[med-svn] [Git][med-team/gubbins][upstream] New upstream version 2.4.1

[Steffen Möller]

Steffen Möller pushed to branch upstream at Debian Med / gubbins


Commits:
d4f542ff by Steffen Moeller at 2020-01-22T12:30:49+01:00
New upstream version 2.4.1
- - - - -


5 changed files:

- Dockerfile
- VERSION
- python/setup.py
- src/branch_sequences.c
- src/gubbins.c


Changes:

=====================================
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
=====================================
@@ -1 +1 @@
-2.4.0
+2.4.1


=====================================
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 at 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
=====================================
@@ -71,22 +71,22 @@ 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();
 
 	char * sample_names[number_of_samples];
-    get_sample_names_from_parse_phylip(sample_names);
+	get_sample_names_from_parse_phylip(sample_names);
 
-    char * reference_sequence_bases;
-    reference_sequence_bases = (char *) calloc((number_of_snps+1),sizeof(char));
+	char * reference_sequence_bases;
+	reference_sequence_bases = (char *) calloc((number_of_snps+1),sizeof(char));
 
 	get_sequence_for_sample_name(reference_sequence_bases, sample_names[0]);
 	int internal_nodes[number_of_samples];
@@ -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);
 	



View it on GitLab: https://salsa.debian.org/med-team/gubbins/commit/d4f542ff7e0e7148a9575cfb2b11de8916e5e4e4

-- 
View it on GitLab: https://salsa.debian.org/med-team/gubbins/commit/d4f542ff7e0e7148a9575cfb2b11de8916e5e4e4
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