From eb2249d4389017d09d299a970ce999498fec4ad6 Mon Sep 17 00:00:00 2001
From: Nick Croucher <n.croucher@imperial.ac.uk>
Date: Fri, 11 Oct 2024 08:35:37 +0100
Subject: [PATCH] Add full network variable to lineage assignment call

---
 PopPUNK/lineages.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/PopPUNK/lineages.py b/PopPUNK/lineages.py
index 36afe729..48398864 100755
--- a/PopPUNK/lineages.py
+++ b/PopPUNK/lineages.py
@@ -392,7 +392,9 @@ def query_db(args):
                     accessory,
                     args.gpu_dist,
                     args.gpu_graph,
-                    save_partial_query_graph = False)
+                    save_partial_query_graph = False,
+                    True # Use full network - does not make sense to use references for lineages
+                    )
 
     # Process clustering
     query_strains = {}