From 176a5a4701d215f1cb475fa2adcaf2f20572ffd5 Mon Sep 17 00:00:00 2001
From: Shing Zhan <shing.zhan@gmail.com>
Date: Mon, 26 Feb 2024 12:01:56 +0000
Subject: [PATCH] Recode allele to print in VCF

---
 python/tests/beagle_numba.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/tests/beagle_numba.py b/python/tests/beagle_numba.py
index 17cc107b41..f01252acbc 100644
--- a/python/tests/beagle_numba.py
+++ b/python/tests/beagle_numba.py
@@ -864,8 +864,8 @@ def write_vcf(ref_ts, impdata, out_file, chr_name="1"):
             line_str = chr_name + "\t"
             line_str += str(int(impdata.site_pos[i])) + "\t"
             line_str += str(i) + "\t"
-            REF = impdata.get_ref_allele_at_site(i)
-            ALT = impdata.get_alt_allele_at_site(i)
+            REF = _ACGT_ALLELES[impdata.get_ref_allele_at_site(i)]
+            ALT = _ACGT_ALLELES[impdata.get_alt_allele_at_site(i)]
             line_str += REF + "\t"
             line_str += ALT + "\t"
             # QUAL