From 9b5416d6a3870c5a51bbd02f3ff4e04615c3ae3d Mon Sep 17 00:00:00 2001
From: Martin Hunt <mh12@sanger.ac.uk>
Date: Fri, 19 Feb 2016 09:30:36 +0000
Subject: [PATCH 1/2] Do not use nosimplify

---
 circlator/merge.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/circlator/merge.py b/circlator/merge.py
index c340024..f9bdb1b 100644
--- a/circlator/merge.py
+++ b/circlator/merge.py
@@ -67,7 +67,7 @@ def _run_nucmer(self, ref, qry, outfile):
             diagdiff=self.nucmer_diagdiff,
             maxmatch=True,
             breaklen=self.nucmer_breaklen,
-            simplify=False,
+            simplify=True,
             verbose=self.verbose
         )
         n.run()

From f52611b721127b832adbc7897b9bcb7f2c9c2584 Mon Sep 17 00:00:00 2001
From: Martin Hunt <mh12@sanger.ac.uk>
Date: Fri, 19 Feb 2016 09:32:44 +0000
Subject: [PATCH 2/2] version bumps

---
 circlator/common.py | 2 +-
 setup.py            | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/circlator/common.py b/circlator/common.py
index 67a1f92..03c0036 100644
--- a/circlator/common.py
+++ b/circlator/common.py
@@ -4,7 +4,7 @@
 
 class Error (Exception): pass
 
-version = '1.1.3'
+version = '1.1.4'
 
 def syscall(cmd, allow_fail=False, verbose=False):
     if verbose:
diff --git a/setup.py b/setup.py
index bde89dd..4dd5531 100644
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@
 
 setup(
     name='circlator',
-    version='1.1.3',
+    version='1.1.4',
     description='circlator: a tool to circularise genome assemblies',
     packages = find_packages(),
     package_data={'circlator': ['data/*']},
@@ -22,7 +22,7 @@
         'pyfastaq >= 3.10.0',
         'pysam >= 0.8.1',
         'pymummer>=0.6.1',
-        'bio_assembly_refinement>=0.4.0',
+        'bio_assembly_refinement>=0.5.0',
     ],
     license='GPLv3',
     classifiers=[