From ead12605d635e2097038e37e6875b4efa433cb3b Mon Sep 17 00:00:00 2001
From: Biowilko <sam1.wilkinson1@gmail.com>
Date: Mon, 21 Oct 2024 11:42:50 +0100
Subject: [PATCH] Fix correctly paired logic

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

diff --git a/artic/align_trim.py b/artic/align_trim.py
index 2a1b3f69..7898294a 100755
--- a/artic/align_trim.py
+++ b/artic/align_trim.py
@@ -214,9 +214,8 @@ def handle_segment(
     # check if primers are correctly paired and then assign read group
     # NOTE: removed this as a function as only called once
     # TODO: will try improving this / moving it to the primer scheme processing code
-    correctly_paired = p1[2]["Primer_ID"].replace("_LEFT", "") == p2[2][
-        "Primer_ID"
-    ].replace("_RIGHT", "")
+    correctly_paired = p1[2]["Primer_ID"].split("_")[1] == p2[2]["Primer_ID"].split("_")[1]
+
 
     if not args.no_read_groups:
         if correctly_paired: