[med-svn] [gubbins] 01/04: Imported Upstream version 1.4.7

[Andreas Tille]

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tille pushed a commit to branch master
in repository gubbins.

commit e5b0fa02c34a1f7add9014a93085488662b63c52
Author: Andreas Tille <tille at debian.org>
Date:   Sat Mar 19 22:09:15 2016 +0100

    Imported Upstream version 1.4.7
---
 VERSION                                                                 | 2 +-
 python/gubbins/common.py                                                | 1 +
 python/gubbins/tests/data/non_bi_tree.tre.expected                      | 2 +-
 .../robinson_foulds_distance_tree1.tre.reroot_tree_at_midpoint_expected | 2 +-
 src/snp_sites.c                                                         | 2 +-
 5 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/VERSION b/VERSION
index e516bb9..be05bba 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.4.5
+1.4.7
diff --git a/python/gubbins/common.py b/python/gubbins/common.py
index 48f8c06..0cc8c2c 100644
--- a/python/gubbins/common.py
+++ b/python/gubbins/common.py
@@ -515,6 +515,7 @@ class GubbinsCommon():
     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
index 2fb3948..d5e8fad 100644
--- 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/python/gubbins/tests/data/robinson_foulds_distance_tree1.tre.reroot_tree_at_midpoint_expected b/python/gubbins/tests/data/robinson_foulds_distance_tree1.tre.reroot_tree_at_midpoint_expected
index ce9ff25..fd5880a 100644
--- a/python/gubbins/tests/data/robinson_foulds_distance_tree1.tre.reroot_tree_at_midpoint_expected
+++ b/python/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;
diff --git a/src/snp_sites.c b/src/snp_sites.c
index 45b6312..68a2275 100644
--- a/src/snp_sites.c
+++ b/src/snp_sites.c
@@ -85,7 +85,7 @@ int generate_snp_sites(char filename[],  int exclude_gaps, char suffix[])
 		internal_nodes[a] = 0;
 	}
 	
-	char* bases_for_snps[number_of_snps];
+	char** bases_for_snps = malloc(number_of_snps * sizeof(char *));
 	
 	for(i = 0; i < number_of_snps; i++)
 	{

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