Replace mutable default arguments with None across public APIs

Switch run_isovar, apply_filters, evaluate_filters, and DataFrameBuilder
from mutable module-level defaults to None with fresh copies created
inside each function/constructor. Prevents accidental cross-call
contamination if a caller mutates the returned defaults.

Fixes #136

Author: iskandr

.claude/worktrees/agent-a2bf1121

@@ -0,0 +1 @@
+Subproject commit d7cbc775b76cae1bf9f0455bfe5f5db7a129273f

isovar/__init__.py

@@ -10,7 +10,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-__version__ = "1.4.6"
+__version__ = "1.4.7"
 
 
 from .allele_read import AlleleRead

isovar/dataframe_builder.py

@@ -32,10 +32,10 @@ def __init__(
             self,
             element_class,
             field_names=None,
-            exclude=set([]),
-            converters={},
-            rename_dict={},
-            extra_column_fns={},
+            exclude=None,
+            converters=None,
+            rename_dict=None,
+            extra_column_fns=None,
             variant_columns=True,
             convert_collections_to_size=True):
         """
@@ -77,6 +77,14 @@ def __init__(
             then collection values cause a runtime error.
         """
         self.element_class = element_class
+        if exclude is None:
+            exclude = set()
+        if converters is None:
+            converters = {}
+        if rename_dict is None:
+            rename_dict = {}
+        if extra_column_fns is None:
+            extra_column_fns = {}
         self.rename_dict = rename_dict
         self.converters = converters
         self.variant_columns = variant_columns

isovar/filtering.py

@@ -103,7 +103,7 @@ def evaluate_boolean_filters(isovar_result, filter_flags):
 def evaluate_filters(
         isovar_result,
         filter_thresholds,
-        filter_flags=[]):
+        filter_flags=None):
     """
     Creates a dictionary whose keys are named of different
     filter conditions and values are booleans, where True
@@ -133,6 +133,8 @@ def evaluate_filters(
     Dictionary of filter names mapped to boolean value indicating
     whether this locus passed the filter.
     """
+    if filter_flags is None:
+        filter_flags = []
     filter_values_dict = evaluate_boolean_filters(isovar_result, filter_flags)
     filter_values_dict.update(
         evaluate_threshold_filters(isovar_result, filter_thresholds))
@@ -141,8 +143,8 @@ def evaluate_filters(
 
 def apply_filters(
         isovar_result,
-        filter_thresholds={},
-        filter_flags=[]):
+        filter_thresholds=None,
+        filter_flags=None):
     """
     Given an IsovarResult object, evaluates given filters
     for each object, and returns a copy of the IsovarResult with new fiter
@@ -168,6 +170,10 @@ def apply_filters(
 
     Returns IsovarResult
     """
+    if filter_thresholds is None:
+        filter_thresholds = {}
+    if filter_flags is None:
+        filter_flags = []
     filter_values = OrderedDict(isovar_result.filter_values.items())
     new_filter_values = evaluate_filters(
         isovar_result,

isovar/main.py

@@ -77,8 +77,8 @@ def run_isovar(
         transcript_id_whitelist=None,
         read_collector=None,
         protein_sequence_creator=None,
-        filter_thresholds=DEFAULT_FILTER_THRESHOLDS,
-        filter_flags=DEFAULT_FILTER_FLAGS,
+        filter_thresholds=None,
+        filter_flags=None,
         min_shared_fragments_for_phasing=MIN_SHARED_FRAGMENTS_FOR_PHASING,
         decompression_threads=1):
     """
@@ -130,6 +130,12 @@ def run_isovar(
     `protein_sequences` field of the IsovarVar result will be empty
     if no sequences could be determined.
     """
+    if filter_thresholds is None:
+        filter_thresholds = OrderedDict(DEFAULT_FILTER_THRESHOLDS)
+
+    if filter_flags is None:
+        filter_flags = list(DEFAULT_FILTER_FLAGS)
+
     if isinstance(variants, str):
         variants = load_vcf(variants)