style: formatting

gumpy/variantfile.py

@@ -1,6 +1,7 @@
 """
 Classes used to parse and store VCF data
 """
+
 import copy
 import pathlib
 import warnings
@@ -81,9 +82,7 @@ def __init__(self, record: pysam.libcbcf.VariantRecord, sample: str | int):
             self.is_filter_pass = False
         else:
             self.filter = str(record.filter.items()[0][0])
-            self.is_filter_pass = (
-                True if record.filter.items()[0][0] == "PASS" else False
-            )
+            self.is_filter_pass = True if record.filter.items()[0][0] == "PASS" else False
 
         # Get the info field
         self.info = {}
@@ -378,9 +377,7 @@ def _find_minor_populations(self):
             simple_calls.append((idx, pos, t, bases))
         seen = []
 
-        allelic_depth_tag = (
-            "COV" if "COV" in self.format_fields_metadata.keys() else "AD"
-        )
+        allelic_depth_tag = "COV" if "COV" in self.format_fields_metadata.keys() else "AD"
 
         for idx, type_ in self.calls.keys():
             # Check if we've delt with this vcf already
@@ -523,7 +520,9 @@ def __find_calls(self):
                 variant_type = "ref"
 
             if index in record_positions:
-                raise ValueError("Multiple calls at position " + str(index) + " in VCF file")
+                raise ValueError(
+                    "Multiple calls at position " + str(index) + " in VCF file"
+                )
             record_positions.add(index)
 
             # if the REF, ALT pair are the same length, check if we can decompose
@@ -801,9 +800,7 @@ def __get_variants(self):
             alts.append(alt)
             variants.append(variant)
             for key in self.calls[(index, type_)]["original_vcf_row"]:
-                metadata[key].append(
-                    self.calls[(index, type_)]["original_vcf_row"][key]
-                )
+                metadata[key].append(self.calls[(index, type_)]["original_vcf_row"][key])
 
         # Remove ref calls as required
         for key in to_drop: