From d4e4deb0c1d1d4e0dab22e4f4a19fa7e7c680013 Mon Sep 17 00:00:00 2001
From: Lauren Coombe <lauren.e.coombe@gmail.com>
Date: Tue, 12 Sep 2023 12:57:17 -0700
Subject: [PATCH] Bugfix for cases where there are no output paths, and
 overlap=True (#100)

---
 bin/ntjoin_assemble.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/bin/ntjoin_assemble.py b/bin/ntjoin_assemble.py
index 922e91d..c5144ef 100755
--- a/bin/ntjoin_assemble.py
+++ b/bin/ntjoin_assemble.py
@@ -722,6 +722,8 @@ def adjust_for_trimming(self, fasta_filename, paths):
         mx_info = defaultdict(dict)  # path_index -> mx -> pos
         mxs = {}  # path_index -> [mx]
         cur_path_index = 0
+        if not paths:
+            return # If list of paths is empty
         cur_valid_segments = {f"{node.contig}_{node.start}_{node.end}"
                                   for node in paths[cur_path_index]}
         with btllib.Indexlr(fasta_filename, self.args.overlap_k, self.args.overlap_w,