_min' = {arg_dict['control_dp_min']}) requires '--control_dp_tag' to be set"
-        error_message(err_msg, logger)
-    
-    if arg_dict['control_af_tag'] == "_NA_" and (arg_dict['control_af_max'] is not None or arg_dict['control_ad_max'] is not None):
-        err_msg = f"Maximum AF/AD control ('control_af_max' = {arg_dict['control_af_max']}, 'control_ad_max' = {arg_dict['control_ad_max']}) requires '--control_af_tag' to be set"
-        error_message(err_msg, logger)
 
     # Check that coding target size region of sequencing assay is set correctly
     if float(arg_dict['effective_target_size_mb']) < 0 or float(arg_dict['effective_target_size_mb']) > float(pcgr_vars.CODING_EXOME_SIZE_MB):