[med-svn] [ariba] branch upstream updated (3ba4058 -> 5fd2631)

[Sascha Steinbiss]

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satta pushed a change to branch upstream
in repository ariba.

      from  3ba4058   New upstream version 2.9.4+ds
       new  5fd2631   New upstream version 2.10.0+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:
 ariba/__init__.py                                  |  1 +
 ariba/flag.py                                      |  3 ++
 ariba/mic_plotter.py                               |  2 +-
 ariba/ref_preparer.py                              |  8 ++++-
 ariba/reference_data.py                            | 19 +++++++----
 ariba/report_filter.py                             |  3 ++
 ariba/report_flag_expander.py                      | 37 ++++++++++++++++++++++
 ariba/tasks/__init__.py                            |  1 +
 ariba/tasks/expandflag.py                          |  8 +++++
 .../01.filter.check_genes.log                      | 10 +++---
 .../data/reference_data_test_remove_bad_genes.log  | 10 +++---
 ariba/tests/data/report_flag_expander.run.in.tsv   |  3 ++
 ariba/tests/data/report_flag_expander.run.out.tsv  |  3 ++
 ariba/tests/flag_test.py                           |  8 +++++
 ariba/tests/reference_data_test.py                 | 17 ++++++----
 ariba/tests/report_filter_test.py                  | 15 +++++++++
 ariba/tests/report_flag_expander_test.py           | 20 ++++++++++++
 scripts/ariba                                      | 12 +++++++
 setup.py                                           |  2 +-
 19 files changed, 157 insertions(+), 25 deletions(-)
 create mode 100644 ariba/report_flag_expander.py
 create mode 100644 ariba/tasks/expandflag.py
 create mode 100644 ariba/tests/data/report_flag_expander.run.in.tsv
 create mode 100644 ariba/tests/data/report_flag_expander.run.out.tsv
 create mode 100644 ariba/tests/report_flag_expander_test.py

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