From c58af6a9ba3810ae53637312de0858f79734a0f2 Mon Sep 17 00:00:00 2001
From: Leon Rauschning <99650940+lrauschning@users.noreply.github.com>
Date: Thu, 27 Jun 2024 15:03:19 +0200
Subject: [PATCH] emit warning if synal matching fails

---
 msyd/pyxfiles/pansyn.pyx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/msyd/pyxfiles/pansyn.pyx b/msyd/pyxfiles/pansyn.pyx
index 53b4daa..37ca38f 100755
--- a/msyd/pyxfiles/pansyn.pyx
+++ b/msyd/pyxfiles/pansyn.pyx
@@ -203,6 +203,9 @@ def match_synal(syn, aln, ref='a'):
             alnr = next(alniter)[1]
         except StopIteration:
             break
+
+    if len(ret) <= 0.1*len(syn):
+        logger.error("Less than 10% of syns had a matching alignment! Check that syri was run on the same alignment as was provided!")
     return pd.DataFrame(list(ret))