[med-svn] [Git][med-team/gubbins][master] 7 commits: New upstream version 2.4.1
Steffen Möller
gitlab at salsa.debian.org
Wed Jan 22 11:41:44 GMT 2020
Steffen Möller pushed to branch master at Debian Med / gubbins
Commits:
d4f542ff by Steffen Moeller at 2020-01-22T12:30:49+01:00
New upstream version 2.4.1
- - - - -
784e614c by Steffen Moeller at 2020-01-22T12:30:49+01:00
routine-update: New upstream version
- - - - -
61941701 by Steffen Moeller at 2020-01-22T12:30:51+01:00
Update upstream source from tag 'upstream/2.4.1'
Update to upstream version '2.4.1'
with Debian dir c6374cc91ece41771a972bd5f058c1bcbfeb7ab9
- - - - -
f46c9565 by Steffen Moeller at 2020-01-22T12:30:55+01:00
R-U: Trailing whitespace in debian/changelog
- - - - -
14be1edf by Steffen Moeller at 2020-01-22T12:30:58+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.
- - - - -
12ca8ba5 by Steffen Moeller at 2020-01-22T12:31:36+01:00
routine-update: Ready to upload to unstable
- - - - -
4b1d3dda by Steffen Moeller at 2020-01-22T12:41:10+01:00
Preparing for new upstream version
- - - - -
8 changed files:
- Dockerfile
- VERSION
- debian/changelog
- debian/control
- debian/upstream/metadata
- 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
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+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 at debian.org> Wed, 22 Jan 2020 12:30:58 +0100
+
gubbins (2.4.0-2) unstable; urgency=medium
* Team upload.
@@ -6,7 +17,7 @@ gubbins (2.4.0-2) unstable; urgency=medium
hard dependency (suggested by Sascha)
-- Steffen Moeller <moeller at debian.org> Thu, 09 Jan 2020 02:31:16 +0100
-
+
gubbins (2.4.0-1) 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 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/compare/c62bd388f4e5ea7a28ff28bbb1cc8743bfdf1fbf...4b1d3dda422b9f633e35247039e70a9e41b99d46
--
View it on GitLab: https://salsa.debian.org/med-team/gubbins/compare/c62bd388f4e5ea7a28ff28bbb1cc8743bfdf1fbf...4b1d3dda422b9f633e35247039e70a9e41b99d46
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