Package: discosnp / 2.3.0-2

Metadata

Package Version Patches format
discosnp 2.3.0-2 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
use_debian_packaged_gatb core.patch | (download)

CMakeLists.txt | 4 2 + 2 - 0 !
tools/QHC/CMakeLists.txt | 4 3 + 1 - 0 !
tools/kissnp2/CMakeLists.txt | 6 4 + 2 - 0 !
tools/kissreads2/CMakeLists.txt | 6 4 + 2 - 0 !
tools/read_file_names/CMakeLists.txt | 6 4 + 2 - 0 !
5 files changed, 17 insertions(+), 9 deletions(-)

 use cmake input file of debian packaged gatb-core


no_install_to_wrong_dir.patch | (download)

CMakeLists.txt | 12 6 + 6 - 0 !
1 file changed, 6 insertions(+), 6 deletions(-)

 failed to fix these install dirs, deactivate completely and use dh_install


path_to_readme_file_names.patch | (download)

run_discoSnp++.sh | 10 5 + 5 - 0 !
run_discoSnpRad.sh | 10 5 + 5 - 0 !
scripts_RAD/discoRAD_finalization.sh | 2 1 + 1 - 0 !
3 files changed, 11 insertions(+), 11 deletions(-)

 there is no point in delivering read_file_names in /usr/bin
 It is available in /usr/share/discosnp/bin/read_file_names - this patch adapts
 the scripts using it.
 .
 Some other issues of these scripts are fixed as well.


spelling.patch | (download)

tools/kissnp2/src/Kissnp2.cpp | 6 3 + 3 - 0 !
tools/kissreads2/src/Kissreads2.cpp | 2 1 + 1 - 0 !
2 files changed, 4 insertions(+), 4 deletions(-)

 fix spelling


fix_scripts.patch | (download)

scripts_RAD/discoRAD_finalization.sh | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 add missing shebang line


adapt_test_scripts.patch | (download)

test/large_test/local_large_test.sh | 2 1 + 1 - 0 !
test/simple_test.sh | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 adapt test scripts to debian path


2to3.patch | (download)

scripts/ClassVCF_creator.py | 16 8 + 8 - 0 !
scripts/VCF_creator.py | 4 2 + 2 - 0 !
scripts/discoSnp++_to_csv.py | 2 1 + 1 - 0 !
scripts/filterOnBestDP_multiple_variant_at_same_pos.py | 6 3 + 3 - 0 !
scripts/filter_out_using_MAF.py | 6 3 + 3 - 0 !
scripts/filter_out_using_ratio_of_covered_files.py | 2 1 + 1 - 0 !
scripts/functionObjectVCF_creator.py | 8 4 + 4 - 0 !
scripts/one2zeroBased_vcf.py | 2 1 + 1 - 0 !
scripts_RAD/1SNP_by_cluster.py | 4 2 + 2 - 0 !
scripts_RAD/filter_paralogs.py | 2 1 + 1 - 0 !
scripts_RAD/filter_vcf_by_indiv_cov_and_max_missing.py | 26 13 + 13 - 0 !
11 files changed, 39 insertions(+), 39 deletions(-)

 result of 2to3