[med-svn] [ariba] branch master updated (285b94a -> 8d2b3e7)

[Sascha Steinbiss]

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

satta pushed a change to branch master
in repository ariba.

      from  285b94a   Realise that 2.7.2+ds-1 was not yet uploaded - fix changelog and re-upload to experimental
       new  83edd46   New upstream version 2.9.0+ds
       new  8d2b3e7   Merge tag 'upstream/2.9.0+ds'

The 2 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                                          |  10 +-
 ariba/__init__.py                                  |   1 +
 ariba/assembly_compare.py                          |  33 ++
 ariba/assembly_variants.py                         |  23 +-
 ariba/cluster.py                                   |   4 +-
 ariba/ext/vcfcall_ariba.cpp                        |   3 +-
 ariba/mic_plotter.py                               | 651 +++++++++++++++++++++
 ariba/ref_genes_getter.py                          |  53 ++
 ariba/summary.py                                   |  37 +-
 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/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 ++--
 scripts/ariba                                      |  55 +-
 setup.py                                           |   3 +-
 40 files changed, 1494 insertions(+), 162 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

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git