From 16d8a7210f22d233cead250d863f37203ba7eca0 Mon Sep 17 00:00:00 2001
From: nds <nds@sanger.ac.uk>
Date: Thu, 12 Feb 2015 10:59:23 +0000
Subject: [PATCH] Added --nosimplify toggle to nucmer command

---
 pymummer/nucmer.py            | 5 +++++
 pymummer/tests/nucmer_test.py | 3 ++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/pymummer/nucmer.py b/pymummer/nucmer.py
index 67bd7fb..79c1b1b 100644
--- a/pymummer/nucmer.py
+++ b/pymummer/nucmer.py
@@ -19,6 +19,7 @@ def __init__(
       breaklen=None,
       coords_header=True,
       maxmatch=False,
+      simplify=True,
       show_snps=False,
       snps_header=True,
       verbose=False,
@@ -31,6 +32,7 @@ def __init__(
         self.breaklen = breaklen
         self.coords_header = coords_header
         self.maxmatch = maxmatch
+        self.simplify = simplify
         self.show_snps = show_snps
         self.snps_header = snps_header
         self.verbose = verbose
@@ -46,6 +48,9 @@ def _nucmer_command(self, ref, qry, outprefix):
 
         if self.maxmatch:
             command += ' --maxmatch'
+            
+        if not self.simplify:
+        	command += ' --nosimplify'
 
         return command + ' ' + ref + ' ' + qry
 
diff --git a/pymummer/tests/nucmer_test.py b/pymummer/tests/nucmer_test.py
index c962b3d..8ba072a 100644
--- a/pymummer/tests/nucmer_test.py
+++ b/pymummer/tests/nucmer_test.py
@@ -13,7 +13,8 @@ def test_nucmer_command(self):
         tests = [
             [nucmer.Runner('ref', 'qry', 'outfile'), 'nucmer -p pre ref qry'],
             [nucmer.Runner('ref', 'qry', 'outfile', breaklen=42), 'nucmer -p pre -b 42 ref qry'],
-            [nucmer.Runner('ref', 'qry', 'outfile', maxmatch=True), 'nucmer -p pre --maxmatch ref qry']
+            [nucmer.Runner('ref', 'qry', 'outfile', maxmatch=True), 'nucmer -p pre --maxmatch ref qry'],
+            [nucmer.Runner('ref', 'qry', 'outfile', simplify=False), 'nucmer -p pre --nosimplify ref qry']
         ]
 
         for l in tests: