From 847ca5310714e4131e1a244095bb6b5f9c40808b Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshtm.ac.uk>
Date: Thu, 31 Oct 2024 12:46:22 +0000
Subject: [PATCH] fix for pilot VCFs

---
 pathogenprofiler/vcf.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/pathogenprofiler/vcf.py b/pathogenprofiler/vcf.py
index d8a084b..e01f03c 100644
--- a/pathogenprofiler/vcf.py
+++ b/pathogenprofiler/vcf.py
@@ -223,10 +223,9 @@ def load_ann(
                 else:
                     if 'QNAME' in var.info:
                         freq = 1.0
-                    elif sv:
-                        freq = af_dict[alt]
                     else:
-                        raise NotImplementedError
+                        freq = af_dict[alt]
+
                     
                 tmp_var = Variant(
                     chrom = chrom,