From 1fa9fcce4d1f3e2e9cae13a849133b85c6824b1b Mon Sep 17 00:00:00 2001
From: wdecoster <decosterwouter@gmail.com>
Date: Tue, 2 Jul 2024 15:12:09 +0200
Subject: [PATCH] fix equal short sequences being 1|2 for short alleles

---
 Cargo.toml | 2 +-
 src/vcf.rs | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index e461ff7..8eb0bc9 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "STRdust"
-version = "0.8.3"
+version = "0.8.4"
 edition = "2021"
 
 
diff --git a/src/vcf.rs b/src/vcf.rs
index 93a0db7..7e233dc 100644
--- a/src/vcf.rs
+++ b/src/vcf.rs
@@ -106,7 +106,7 @@ impl VCFRecord {
             "."
         } else if levenshtein(&allele2.seq, &repeat_ref_sequence) < repeat_ref_sequence.len() / 20 {
             "0"
-        } else if levenshtein(&allele2.seq, &allele1.seq) < allele1.seq.len() / 20 {
+        } else if allele2.seq == allele1.seq || levenshtein(&allele2.seq, &allele1.seq) < allele1.seq.len() / 20 {
             genotype1
         } else {
             next_alt