code clean

truvari/bench.py

@@ -348,7 +348,6 @@ def write_match(self, match):
         Writer is responsible for handling FPs between sizefilt-sizemin
         """
         box = self.stats_box
-        skip = False
         if match.base:
             box["base cnt"] += 1
             annotate_entry(match.base, match, self.n_headers['b'])

truvari/comparisons.py

@@ -147,7 +147,7 @@ def entry_is_filtered(entry, values=None):
 def entry_is_present(entry, sample=None, allow_missing=True):
     """
     Checks if entry's sample genotype is present and is heterozygous or homozygous (a.k.a. present)
-    If allow_missing, just check for a 1 in the genotype. Otherwise, a missing ('.') genotype isn't 
+    If allow_missing, just check for a 1 in the genotype. Otherwise, a missing ('.') genotype isn't
     considered present
 
     :param `entry`: entry to check

truvari/consistency.py

@@ -24,7 +24,7 @@ def parse_vcf(fn, no_dups=False):
         is_dup = key in seen
         if no_dups and is_dup:
             continue
-        elif is_dup:
+        if is_dup:
             key += f".{str(seen[key])}"
         seen[key] += 1
         yield key