Dockerfile

@@ -20,7 +20,9 @@ RUN apt-get update && apt-get install --no-install-recommends -y \
     python3 \
     python3-dev \
     python3-setuptools \
-    python3-pip
+    python3-pip \
+    gdb \
+    valgrind
 
 # Install python dependencies 
 RUN pip3 install --trusted-host pypi.python.org --upgrade pip

VERSION

-2.4.0
+2.4.1

debian/changelog

+gubbins (2.4.1-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Standards-Version: 4.5.0
+  * Remove trailing whitespace in debian/changelog (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.
+  * Specified raxml version from Dockerfile - test complained on i386
+
+ -- Steffen Moeller <moeller@debian.org>  Wed, 22 Jan 2020 12:30:58 +0100
+
 gubbins (2.4.0-2) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 12),
                dh-python,
                fasttree,
                iqtree,
-               raxml,
+               raxml (>= 8.2.12),
                python3-setuptools,
                zlib1g-dev,
                check,
@@ -18,7 +18,7 @@ Build-Depends: debhelper-compat (= 12),
                python3-reportlab,
                python3-nose,
                pkg-config
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/gubbins
 Vcs-Git: https://salsa.debian.org/med-team/gubbins.git
 Homepage: https://sanger-pathogens.github.io/gubbins/

debian/upstream/metadata

@@ -24,5 +24,7 @@ Registry:
   Entry: NA
 - Name: conda:bioconda
   Entry: gubbins
-Repository: https://github.com/sanger-pathogens/gubbins
+Repository: https://github.com/sanger-pathogens/gubbins.git
 Repository-Browse: https://github.com/sanger-pathogens/gubbins
+Bug-Database: https://github.com/sanger-pathogens/gubbins/issues
+Bug-Submit: https://github.com/sanger-pathogens/gubbins/issues/new

python/setup.py

@@ -4,7 +4,7 @@ import setuptools
 
 setuptools.setup(
     name='gubbins',
-    version='2.4.0',
+    version='2.4.1',
     description='Frontend to the Gubbins BioInformatics tool',
     author='Andrew J. Page',
     author_email='gubbins-help@sanger.ac.uk',

src/branch_sequences.c

@@ -574,7 +574,7 @@ int get_blocks(int ** block_coordinates, int genome_size,int * snp_site_coords,i
 	int x =0;
 	for(x=0; x< number_of_snps; x++)
 	{
-		if(original_sequence[x]  == 'N' || original_sequence[x]  == '-' )
+		if((original_sequence[x] == 'N' || original_sequence[x] == '-' ) && snp_locations[x] != 0)
 		{
 		  gaps_in_original_genome_space[snp_locations[x]-1] = 1;
 	  }

src/gubbins.c

@@ -71,14 +71,14 @@ void extract_sequences(char vcf_filename[], char tree_filename[],char multi_fast
 	
 	number_of_snps  = number_of_snps_in_phylip();
 	
-	int* snp_locations = calloc(number_of_snps, sizeof(int));
+	int* snp_locations = calloc((number_of_snps+1), sizeof(int));
 	
 	get_integers_from_column_in_vcf(vcf_file_pointer, snp_locations, number_of_snps, column_number_for_column_name(column_names, "POS", number_of_columns));
 
 	root_node = build_newick_tree(tree_filename, vcf_file_pointer,snp_locations, number_of_snps, column_names, number_of_columns, length_of_original_genome,min_snps,window_min, window_max);
 	fclose(vcf_file_pointer);
 
-	int* filtered_snp_locations = calloc(number_of_snps, sizeof(int));
+	int* filtered_snp_locations = calloc((number_of_snps+1), sizeof(int));
 	int number_of_filtered_snps;
 	int number_of_samples = number_of_samples_from_parse_phylip();
 
@@ -97,7 +97,7 @@ void extract_sequences(char vcf_filename[], char tree_filename[],char multi_fast
 	}
 
 	number_of_filtered_snps = refilter_existing_snps(reference_sequence_bases, number_of_snps, snp_locations, filtered_snp_locations,internal_nodes);
-	char ** filtered_bases_for_snps = (char **) calloc(number_of_filtered_snps, sizeof(char *));
+	char ** filtered_bases_for_snps = (char **) calloc((number_of_filtered_snps+1), sizeof(char *));
 
 	filter_sequence_bases_and_rotate(reference_sequence_bases, filtered_bases_for_snps, number_of_filtered_snps);