[med-svn] [unanimity] 02/04: Merge tag 'upstream/2.0.4+dfsg'

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository unanimity.

commit 6e8f934711bf2757e7817b26f997c0c202a4b495
Merge: d9039ac 61ac353
Author: Afif Elghraoui <afif at debian.org>
Date:   Wed Dec 14 21:46:43 2016 -0800

    Merge tag 'upstream/2.0.4+dfsg'
    
    Upstream version 2.0.4+dfsg

 .gitmodules                                        |  20 +-
 CHANGELOG.md                                       |  12 +
 CMakeLists.txt                                     |   2 +-
 README.md                                          |   4 +-
 build.sh                                           | 103 +++
 cmake/uny-dependencies.cmake                       |  14 +-
 .../ZScoreMath.rst                                 | 267 ++++++
 .../img/consensus-modalities.pdf                   | Bin 0 -> 184757 bytes
 .../img/consensus-modalities.png                   | Bin 0 -> 270181 bytes
 .../img/hmms.pdf                                   | Bin 0 -> 194111 bytes
 .../img/hmms.png                                   | Bin 0 -> 373013 bytes
 .../index.rst                                      | 281 +++++-
 .../pacbioHMM.svg.png                              | Bin 0 -> 61715 bytes
 doc/INSTALL.md                                     |  13 +-
 include/pacbio/ccs/Consensus.h                     |  87 +-
 .../pacbio/ccs/ConsensusSettings.h                 |  64 +-
 include/pacbio/consensus/AbstractIntegrator.h      |  24 +-
 include/pacbio/consensus/AbstractMatrix.h          |  19 +-
 include/pacbio/consensus/Evaluator.h               |  68 +-
 .../pacbio/consensus/MatrixViewConvention.h        |  29 +-
 include/pacbio/consensus/MonoMolecularIntegrator.h |  15 +-
 .../pacbio/consensus/MultiMolecularIntegrator.h    |  11 +-
 include/pacbio/consensus/Mutation.h                |   8 +
 include/pacbio/consensus/Polish.h                  |  10 +
 include/pacbio/consensus/Template.h                |   2 +-
 .../pacbio/data/PlainOption.h                      |  48 +-
 include/pacbio/data/Read.h                         |   4 +
 include/pacbio/denovo/PoaGraph.h                   |   2 +
 include/pacbio/denovo/SparsePoa.h                  |   2 +
 scripts/task_pbccs_ccs                             | 218 -----
 src/AbstractIntegrator.cpp                         |   2 +-
 src/CMakeLists.txt                                 |   4 +-
 src/ConsensusSettings.cpp                          | 300 +++++++
 src/Evaluator.cpp                                  |  18 +
 src/EvaluatorImpl.cpp                              |  55 +-
 src/EvaluatorImpl.h                                |   5 +
 src/ModelSelection.cpp                             |   5 +-
 src/Read.cpp                                       |   6 +-
 src/Recursor.h                                     | 201 +++--
 src/Sequence.cpp                                   |   2 +-
 src/SparsePoa.cpp                                  |   7 +-
 src/Timer.cpp                                      |   2 +-
 src/Utility.cpp                                    |   5 +-
 src/align/AlignConfig.cpp                          |   2 +-
 src/main/ccs.cpp                                   | 236 ++---
 .../Polish.h => src/matrix/BasicDenseMatrix.cpp    |  50 +-
 src/{EvaluatorImpl.h => matrix/BasicDenseMatrix.h} |  94 +-
 src/matrix/ScaledMatrix.h                          |  14 +
 src/matrix/SparseMatrix.h                          |  23 +-
 src/poa/PoaGraph.cpp                               |   5 +
 src/poa/PoaGraphImpl.cpp                           |  17 +
 src/poa/PoaGraphImpl.h                             |   1 +
 swig/Matrix.i                                      |   2 +
 swig/Mutation.i                                    |  10 +
 swig/State.i                                       |   6 +-
 tests/CMakeLists.txt                               |   1 -
 tests/cram/100zmws.t                               |  25 +-
 tests/cram/100zmws_byStrand.t                      | 113 +--
 tests/cram/tiny.t                                  |   2 +-
 tests/python/test_tool_contract.py                 |   2 +-
 tests/unit/TestConsensus.cpp                       |  10 +-
 tests/unit/TestIntegrator.cpp                      |   9 +-
 tests/unit/TestLoadModels.cpp                      |   4 +-
 tests/unit/TestPolish.cpp                          |   2 +-
 third-party/cpp-optparse/OptionParser.cpp          | 959 ++++++++++-----------
 third-party/cpp-optparse/OptionParser.h            | 279 ++++--
 third-party/cpp-optparse/test.cpp                  | 277 +++---
 third-party/cram-0.7/cram/__init__.py              |   6 +
 third-party/cram-0.7/cram/__main__.py              |  10 +
 third-party/cram-0.7/cram/_cli.py                  | 134 +++
 third-party/cram-0.7/cram/_diff.py                 | 158 ++++
 third-party/cram-0.7/cram/_encoding.py             | 106 +++
 third-party/cram-0.7/cram/_main.py                 | 211 +++++
 third-party/cram-0.7/cram/_process.py              |  54 ++
 third-party/cram-0.7/cram/_run.py                  |  77 ++
 third-party/cram-0.7/cram/_test.py                 | 230 +++++
 third-party/cram-0.7/cram/_xunit.py                | 173 ++++
 third-party/cram-0.7/scripts/cram                  |   9 +
 tools/Darwin/clang-format                          | Bin 2490044 -> 0 bytes
 tools/Linux/clang-format                           | Bin 2754467 -> 0 bytes
 tools/check-formatting                             |  33 -
 tools/format-all                                   |   8 -
 tools/git-clang-format                             | 485 -----------
 tools/win32/clang-format.exe                       | Bin 1315328 -> 0 bytes
 84 files changed, 3716 insertions(+), 2060 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/unanimity.git