From 7dd66bcbae10f1756d440fad7349fd8d84b3f381 Mon Sep 17 00:00:00 2001
From: Shing Zhan <shing.zhan@gmail.com>
Date: Wed, 7 Jun 2023 23:12:42 +0100
Subject: [PATCH] Switch order of checks

---
 src/util.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/util.py b/src/util.py
index 96ca2d8..37539b7 100644
--- a/src/util.py
+++ b/src/util.py
@@ -199,16 +199,16 @@ def make_compatible_samples(
     if not isinstance(ts, tskit.TreeSequence):
         raise TypeError(f"ts must be a TreeSequence object.")
 
-    # Check all sites in ts are biallelic.
-    for v in ts.variants():
-        if len(set(v.alleles) - {None}) != 2:
-            raise ValueError(f"All sites in ts must be biallelic.")
-
     # Check all sites in sd are mono- or biallelic.    
     for v in sd.variants():
         if len(set(v.alleles) - {None}) > 2:
             raise ValueError(f"All sites in sd must be mono- or biallelic.")
 
+    # Check all sites in ts are biallelic.
+    for v in ts.variants():
+        if len(set(v.alleles) - {None}) != 2:
+            raise ValueError(f"All sites in ts must be biallelic.")
+
     sd_site_pos = sd.sites_position[:]
     ts_site_pos = ts.sites_position
     all_site_pos = sorted(set(sd_site_pos).union(set(ts_site_pos)))