Added --nosimplify toggle to nucmer command

sanger-pathogens · Feb 12, 2015 · 16d8a72 · 16d8a72
1 parent 12748de
commit 16d8a72
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Showing 2 changed files with 7 additions and 1 deletion.
diff --git 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
@@ -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: