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commit efc4d604aa03219b033e379af1d24710c10c57ee Merge: f85b24c 4c36268 Author: Sascha Steinbiss <sa...@debian.org> Date: Wed Oct 12 16:00:06 2016 +0000 Merge tag 'upstream/2.3.0+ds' Upstream version 2.3.0+ds Dockerfile | 19 + README.md | 38 +- ariba/assembly.py | 18 +- ariba/cluster.py | 24 +- ariba/clusters.py | 15 +- ariba/ext/minimap_ariba.cpp | 51 +- ariba/external_progs.py | 6 +- ariba/mash.py | 15 +- ariba/ref_genes_getter.py | 43 +- ariba/ref_preparer.py | 13 +- ariba/reference_data.py | 18 +- ariba/report.py | 188 ++++--- ariba/samtools_variants.py | 5 +- ariba/summary.py | 20 +- ariba/summary_cluster.py | 101 ++-- ariba/summary_cluster_variant.py | 67 ++- ariba/tasks/getref.py | 3 +- ariba/tasks/prepareref.py | 1 + ariba/tasks/run.py | 4 + ariba/test_run_data/metadata.tsv | 1 + ariba/test_run_data/reads_1.fq | 4 + ariba/test_run_data/reads_2.fq | 4 + .../test_run_data/ref_fasta_to_make_reads_from.fa | 5 + ariba/test_run_data/ref_seqs.fa | 5 + ariba/tests/assembly_test.py | 14 +- ariba/tests/cluster_test.py | 133 +++-- ariba/tests/clusters_test.py | 11 + .../data/cluster_test_full_run_delete_codon.fa | 3 + .../data/cluster_test_full_run_delete_codon.tsv | 1 + .../for_reads.fa | 20 + .../cluster_test_full_run_delete_codon/reads_1.fq | 588 ++++++++++++++++++++ .../cluster_test_full_run_delete_codon/reads_2.fq | 588 ++++++++++++++++++++ .../references.fa | 3 + .../data/cluster_test_full_run_insert_codon.fa | 3 + .../data/cluster_test_full_run_insert_codon.tsv | 1 + .../for_reads.fa | 20 + .../cluster_test_full_run_insert_codon/reads_1.fq | 592 +++++++++++++++++++++ .../cluster_test_full_run_insert_codon/reads_2.fq | 592 +++++++++++++++++++++ .../references.fa | 3 + .../data/cluster_test_full_run_multiple_vars.fa | 5 + .../data/cluster_test_full_run_multiple_vars.tsv | 2 + .../for_reads.fa | 20 + .../cluster_test_full_run_multiple_vars/reads_1.fq | 584 ++++++++++++++++++++ .../cluster_test_full_run_multiple_vars/reads_2.fq | 584 ++++++++++++++++++++ .../references.fa | 5 + .../data/cluster_test_full_run_ok_non_coding.fa | 2 +- ...cluster_test_full_run_ref_not_in_cluster.in.fa} | 2 +- ...cluster_test_full_run_ref_not_in_cluster.in.tsv | 6 + ...uster_test_full_run_ref_not_in_cluster.mash.fa} | 7 +- ...er_test_full_run_ref_not_in_cluster.mash.fa.msh | Bin 0 -> 2760 bytes .../reads_1.fq | 144 +++++ .../reads_2.fq | 144 +++++ .../references.fa} | 2 +- ...sters_minimap_reads_to_all_refs.out.clstr_count | 4 +- .../clusters_minimap_reads_to_all_refs.out.hist | 37 +- ariba/tests/data/clusters_test_dummy_db.fa.msh | Bin 0 -> 504 bytes ariba/tests/data/clusters_test_write_report.tsv | 2 +- ariba/tests/data/reference_data_init_ok.rename.tsv | 2 + .../tests/data/reference_data_load_rename_file.tsv | 2 + ariba/tests/data/report_filter_test_init_bad.tsv | 8 +- ariba/tests/data/report_filter_test_init_good.tsv | 10 +- .../data/report_filter_test_load_report_bad.tsv | 8 +- .../data/report_filter_test_load_report_good.tsv | 10 +- .../tests/data/report_filter_test_run.expected.tsv | 12 +- ariba/tests/data/report_filter_test_run.in.tsv | 18 +- .../tests/data/report_filter_test_write_report.tsv | 8 +- .../summary_gather_unfiltered_output_data.in.1.tsv | 12 +- .../summary_gather_unfiltered_output_data.in.2.tsv | 12 +- ...ample_test_column_names_tuples_and_het_snps.tsv | 16 +- .../summary_sample_test_column_summary_data.tsv | 16 +- .../data/summary_sample_test_load_file.in.tsv | 14 +- .../summary_sample_test_non_synon_variants.tsv | 12 +- .../tests/data/summary_sample_test_var_groups.tsv | 14 +- .../tests/data/summary_test_load_input_files.1.tsv | 6 +- .../tests/data/summary_test_load_input_files.2.tsv | 10 +- ariba/tests/data/summary_test_whole_run.in.1.tsv | 34 +- ariba/tests/data/summary_test_whole_run.in.2.tsv | 15 +- ariba/tests/data/summary_test_whole_run.out.csv | 6 +- ariba/tests/data/summary_to_matrix.1.tsv | 10 +- ariba/tests/data/summary_to_matrix.2.tsv | 12 +- ariba/tests/read_filter_test.py | 8 +- ariba/tests/ref_preparer_test.py | 1 + ariba/tests/reference_data_test.py | 17 + ariba/tests/report_filter_test.py | 58 +- ariba/tests/samtools_variants_test.py | 22 +- ariba/tests/summary_cluster_test.py | 248 +++++---- ariba/tests/summary_cluster_variant_test.py | 73 ++- ariba/tests/summary_test.py | 56 +- scripts/ariba | 61 ++- setup.py | 2 +- 90 files changed, 4981 insertions(+), 622 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit