This is an automated email from the git hooks/post-receive script.

satta pushed a change to branch upstream
in repository ariba.

      from  d73cf5b   Imported Upstream version 2.2.5+ds
       new  4c36268   New upstream version 2.3.0+ds

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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 +
 ....tsv => cluster_test_full_run_delete_codon.tsv} |   0
 .../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 +
 ....tsv => cluster_test_full_run_insert_codon.tsv} |   0
 .../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 +
 ...e.fa => cluster_test_full_run_multiple_vars.fa} |   0
 ...tsv => cluster_test_full_run_multiple_vars.tsv} |   1 +
 .../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                                  |   0
 .../data/cluster_test_full_run_ok_non_coding.fa    |   2 +-
 ...cluster_test_full_run_ref_not_in_cluster.in.fa} |   0
 ...luster_test_full_run_ref_not_in_cluster.in.tsv} |   0
 ...uster_test_full_run_ref_not_in_cluster.mash.fa} |   5 +-
 ...er_test_full_run_ref_not_in_cluster.mash.fa.msh | Bin 0 -> 2760 bytes
 .../reads_1.fq                                     |   0
 .../reads_2.fq                                     |   0
 .../references.fa                                  |   0
 ...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, 4671 insertions(+), 619 deletions(-)
 create mode 100644 Dockerfile
 create mode 100644 ariba/tests/data/cluster_test_full_run_delete_codon.fa
 copy ariba/tests/data/{cluster_test_full_run_partial_asmbly.tsv => 
cluster_test_full_run_delete_codon.tsv} (100%)
 create mode 100644 
ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa
 create mode 100644 
ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq
 create mode 100644 
ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq
 create mode 100644 
ariba/tests/data/cluster_test_full_run_delete_codon/references.fa
 create mode 100644 ariba/tests/data/cluster_test_full_run_insert_codon.fa
 copy ariba/tests/data/{cluster_test_full_run_partial_asmbly.tsv => 
cluster_test_full_run_insert_codon.tsv} (100%)
 create mode 100644 
ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa
 create mode 100644 
ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq
 create mode 100644 
ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq
 create mode 100644 
ariba/tests/data/cluster_test_full_run_insert_codon/references.fa
 copy ariba/tests/data/{cluster_test_full_run_ok_presence_absence.fa => 
cluster_test_full_run_multiple_vars.fa} (100%)
 copy ariba/tests/data/{cluster_test_full_run_partial_asmbly.tsv => 
cluster_test_full_run_multiple_vars.tsv} (50%)
 create mode 100644 
ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa
 create mode 100644 
ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq
 create mode 100644 
ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq
 copy ariba/tests/data/{cluster_test_full_run_ok_presence_absence => 
cluster_test_full_run_multiple_vars}/references.fa (100%)
 copy ariba/tests/data/{cluster_test_full_run_ok_non_coding/references.fa => 
cluster_test_full_run_ref_not_in_cluster.in.fa} (100%)
 copy ariba/tests/data/{cluster_test_full_run_ok_non_coding.metadata.tsv => 
cluster_test_full_run_ref_not_in_cluster.in.tsv} (100%)
 copy ariba/tests/data/{cluster_test_full_run_ok_non_coding/references.fa => 
cluster_test_full_run_ref_not_in_cluster.mash.fa} (65%)
 create mode 100644 
ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.mash.fa.msh
 copy ariba/tests/data/{cluster_test_full_run_ok_non_coding => 
cluster_test_full_run_ref_not_in_cluster}/reads_1.fq (100%)
 copy ariba/tests/data/{cluster_test_full_run_ok_non_coding => 
cluster_test_full_run_ref_not_in_cluster}/reads_2.fq (100%)
 copy ariba/tests/data/{cluster_test_full_run_ok_non_coding => 
cluster_test_full_run_ref_not_in_cluster}/references.fa (100%)
 create mode 100644 ariba/tests/data/clusters_test_dummy_db.fa.msh
 create mode 100644 ariba/tests/data/reference_data_init_ok.rename.tsv
 create mode 100644 ariba/tests/data/reference_data_load_rename_file.tsv

-- 
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

Reply via email to