| 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
|
