Merge pull request #47 from martinghunt/nucmer_simplify_true

Nucmer simplify true
sanger-pathogens · Feb 19, 2016 · 204bd0d · 204bd0d
2 parents 3e5092c + f52611b
commit 204bd0d
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git 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/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()

diff --git 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=[