[med-svn] [consensuscore2] 05/09: Merge tag 'upstream/0.12.0'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository consensuscore2.

commit bb8c8c1c60d60ecdbaa32c200fab28a947984914
Merge: 4a39c87 4d0299d
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sun Jul 3 16:25:31 2016 -0700

    Merge tag 'upstream/0.12.0'
    
    Upstream version 0.12.0

 CMakeLists.txt                                     |   2 +-
 README.md                                          |   2 +-
 circle.yml                                         |   8 +-
 include/pacbio/consensus/Coverage.h                |   3 +-
 include/pacbio/consensus/Evaluator.h               |  34 ++
 include/pacbio/consensus/Exceptions.h              |  34 ++
 include/pacbio/consensus/Integrator.h              |  35 ++
 include/pacbio/consensus/ModelConfig.h             |  39 +-
 include/pacbio/consensus/Mutation.h                |  34 ++
 include/pacbio/consensus/Polish.h                  |  46 ++-
 include/pacbio/consensus/Read.h                    |  37 ++
 include/pacbio/consensus/Sequence.h                |  36 ++
 include/pacbio/consensus/Template.h                |  75 +++-
 include/pacbio/consensus/Version.h.in              |  37 ++
 include/pacbio/consensus/align/AffineAlignment.h   |   2 +-
 include/pacbio/consensus/align/AlignConfig.h       |   2 +-
 include/pacbio/consensus/align/LinearAlignment.h   |   2 +-
 include/pacbio/consensus/align/PairwiseAlignment.h |   2 +-
 include/pacbio/consensus/poa/PoaConsensus.h        |   2 +-
 include/pacbio/consensus/poa/PoaGraph.h            |   2 +-
 include/pacbio/consensus/poa/RangeFinder.h         |  35 ++
 setup.py                                           | 135 +++++--
 src/Coverage.cpp                                   |   2 +-
 src/Evaluator.cpp                                  |  40 +-
 src/EvaluatorImpl.cpp                              |  40 +-
 src/EvaluatorImpl.h                                |  41 +-
 src/Integrator.cpp                                 |  66 +++-
 src/ModelConfig.cpp                                |  34 ++
 src/ModelFactory.cpp                               |  34 ++
 src/ModelFactory.h                                 |  34 ++
 src/Mutation.cpp                                   |  34 ++
 src/Polish.cpp                                     | 159 ++++++--
 src/Read.cpp                                       |  49 +++
 src/Recursor.cpp                                   |  34 ++
 src/Recursor.h                                     |  25 +-
 src/Sequence.cpp                                   |  34 ++
 src/Template.cpp                                   |  65 +++-
 src/align/AffineAlignment.cpp                      |   2 +-
 src/align/AlignConfig.cpp                          |   8 +-
 src/align/LinearAlignment.cpp                      |   2 +-
 src/align/PairwiseAlignment.cpp                    |   2 +-
 src/matrix/ScaledMatrix.cpp                        |  34 ++
 src/matrix/ScaledMatrix.h                          |  55 ++-
 src/matrix/SparseMatrix.cpp                        |   2 +-
 src/matrix/SparseMatrix.h                          |   2 +-
 src/matrix/SparseVector.h                          |   2 +-
 src/models/P6C4NoCovModel.cpp                      |  76 +++-
 src/models/SP1C1BetaNoCovModel.cpp                 | 174 ---------
 src/models/SP1C1PwModel.cpp                        | 301 ---------------
 src/models/S_P1C1Beta_Model.cpp                    | 239 ++++++++++++
 src/models/S_P1C1v1_Model.cpp                      | 423 +++++++++++++++++++++
 src/models/S_P1C1v2_Model.cpp                      | 422 ++++++++++++++++++++
 src/poa/PoaConsensus.cpp                           |   2 +-
 src/poa/PoaGraph.cpp                               |   2 +-
 src/poa/PoaGraphImpl.cpp                           |  34 ++
 src/poa/PoaGraphImpl.h                             |  34 ++
 src/poa/PoaGraphTraversals.cpp                     |   2 +-
 src/poa/RangeFinder.cpp                            |  34 ++
 src/poa/VectorL.h                                  |  34 ++
 swig/ConsensusCore2.i.in                           |  12 +
 tests/Mutations.cpp                                |  34 ++
 tests/Mutations.h                                  |  36 ++
 tests/RandomDNA.cpp                                |  43 ++-
 tests/RandomDNA.h                                  |  36 ++
 tests/TestIntegrator.cpp                           | 136 ++++---
 tests/TestTemplate.cpp                             |  14 +
 66 files changed, 2778 insertions(+), 714 deletions(-)

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