From fbfba1374e9ddc67e9dd0699b11e9146cc8ef7e6 Mon Sep 17 00:00:00 2001 From: Adam English Date: Thu, 11 Jan 2024 11:54:46 -0500 Subject: [PATCH] code clean --- truvari/bench.py | 1 - truvari/comparisons.py | 2 +- truvari/consistency.py | 2 +- 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/truvari/bench.py b/truvari/bench.py index 4a50fa37..9f829d37 100644 --- a/truvari/bench.py +++ b/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']) diff --git a/truvari/comparisons.py b/truvari/comparisons.py index ca99c5c1..332bbfd9 100644 --- a/truvari/comparisons.py +++ 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 diff --git a/truvari/consistency.py b/truvari/consistency.py index c057247e..9761c6a9 100644 --- a/truvari/consistency.py +++ b/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