From a1bb2b67684f04f981e345c9f783afc72d3f81cf Mon Sep 17 00:00:00 2001 From: andrewjpage Date: Thu, 16 Apr 2015 16:08:24 +0100 Subject: [PATCH 1/2] max window size --- python/gubbins/common.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/python/gubbins/common.py b/python/gubbins/common.py index 65a7912a..df3b3343 100644 --- a/python/gubbins/common.py +++ b/python/gubbins/common.py @@ -248,27 +248,27 @@ def parse_and_run(self): current_tree_name = GubbinsCommon.fasttree_current_tree_name(base_filename, i) tree_building_command = GubbinsCommon.fasttree_tree_building_command(i, self.args.starting_tree,current_tree_name,base_filename,previous_tree_name,FASTTREE_EXEC, FASTTREE_PARAMS,base_filename ) fastml_command = GubbinsCommon.fasttree_fastml_command(FASTML_EXEC, starting_base_filename+".snp_sites.aln", base_filename, i) - gubbins_command = GubbinsCommon.fasttree_gubbins_command(base_filename,starting_base_filename+".gaps", i,self.args.alignment_filename,GUBBINS_EXEC,self.args.min_snps,self.args.alignment_filename, self.args.min_window_size,self.max_window_size) + gubbins_command = GubbinsCommon.fasttree_gubbins_command(base_filename,starting_base_filename+".gaps", i,self.args.alignment_filename,GUBBINS_EXEC,self.args.min_snps,self.args.alignment_filename, self.args.min_window_size,self.args.max_window_size) elif i == 2: previous_tree_name = current_tree_name current_tree_name = GubbinsCommon.raxml_current_tree_name(base_filename_without_ext,current_time, i) tree_building_command = GubbinsCommon.raxml_tree_building_command(i,base_filename_without_ext,base_filename,current_time,RAXML_EXEC,previous_tree_name, self.args.verbose) fastml_command = GubbinsCommon.raxml_fastml_command(FASTML_EXEC, starting_base_filename+".snp_sites.aln", base_filename_without_ext,current_time, i) - gubbins_command = GubbinsCommon.raxml_gubbins_command(base_filename_without_ext,starting_base_filename+".gaps",current_time, i,self.args.alignment_filename,GUBBINS_EXEC,self.args.min_snps,self.args.alignment_filename, self.args.min_window_size,self.max_window_size) + gubbins_command = GubbinsCommon.raxml_gubbins_command(base_filename_without_ext,starting_base_filename+".gaps",current_time, i,self.args.alignment_filename,GUBBINS_EXEC,self.args.min_snps,self.args.alignment_filename, self.args.min_window_size,self.args.max_window_size) else: previous_tree_name = GubbinsCommon.raxml_previous_tree_name(base_filename_without_ext,base_filename, current_time,i) current_tree_name = GubbinsCommon.raxml_current_tree_name(base_filename_without_ext,current_time, i) tree_building_command = GubbinsCommon.raxml_tree_building_command(i,base_filename_without_ext,base_filename,current_time,RAXML_EXEC,previous_tree_name, self.args.verbose) fastml_command = GubbinsCommon.raxml_fastml_command(FASTML_EXEC, starting_base_filename+".snp_sites.aln", base_filename_without_ext,current_time, i) - gubbins_command = GubbinsCommon.raxml_gubbins_command(base_filename_without_ext,starting_base_filename+".gaps",current_time, i,self.args.alignment_filename,GUBBINS_EXEC,self.args.min_snps,self.args.alignment_filename, self.args.min_window_size,self.max_window_size) + gubbins_command = GubbinsCommon.raxml_gubbins_command(base_filename_without_ext,starting_base_filename+".gaps",current_time, i,self.args.alignment_filename,GUBBINS_EXEC,self.args.min_snps,self.args.alignment_filename, self.args.min_window_size,self.args.max_window_size) elif self.args.tree_builder == "raxml": previous_tree_name = GubbinsCommon.raxml_previous_tree_name(base_filename_without_ext,base_filename, current_time,i) current_tree_name = GubbinsCommon.raxml_current_tree_name(base_filename_without_ext,current_time, i) tree_building_command = GubbinsCommon.raxml_tree_building_command(i,base_filename_without_ext,base_filename,current_time,RAXML_EXEC,previous_tree_name, self.args.verbose) fastml_command = GubbinsCommon.raxml_fastml_command(FASTML_EXEC, starting_base_filename+".snp_sites.aln", base_filename_without_ext,current_time, i) - gubbins_command = GubbinsCommon.raxml_gubbins_command(base_filename_without_ext,starting_base_filename+".gaps",current_time, i,self.args.alignment_filename,GUBBINS_EXEC,self.args.min_snps,self.args.alignment_filename, self.args.min_window_size,self.max_window_size) + gubbins_command = GubbinsCommon.raxml_gubbins_command(base_filename_without_ext,starting_base_filename+".gaps",current_time, i,self.args.alignment_filename,GUBBINS_EXEC,self.args.min_snps,self.args.alignment_filename, self.args.min_window_size,self.args.max_window_size) elif self.args.tree_builder == "fasttree": previous_tree_name = GubbinsCommon.fasttree_previous_tree_name(base_filename, i) @@ -278,7 +278,7 @@ def parse_and_run(self): tree_building_command = GubbinsCommon.fasttree_tree_building_command(i, self.args.starting_tree,current_tree_name,previous_tree_name,previous_tree_name,FASTTREE_EXEC,FASTTREE_PARAMS,base_filename ) fastml_command = GubbinsCommon.fasttree_fastml_command(FASTML_EXEC, starting_base_filename+".snp_sites.aln", base_filename, i) - gubbins_command = GubbinsCommon.fasttree_gubbins_command(base_filename,starting_base_filename+".gaps", i,self.args.alignment_filename,GUBBINS_EXEC,self.args.min_snps,self.args.alignment_filename, self.args.min_window_size,self.max_window_size) + gubbins_command = GubbinsCommon.fasttree_gubbins_command(base_filename,starting_base_filename+".gaps", i,self.args.alignment_filename,GUBBINS_EXEC,self.args.min_snps,self.args.alignment_filename, self.args.min_window_size,self.args.max_window_size) if self.args.verbose > 0: print tree_building_command From 374aa52a09519df01f1d2d987f6e49725e15cf43 Mon Sep 17 00:00:00 2001 From: andrewjpage Date: Thu, 16 Apr 2015 16:09:40 +0100 Subject: [PATCH 2/2] max window size bug --- VERSION | 2 +- debian/changelog | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 1892b926..31e5c843 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.3.2 +1.3.3 diff --git a/debian/changelog b/debian/changelog index 64f97b63..0de6f984 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +gubbins (1.3.3~trusty1) trusty; urgency=low + + * Max window size arg bug + + -- Andrew Page Thu, 16 Apr 2015 16:09:00 +0000 + gubbins (1.3.2~trusty1) trusty; urgency=low * pass in self to window size check