This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository gubbins.
commit e5b0fa02c34a1f7add9014a93085488662b63c52 Author: Andreas Tille <[email protected]> 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++) { -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gubbins.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
