[med-svn] [pbgenomicconsensus] branch master updated (3a15e9b -> 2b9c726)

[Afif Elghraoui]

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

afif pushed a change to branch master
in repository pbgenomicconsensus.

      from  3a15e9b   releasing package pbgenomicconsensus version 2.0.0+20160420-2
       new  db3cde2   Imported Upstream version 2.1.0
       new  c2bef03   Merge tag 'upstream/2.1.0'
       new  82f8f8c   Update manpage for new release
       new  cc6cffd   Enable Arrow: add its dependency and enable its tests
       new  2b9c726   Add new dependency on pbtestdata required for test suite

The 5 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:
 CHANGELOG                                       |   6 +
 GenomicConsensus/__init__.py                    |   2 +-
 GenomicConsensus/arrow/arrow.py                 |  52 ++++++--
 GenomicConsensus/arrow/evidence.py              | 161 +++++++++++++-----------
 GenomicConsensus/arrow/model.py                 |  49 ++++----
 GenomicConsensus/arrow/utils.py                 |  77 ++++++++----
 GenomicConsensus/main.py                        |  11 +-
 GenomicConsensus/options.py                     |  10 +-
 circle.yml                                      |   4 +
 debian/control                                  |   2 +
 debian/man/variantCaller.1.md                   |   3 +
 debian/patches/disable-arrow-tests.patch        |  28 -----
 debian/patches/series                           |   1 -
 debian/tests/control                            |   2 +
 doc/HowTo.rst                                   |   8 +-
 tests/cram/bad_input.t                          |   2 +-
 tests/cram/extra/arrow-evidence.t               |  28 +++++
 tests/cram/internal/alignment_summary_scaling.t |   4 +-
 tests/cram/internal/arrow-staph.t               |  14 +--
 tests/cram/version.t                            |   2 +-
 tests/unit/test_algorithm_selection.py          |   4 +-
 tests/unit/test_summarize_consensus.py          |   2 +-
 tests/unit/test_tool_contract.py                |  72 +++++------
 23 files changed, 322 insertions(+), 222 deletions(-)
 delete mode 100644 debian/patches/disable-arrow-tests.patch
 create mode 100644 tests/cram/extra/arrow-evidence.t

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