[med-svn] [pbgenomicconsensus] 02/05: Merge tag 'upstream/2.1.0'

[Afif Elghraoui]

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commit c2bef03f997b0440318ffd7a509e4bb7f1f22818
Merge: 3a15e9b db3cde2
Author: Afif Elghraoui <afif at debian.org>
Date:   Sat Jul 23 15:54:45 2016 -0700

    Merge tag 'upstream/2.1.0'
    
    Upstream version 2.1.0

 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(-)

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