--- a/filter_vcf.py	Mon Dec 21 10:50:17 2015 -0500
+++ b/filter_vcf.py	Mon Dec 21 11:12:19 2015 -0500
@@ -6,6 +6,8 @@
 @author: alex
 '''
 import argparse
+import logging
+import yaml
 
 from phe.variant import VariantSet
 
@@ -15,20 +17,47 @@
     args = argparse.ArgumentParser()
 
     args.add_argument("--vcf", "-v", required=True, help="VCF file to (re)filter.")
-    args.add_argument("--filters", "-f", required=True, help="Filter(s) to apply as key:threshold pairs, separated by comma.")
+
+    group = args.add_mutually_exclusive_group()
+
+    group.add_argument("--filters", "-f", help="Filter(s) to apply as key:threshold pairs, separated by comma.")
+    group.add_argument("--config", "-c", help="Config with filters in YAML format. E.g.filters:-key:value")
+
     args.add_argument("--output", "-o", required=True, help="Location for filtered VCF to be written.")
 
+    args.add_argument("--only-good", action="store_true", default=False, help="Write only variants that PASS all filters (default all variants are written).")
+
+    args.add_argument("--debug", action="store_true", default=False, help="Make output more verbose.")
+
     return args.parse_args()
 
+def load_config(config_path):
+    with open(config_path) as fp:
+        config = yaml.load(fp)
+
+    return config.get("filters", {})
 
 def main():
     args = get_args()
 
+    log_level = logging.DEBUG if args.debug else logging.INFO
+    logging.basicConfig(format="[%(asctime)s] %(levelname)s: %(message)s",
+                            level=log_level)
+
+    if args.config is not None:
+        args.filters = load_config(args.config)
+    elif args.filters is None:
+        logging.error("Either --config or --filters needs to be specified.")
+        return 1
+
     var_set = VariantSet(args.vcf, filters=args.filters)
 
-    var_set.filter_variants()
+    if args.filters:
+        var_set.filter_variants()
 
-    var_set.serialise(args.output)
+    var_set.write_variants(args.output, only_good=args.only_good)
+
+
 
 if __name__ == '__main__':
     exit(main())