[med-svn] [pbgenomicconsensus] branch upstream updated (0b4bc9e -> db3cde2)

[Afif Elghraoui]

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

afif pushed a change to branch upstream
in repository pbgenomicconsensus.

      from  0b4bc9e   Imported Upstream version 2.0.0+20160420
       new  db3cde2   Imported Upstream version 2.1.0

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:
 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 +
 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 +++++------
 18 files changed, 315 insertions(+), 193 deletions(-)
 create mode 100644 tests/cram/extra/arrow-evidence.t

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