[med-svn] [ariba] branch upstream updated (eebec95 -> a3fddfd)

[Sascha Steinbiss]

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

satta pushed a change to branch upstream
in repository ariba.

      from  eebec95   New upstream version 2.7.2+ds
       new  83edd46   New upstream version 2.9.0+ds
       new  b69312e   New upstream version 2.9.0+ds
       new  a3fddfd   New upstream version 2.9.2+ds

The 3 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:
 README.md                                          |  32 +-
 ariba/__init__.py                                  |   1 +
 ariba/assembly.py                                  |   1 +
 ariba/assembly_compare.py                          |  33 ++
 ariba/assembly_variants.py                         |  23 +-
 ariba/cluster.py                                   |   5 +-
 ariba/clusters.py                                  |   2 -
 ariba/ext/vcfcall_ariba.cpp                        |   3 +-
 ariba/external_progs.py                            |   7 +
 ariba/mapping.py                                   |   4 +
 ariba/mic_plotter.py                               | 651 +++++++++++++++++++++
 ariba/ref_genes_getter.py                          |  53 ++
 ariba/summary.py                                   |  38 +-
 ariba/summary_cluster.py                           |  23 +-
 ariba/summary_cluster_variant.py                   |  58 +-
 ariba/summary_sample.py                            |   2 +-
 ariba/tasks/__init__.py                            |   1 +
 ariba/tasks/micplot.py                             |  39 ++
 ariba/tasks/summary.py                             |  10 +-
 ariba/tests/assembly_compare_test.py               |  31 +
 ariba/tests/assembly_variants_test.py              |  17 +-
 ariba/tests/data/mic_plotter_load_mic_file.tsv     |   7 +
 ariba/tests/data/mic_plotter_load_summary_file.tsv |   3 +
 ...oxplot_tsv.antibio1.exclude.no_combinations.tsv |   3 +
 ...mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv |   2 +
 ..._to_boxplot_tsv.antibio1.no.no_combinations.tsv |   4 +
 .../mic_plotter_to_boxplot_tsv.antibio1.no.tsv     |   3 +
 ...to_boxplot_tsv.antibio1.yes.no_combinations.tsv |   5 +
 .../mic_plotter_to_boxplot_tsv.antibio1.yes.tsv    |   3 +
 ...oxplot_tsv.antibio2.exclude.no_combinations.tsv |   4 +
 ...mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv |   3 +
 ..._to_boxplot_tsv.antibio2.no.no_combinations.tsv |   4 +
 .../mic_plotter_to_boxplot_tsv.antibio2.no.tsv     |   3 +
 ...to_boxplot_tsv.antibio2.yes.no_combinations.tsv |   4 +
 .../mic_plotter_to_boxplot_tsv.antibio2.yes.tsv    |   3 +
 ariba/tests/data/summary_test_load_fofn            |   4 +
 ariba/tests/data/summary_test_whole_run.out.csv    |   6 +-
 ariba/tests/mapping_test.py                        |   3 +
 ariba/tests/mic_plotter_test.py                    | 283 +++++++++
 ariba/tests/summary_cluster_test.py                |  16 +-
 ariba/tests/summary_cluster_variant_test.py        | 104 ++--
 ariba/tests/summary_sample_test.py                 |   9 +-
 ariba/tests/summary_test.py                        | 129 ++--
 install_dependencies.sh                            |  10 +-
 scripts/ariba                                      |  55 +-
 setup.py                                           |   3 +-
 46 files changed, 1529 insertions(+), 178 deletions(-)
 create mode 100644 ariba/mic_plotter.py
 create mode 100644 ariba/tasks/micplot.py
 create mode 100644 ariba/tests/data/mic_plotter_load_mic_file.tsv
 create mode 100644 ariba/tests/data/mic_plotter_load_summary_file.tsv
 create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv
 create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv
 create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv
 create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv
 create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv
 create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv
 create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv
 create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv
 create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv
 create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv
 create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv
 create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv
 create mode 100644 ariba/tests/data/summary_test_load_fofn
 create mode 100644 ariba/tests/mic_plotter_test.py

-- 
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