Added parsing the model_specific_settings.conf file

Author: zhengzhenxian

README.md

@@ -81,7 +81,9 @@ Performance comparison between “ClairS v0.4.0 with the SS model”, “ClairS
 ------
 
 ## Latest Updates
-*v0.4.2 (Jue 29, 2025)* : Added `--snv_min_qual` and `--indel_min_qual` options to independently set the minimum QUAL threshold for SNVs and Indels to be marked as 'PASS', while deprecating the legacy `--qual` option.
+*v0.4.3 (Jul 9, 2025)* : Added parsing the `model_specific_settings.conf` file in the folder of a model and set parameters accordingly. Initially in this version, `snv_min_qual=` and `indel_min_qual=` are supported in the configuration file. 
+
+*v0.4.2 (Jun 29, 2025)* : Added `--snv_min_qual` and `--indel_min_qual` options to independently set the minimum QUAL threshold for SNVs and Indels to be marked as 'PASS', while deprecating the legacy `--qual` option.
 
 *v0.4.1 (Nov 29)* : Added ssrs model for PacBio Revio (`hifi_revio_ssrs`) and illumina (`ilmn_ssrs`) platforms.
 

run_clairs

@@ -667,6 +667,18 @@ def check_args(args):
             elif args.indel_min_qual is None:
                 args.qual = args.indel_min_qual = param.min_thred_qual[args.platform] if args.platform in param.min_thred_qual else param.min_thred_qual['ont']
 
+    model_path = os.path.dirname(args.pileup_model_path)
+    config_file = os.path.join(model_path, 'model_specific_settings.conf')
+    if os.path.exists(config_file):
+        with open(config_file, 'r') as config_fp:
+            for line in config_fp:
+                if line.startswith('snv_min_qual'):
+                    args.snv_min_qual = int(line.split('=')[1].strip())
+                    print("[INFO] Set SNV minimum quality `--snv_min_qual` to {} according to the parameter config file".format(args.snv_min_qual))
+                elif line.startswith('indel_min_qual'):
+                    args.indel_min_qual = int(line.split('=')[1].strip())
+                    print("[INFO] Set Indel minimum quality `--indel_min_qual` to {} according to the parameter config file".format(args.indel_min_qual))
+
     if args.skip_steps is not None:
         check_skip_steps_legal(args)
     if args.enable_realignment and args.platform != 'ilmn':

shared/param.py

@@ -1,6 +1,6 @@
 # parameters
 caller_name = "clairs"
-version = "0.4.2"
+version = "0.4.3"
 
 from itertools import accumulate