[med-svn] [consensuscore2] branch upstream updated (4d0299d -> 4ed3a06)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository consensuscore2.

      from  4d0299d   Imported Upstream version 0.12.0
       new  4ed3a06   Imported Upstream version 0.13.0+20160719

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
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Summary of changes:
 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/{Sequence.h => PolishResult.h}       |  22 +-
 include/pacbio/consensus/Read.h                    |  13 +-
 include/pacbio/consensus/{Sequence.h => State.h}   |  23 +-
 .../pacbio/consensus/StrandType.h                  |  18 +-
 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, 1218 insertions(+), 1120 deletions(-)
 rename include/pacbio/consensus/{Integrator.h => AbstractIntegrator.h} (61%)
 copy include/pacbio/consensus/{Polish.h => MonoMolecularIntegrator.h} (65%)
 copy include/pacbio/consensus/{Polish.h => MultiMolecularIntegrator.h} (68%)
 copy include/pacbio/consensus/{Sequence.h => PolishResult.h} (83%)
 copy include/pacbio/consensus/{Sequence.h => State.h} (84%)
 copy tests/RandomDNA.h => include/pacbio/consensus/StrandType.h (87%)
 create mode 100644 src/AbstractIntegrator.cpp
 delete mode 100644 src/Integrator.cpp
 create mode 100644 src/MonoMolecularIntegrator.cpp
 create mode 100644 src/MultiMolecularIntegrator.cpp

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