From 6ee1f8e945ecdbc5a400e755bce9410a2eb49d09 Mon Sep 17 00:00:00 2001
From: Adam Ewing <adam.ewing@gmail.com>
Date: Thu, 8 Dec 2016 15:35:20 +1000
Subject: [PATCH] handle case where no contigs are generated

---
 bin/addsv.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bin/addsv.py b/bin/addsv.py
index 4e952a0..ab11059 100644
--- a/bin/addsv.py
+++ b/bin/addsv.py
@@ -406,6 +406,7 @@ def makemut(args, bedline, alignopts):
 
         if len(contigs) == 0:
             sys.stderr.write("WARN\t" + now() + "\t" + mutid + "\tgenerated no contigs, skipping site.\n")
+            return None, None
 
         trn_contigs = None
         if is_transloc: