Package: discosnp / 4.4.4-1

Metadata

Package Version Patches format
discosnp 4.4.4-1 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/create_coverage_h5_file/CMakeLists.txt | 6 4 + 2 - 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 !
6 files changed, 21 insertions(+), 11 deletions(-)

 use cmake input file of debian packaged gatb-core


no_install_to_wrong_dir.patch | (download)

CMakeLists.txt | 14 7 + 7 - 0 !
1 file changed, 7 insertions(+), 7 deletions(-)

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


path_to_readme_file_names.patch | (download)

run_discoSnp++.sh | 13 7 + 6 - 0 !
1 file changed, 7 insertions(+), 6 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 | 8 4 + 4 - 0 !
tools/kissreads2/src/Kissreads2.cpp | 2 1 + 1 - 0 !
2 files changed, 5 insertions(+), 5 deletions(-)

 fix spelling


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)

discoSnpRAD/post-processing_scripts/1SNP_per_cluster.py | 2 1 + 1 - 0 !
discoSnpRAD/post-processing_scripts/README.md | 12 6 + 6 - 0 !
discoSnpRAD/post-processing_scripts/add_cluster_info_to_mapped_vcf.py | 3 1 + 2 - 0 !
discoSnpRAD/post-processing_scripts/filter_by_cluster_size_and_rank.py | 3 1 + 2 - 0 !
discoSnpRAD/post-processing_scripts/filter_paralogs.py | 2 1 + 1 - 0 !
discoSnpRAD/post-processing_scripts/filter_vcf_by_indiv_cov_max_missing_and_maf.py | 2 1 + 1 - 0 !
discoSnpRAD/run_discoSnpRad.sh | 4 2 + 2 - 0 !
doc/discoSnp_user_guide.txt | 2 1 + 1 - 0 !
run_discoSnp++.sh | 2 1 + 1 - 0 !
run_discoSnp++_ML.sh | 4 2 + 2 - 0 !
run_discoSnp++_storagefile.sh | 2 1 + 1 - 0 !
scripts/ClassVCF_creator.py | 10 5 + 5 - 0 !
scripts/VCF_creator.py | 6 3 + 3 - 0 !
scripts/create_IGV_compatible_VCF.sh | 2 1 + 1 - 0 !
scripts/discoSnp++_to_csv.py | 6 3 + 3 - 0 !
scripts/filterOnBestDP_multiple_variant_at_same_pos.py | 10 5 + 5 - 0 !
scripts/filter_out_using_MAF.py | 6 3 + 3 - 0 !
scripts/filter_out_using_ratio_of_covered_files.py | 4 2 + 2 - 0 !
scripts/format_phased_variants_for_haplotyping.py | 4 2 + 2 - 0 !
scripts/from_phased_alleles_to_clusters.sh | 4 2 + 2 - 0 !
scripts/functionObjectVCF_creator.py | 10 5 + 5 - 0 !
scripts/k3000/K3000.py | 2 1 + 1 - 0 !
scripts/k3000/K3000_gfa_to_dat.py | 2 1 + 1 - 0 !
scripts/k3000/K3000_node_ids_to_node_sequences.py | 2 1 + 1 - 0 !
scripts/k3000/run.sh | 2 1 + 1 - 0 !
scripts/keep_extensions_disco_file.py | 2 1 + 1 - 0 !
scripts/redundancy_removal_discosnp.py | 2 1 + 1 - 0 !
scripts/remove_extensions_disco_file.py | 2 1 + 1 - 0 !
scripts/remove_non_biallelic.py | 2 1 + 1 - 0 !
scripts/remove_non_covered_genotypes.py | 4 2 + 2 - 0 !
scripts/run_VCF_creator.sh | 16 8 + 8 - 0 !
scripts/simulations/multiple_samples_simulator.sh | 6 3 + 3 - 0 !
scripts/simulations/random_mut_fasta.py | 2 1 + 1 - 0 !
scripts/simulations/targeted_mut_fasta_corrected.py | 2 1 + 1 - 0 !
scripts/validation_scripts/compare_vcf_disco_pos_allele_only.py | 2 1 + 1 - 0 !
scripts/validation_scripts/eval_disco_one_snp_per_locus.py | 2 1 + 1 - 0 !
36 files changed, 74 insertions(+), 76 deletions(-)

 result of 2to3


shell_syntax.patch | (download)

discoSnpRAD/clustering_scripts/discoRAD_clustering.sh | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix posix shell syntax