[med-svn] [consensuscore2] 02/05: Merge tag 'upstream/0.13.0+20160719'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository consensuscore2.

commit 774c191cf762ea1b8d8d24ac116f7f22cd193fa8
Merge: 0a88513 4ed3a06
Author: Afif Elghraoui <afif at debian.org>
Date:   Sat Jul 23 21:14:27 2016 -0700

    Merge tag 'upstream/0.13.0+20160719'
    
    Upstream version 0.13.0+20160719

 CMakeLists.txt                                     |   2 +-
 circle.yml                                         |  13 +-
 .../{Integrator.h => AbstractIntegrator.h}         | 123 +++----
 include/pacbio/consensus/Evaluator.h               |  42 +--
 include/pacbio/consensus/Exceptions.h              |  22 +-
 include/pacbio/consensus/ModelConfig.h             |  12 +-
 .../{Polish.h => MonoMolecularIntegrator.h}        |  51 +--
 .../{Polish.h => MultiMolecularIntegrator.h}       |  48 +--
 include/pacbio/consensus/Polish.h                  |   3 +-
 .../consensus/{Exceptions.h => PolishResult.h}     |  29 +-
 include/pacbio/consensus/Read.h                    |  13 +-
 include/pacbio/consensus/{Exceptions.h => State.h} |  28 +-
 .../consensus/{Exceptions.h => StrandType.h}       |  26 +-
 include/pacbio/consensus/Template.h                |  46 ++-
 setup.py                                           |   2 +-
 src/AbstractIntegrator.cpp                         | 182 +++++++++
 src/Evaluator.cpp                                  | 146 ++++----
 src/EvaluatorImpl.cpp                              |   4 +-
 src/EvaluatorImpl.h                                |   5 +
 src/Integrator.cpp                                 | 408 ---------------------
 src/MonoMolecularIntegrator.cpp                    | 182 +++++++++
 src/MultiMolecularIntegrator.cpp                   | 134 +++++++
 src/Polish.cpp                                     |  42 ++-
 src/Read.cpp                                       |  30 +-
 src/Recursor.h                                     |   4 +-
 src/Template.cpp                                   |  29 +-
 src/matrix/SparseMatrix.cpp                        |   7 +
 src/matrix/SparseMatrix.h                          |   5 +-
 src/matrix/SparseVector.h                          |  16 +-
 src/models/P6C4NoCovModel.cpp                      |  55 ++-
 src/models/S_P1C1Beta_Model.cpp                    |  41 +--
 src/models/S_P1C1v1_Model.cpp                      |  70 +---
 src/models/S_P1C1v2_Model.cpp                      | 358 +++++++++---------
 swig/Integrator.i                                  |  12 +-
 swig/Polish.i                                      |   9 +-
 swig/Read.i                                        |   2 +
 tests/CMakeLists.txt                               |   4 +
 tests/TestIntegrator.cpp                           |  79 ++--
 tests/TestMutationEnumerator.cpp                   |   3 +-
 tests/TestPolish.cpp                               |  22 +-
 tests/TestTemplate.cpp                             |  49 +--
 41 files changed, 1208 insertions(+), 1150 deletions(-)

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