From 228776264da7ad730f96ca78b9d1af39a652d82d Mon Sep 17 00:00:00 2001
From: Chris Rosenthal <crosenth@uw.edu>
Date: Thu, 3 Oct 2024 12:55:54 -0700
Subject: [PATCH] Adding default value "merged" for --direction

---
 bin/write_seqs.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/bin/write_seqs.py b/bin/write_seqs.py
index e934d50..f711951 100755
--- a/bin/write_seqs.py
+++ b/bin/write_seqs.py
@@ -64,7 +64,8 @@ def main(arguments):
         formatter_class=argparse.RawDescriptionHelpFormatter)
     parser.add_argument(
         'seqtabs', nargs='*',
-        help='One or more headerless CSV files with columns specimen,count,seq')
+        help='One or more headerless CSV files '
+             'with columns specimen,count,seq')
     parser.add_argument(
         '--seqtablist', type=argparse.FileType('r'),
         help='A file listing one seqtab file per line')
@@ -91,6 +92,7 @@ def main(arguments):
     parser.add_argument(
         '--direction',
         choices=['merged', 'R1', 'R2'],
+        default='merged',
         help='label to add to all sequence names')
     parser.add_argument(
         '-j', '--num-processes', type=int, default=1,