Commit d4f542ff authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 2.4.1

parent 292f4685

Dockerfile

+3 −1
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@@ -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

+1 −1
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2.4.0
 
2.4.1

python/setup.py

+1 −1
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@@ -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

+1 −1
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@@ -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

+6 −6
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@@ -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);