* Ensure that filters are only called if they are explicitely set on …

…the command line

src/tb_variant_filter/cli.py

@@ -27,7 +27,9 @@ def filter_vcf_file(args: argparse.ArgumentParser):
 
     variant_filters = []
     for filter_class in get_filters():
-        variant_filters.append(filter_class(args, header))
+        filter = filter_class(args, header)
+        if filter.active:
+            variant_filters.append(filter)
 
     variant_filter = UnionFilter(variant_filters)
     print(variant_filter, file=sys.stderr)

src/tb_variant_filter/filters/__init__.py

@@ -25,6 +25,7 @@
 
 class Filter(object):
     def __init__(self, args: argparse.Namespace, header: Header):
+        self.active = False
         self.header = header
 
     @abstractmethod

src/tb_variant_filter/filters/alt_percentage_filter.py

@@ -31,6 +31,7 @@ def __init__(self, args: argparse.Namespace, header: vcfpy.Header) -> "AltPercen
             and args.min_percentage_alt_filter  # noqa W503
             and hasattr(args, "min_percentage_alt")  # noqa W503
         ):
+            self.active = True
             self.min_percentage = args.min_percentage_alt
 
     @classmethod

src/tb_variant_filter/filters/close_to_indel_filter.py

@@ -29,6 +29,7 @@ def __init__(self, args: argparse.Namespace, header: Header) -> "CloseToIndelFil
         super().__init__(args, header)
         self.intervaltree = IntervalTree()
         if hasattr(args, "close_to_indel_filter") and args.close_to_indel_filter:
+            self.active = True
             # we need to re-open the input file because it was already read to get the header
             reader = Reader(open(args.input_file.name))
             dist = args.indel_window_size

src/tb_variant_filter/filters/min_depth_filter.py

@@ -29,6 +29,7 @@ def __init__(self, args: argparse.Namespace, header: vcfpy.Header) -> "MinDepthF
             and args.min_depth_filter  # noqa W503
             and hasattr(args, "min_depth")  # noqa W503
         ):
+            self.active = True
             self.min_depth = args.min_depth
 
     @classmethod

src/tb_variant_filter/filters/region_filter.py

@@ -74,6 +74,7 @@ def __init__(self, args: argparse.Namespace, header: Header) -> "RegionFilter":
         super().__init__(args, header)
         self.intervaltree = IntervalTree()
         if hasattr(args, "region_filter"):
+            self.active = True
             self.region_names = args.region_filter
             for name in args.region_filter:
                 regions = REGIONS[name].regions

src/tb_variant_filter/filters/snv_only_filter.py

@@ -25,6 +25,7 @@ class SnvOnly(Filter):
     def __init__(self, args: argparse.Namespace, header: vcfpy.Header) -> "SnvOnly":
         super().__init__(args, header)
         if hasattr(args, "snv_only_filter") and args.snv_only_filter:
+            self.active = True
             self.snv_only = True
 
     @classmethod