[med-svn] [ariba] 02/02: Merge tag 'upstream/2.9.0+ds'

[Sascha Steinbiss]

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

satta pushed a commit to branch master
in repository ariba.

commit 8d2b3e7732a26894bcfef1ffa369b4feceb3d770
Merge: 285b94a 83edd46
Author: Sascha Steinbiss <sascha.steinbiss at dcso.de>
Date:   Tue Apr 4 13:45:17 2017 +0200

    Merge tag 'upstream/2.9.0+ds'
    
    Upstream version 2.9.0+ds

 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(-)

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