Merge pull request #163 from andrewjpage/master

midpoint rerooting by default
nickjcroucher · Feb 29, 2016 · 49db81e · 49db81e
2 parents c5c8dec + bcc3b87
commit 49db81e
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Showing 4 changed files with 4 additions and 3 deletions.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-1.4.5
+1.4.6
diff --git a/python/gubbins/common.py b/python/gubbins/common.py
@@ -515,6 +515,7 @@ def reroot_tree_at_midpoint(tree_name):
     GubbinsCommon.split_all_non_bi_nodes(tree.seed_node)
 
     tree.update_bipartitions()
+    tree.reroot_at_midpoint()
     tree.deroot()
     tree.update_bipartitions()
     output_tree_string = tree.as_string(

diff --git a/python/gubbins/tests/data/non_bi_tree.tre.expected b/python/gubbins/tests/data/non_bi_tree.tre.expected
@@ -1 +1 @@
-((sequence_6:0.030557,(sequence_5:0.24819,sequence_8:1.1e-05)N8:9e-06)N7:1e-05,sequence_1:2e-06,((sequence_10:2e-05,(sequence_47:0.300658,(sequence_37:0.300658,(sequence_27:0.300658,(sequence_7:0.300658,sequence_17:0.300658):0):0):0):0)N3:1.1e-05,(sequence_9:0.000196,(sequence_3:8.38574,(sequence_2:0.0002,sequence_4:0.306587)N6:0.00017)N5:1.23278)N4:0.193335)N2:1e-05)N1:0.0;
+(sequence_3:8.38574,(sequence_2:0.0002,sequence_4:0.306587)N6:0.00017,(sequence_9:0.000196,((sequence_10:2e-05,(sequence_47:0.300658,(sequence_37:0.300658,(sequence_27:0.300658,(sequence_7:0.300658,sequence_17:0.300658):0):0):0):0)N3:1.1e-05,((sequence_6:0.030557,(sequence_5:0.24819,sequence_8:1.1e-05)N8:9e-06)N7:1e-05,sequence_1:2e-06)N1:1e-05)N2:0.193335)N4:1.23278):0.0;
diff --git a/...on/gubbins/tests/data/robinson_foulds_distance_tree1.tre.reroot_tree_at_midpoint_expected b/...on/gubbins/tests/data/robinson_foulds_distance_tree1.tre.reroot_tree_at_midpoint_expected
@@ -1 +1 @@
-((sequence_6:0.030557,(sequence_5:0.24819,sequence_8:1.1e-05)N8:9e-06)N7:1e-05,sequence_1:2e-06,((sequence_7:0.300658,sequence_10:2e-05)N3:1.1e-05,(sequence_9:0.000196,(sequence_3:8.38574,(sequence_2:0.0002,sequence_4:0.306587)N6:0.00017)N5:1.23278)N4:0.193335)N2:1e-05)N1:0.0;
+(sequence_3:8.38574,(sequence_2:0.0002,sequence_4:0.306587)N6:0.00017,(sequence_9:0.000196,((sequence_7:0.300658,sequence_10:2e-05)N3:1.1e-05,((sequence_6:0.030557,(sequence_5:0.24819,sequence_8:1.1e-05)N8:9e-06)N7:1e-05,sequence_1:2e-06)N1:1e-05)N2:0.193335)N4:1.23278):0.0;
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		((sequence_6:0.030557,(sequence_5:0.24819,sequence_8:1.1e-05)N8:9e-06)N7:1e-05,sequence_1:2e-06,((sequence_10:2e-05,(sequence_47:0.300658,(sequence_37:0.300658,(sequence_27:0.300658,(sequence_7:0.300658,sequence_17:0.300658):0):0):0):0)N3:1.1e-05,(sequence_9:0.000196,(sequence_3:8.38574,(sequence_2:0.0002,sequence_4:0.306587)N6:0.00017)N5:1.23278)N4:0.193335)N2:1e-05)N1:0.0;
		(sequence_3:8.38574,(sequence_2:0.0002,sequence_4:0.306587)N6:0.00017,(sequence_9:0.000196,((sequence_10:2e-05,(sequence_47:0.300658,(sequence_37:0.300658,(sequence_27:0.300658,(sequence_7:0.300658,sequence_17:0.300658):0):0):0):0)N3:1.1e-05,((sequence_6:0.030557,(sequence_5:0.24819,sequence_8:1.1e-05)N8:9e-06)N7:1e-05,sequence_1:2e-06)N1:1e-05)N2:0.193335)N4:1.23278):0.0;