[med-svn] [ariba] branch upstream updated (784873c -> afa23ce)

[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  784873c   New upstream version 2.4.0+ds
      adds  6f1762d   New upstream version 2.5.0+ds
       new  afa23ce   Merge branch 'upstream' of ssh://git.debian.org/git/debian-med/ariba into upstream

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/assembly_compare.py                          |  3 +-
 ariba/cdhit.py                                     |  2 +-
 ariba/ext/minimap_ariba.cpp                        |  5 ++++
 ariba/ref_preparer.py                              |  2 +-
 ariba/ref_seq_chooser.py                           | 20 ++++++++-----
 ariba/reference_data.py                            |  2 +-
 ..._chooser_full_run_contained_ref_seq.all_refs.fa | 35 ++++++++++++++++++++++
 ...oser_full_run_contained_ref_seq.cluster_refs.fa | 20 +++++++++++++
 ...q_chooser_full_run_contained_ref_seq.contigs.fa | 10 +++++++
 ariba/tests/ref_seq_chooser_test.py                | 14 +++++++++
 scripts/ariba                                      |  2 +-
 setup.py                                           |  4 +--
 12 files changed, 105 insertions(+), 14 deletions(-)
 create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa
 create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa
 create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa

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