[med-svn] [python-pymummer] 02/04: New upstream version 0.10.3

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository python-pymummer.

commit d9ba9a5481189470a204868d83c25892fd115a28
Author: Sascha Steinbiss <satta at debian.org>
Date:   Mon Jan 29 15:47:07 2018 +0100

    New upstream version 0.10.3
---
 LICENSE            |  4 ++++
 pymummer/nucmer.py | 11 ++++++++++-
 setup.py           |  2 +-
 3 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/LICENSE b/LICENSE
index 6b156fe..4faa525 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,3 +1,7 @@
+Copyright (c) 2015 - 2017 by Genome Research Ltd.
+
+This is free software, licensed under:
+
 GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 
diff --git a/pymummer/nucmer.py b/pymummer/nucmer.py
index 1406189..5c7d0b9 100644
--- a/pymummer/nucmer.py
+++ b/pymummer/nucmer.py
@@ -19,6 +19,8 @@ class Runner:
       breaklen=None,
       coords_header=True,
       diagdiff=None,
+      diagfactor=None,
+      maxgap=None,
       maxmatch=False,
       mincluster=None,
       simplify=True,
@@ -35,7 +37,9 @@ class Runner:
         self.min_length = min_length
         self.breaklen = breaklen
         self.diagdiff = diagdiff
+        self.diagfactor = diagfactor
         self.coords_header = coords_header
+        self.maxgap = maxgap
         self.maxmatch = maxmatch
         self.mincluster = mincluster
         self.simplify = simplify
@@ -61,6 +65,12 @@ class Runner:
         if self.diagdiff is not None and not self.use_promer:
             command += ' -D ' + str(self.diagdiff)
 
+        if self.diagfactor:
+            command += ' -d ' + str(self.diagfactor)
+
+        if self.maxgap:
+            command += ' -g ' + str(self.maxgap)
+
         if self.maxmatch:
             command += ' --maxmatch'
 
@@ -73,7 +83,6 @@ class Runner:
         return command + ' ' + ref + ' ' + qry
 
 
-
     def _delta_filter_command(self, infile, outfile):
         '''Construct delta-filter command'''
         command = 'delta-filter'
diff --git a/setup.py b/setup.py
index 5e91cd0..cf3ac30 100644
--- a/setup.py
+++ b/setup.py
@@ -26,7 +26,7 @@ if not found_all_progs:
 
 setup(
     name='pymummer',
-    version='0.10.2',
+    version='0.10.3',
     description='Wrapper for MUMmer',
     packages = find_packages(),
     author='Martin Hunt, Nishadi De Silva',

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