From 2332b92e319ea9fd691dbc914bdc106eaafaa4a0 Mon Sep 17 00:00:00 2001
From: Jared Simpson <jared.simpson@gmail.com>
Date: Thu, 8 Dec 2022 09:48:05 -0500
Subject: [PATCH] skip multi-allelic ambiguity codes instead of failing

---
 workflow/scripts/mixture_check.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/workflow/scripts/mixture_check.py b/workflow/scripts/mixture_check.py
index 885e90e..693217c 100755
--- a/workflow/scripts/mixture_check.py
+++ b/workflow/scripts/mixture_check.py
@@ -109,6 +109,9 @@ def calculate(sample_a, sample_b, variants, counts):
         # if A is an IUPAC code, resolve to the non-B allele
         allele_a = resolve_iupac(allele_a, allele_b)
 
+        if allele_a == None:
+            continue
+
         # skip non-informative positions
         if allele_a == allele_b:
             continue
@@ -180,7 +183,6 @@ def resolve_iupac(code, fixed_base):
         elif b == fixed_base:
             return a
         else:
-            assert(False)
             return None
     else:
         return None
@@ -204,6 +206,9 @@ def load_msa_alleles(alleles_fn):
                 continue
             aa = resolve_iupac(ca, ra)
 
+            if aa == None:
+                continue
+
             v = Variant("contig", int(row['pos']), ra, aa)
             out[sample][v] = ca
     return out