[med-svn] [consensuscore2] branch master updated (0a88513 -> bc4f7d2)

[Afif Elghraoui]

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afif pushed a change to branch master
in repository consensuscore2.

      from  0a88513   releasing package consensuscore2 version 0.12.0-1
       new  4ed3a06   Imported Upstream version 0.13.0+20160719
       new  774c191   Merge tag 'upstream/0.13.0+20160719'
       new  d4ea3f5   Drop obsolete patch
       new  1b8c11f   Allow setup.py to work with both Python 2.x and 3.x
       new  bc4f7d2   releasing package consensuscore2 version 0.13.0+20160719-1

The 5 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:
 CMakeLists.txt                                     |   2 +-
 circle.yml                                         |  13 +-
 debian/changelog                                   |   9 +
 debian/control                                     |   2 +
 debian/patches/match-pyversion.patch               |  14 -
 debian/patches/py3.patch                           |  24 ++
 debian/patches/series                              |   2 +-
 .../{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 +--
 46 files changed, 1254 insertions(+), 1135 deletions(-)
 delete mode 100644 debian/patches/match-pyversion.patch
 create mode 100644 debian/patches/py3.patch
 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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