From 0bb64156eb9ca136c90ffbc856a02e5fddf9decb Mon Sep 17 00:00:00 2001
From: Chris Rosenthal <crosenth@uw.edu>
Date: Wed, 16 Dec 2020 12:47:52 -0800
Subject: [PATCH] trim before simchar

---
 alnvu/util.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/alnvu/util.py b/alnvu/util.py
index dfa8d58..55bbf54 100755
--- a/alnvu/util.py
+++ b/alnvu/util.py
@@ -127,6 +127,14 @@ def reformat(seqs,
         else:
             seqlist.append(cons)
 
+    if seqrange:
+        start, stop = seqrange
+        start -= 1  # seqrange is 1-indexed
+    elif trim_to:
+        start, stop = get_extent(get_seq_from_list(trim_to, seqlist).seq)
+    else:
+        start, stop = 0, len(tabulated)
+
     if compare:
         # replace bases identical to reference; make a copy of the
         # sequence for comparison because the original sequences will
@@ -146,14 +154,6 @@ def reformat(seqs,
 
             seqlist[i] = Seq(name, seqstr)
 
-    if seqrange:
-        start, stop = seqrange
-        start -= 1  # seqrange is 1-indexed
-    elif trim_to:
-        start, stop = get_extent(get_seq_from_list(trim_to, seqlist).seq)
-    else:
-        start, stop = 0, len(tabulated)
-
     mask = []
     for i, counts in enumerate(tabulated):
         show = start <= i < stop