1.8.3 Push

Author: BioWilko

artic/get_scheme.py

@@ -37,14 +37,17 @@ def main():
     )
     args = parser.parse_args()
 
-    get_scheme(
+    bed, ref, version = get_scheme(
         scheme_name=args.scheme_name,
         scheme_version=args.scheme_version,
         scheme_directory=args.scheme_directory,
         scheme_length=args.scheme_length,
         read_file=args.read_file,
     )
 
+    os.system(f"cp {bed} primer.bed")
+    os.system(f"cp {ref} reference.fasta")
+
 
 if __name__ == "__main__":
     main()

artic/vcf_filter.py

@@ -52,12 +52,13 @@ def check_filter(self, v):
         try:
             # We don't really care about the depth here, just skip it if it isn't there
             depth = v.format("DP")[0][0]
+
+            if depth < self.min_depth:
+                return False
+
         except Exception:
             pass
 
-        if depth < self.min_depth:
-            return False
-
         return True
 
 

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "artic"
-version = "1.8.3"
+version = "1.8.4"
 authors = [
     { name = "Nick Loman", email = "[email protected]" },
 ]