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commit 6e8f934711bf2757e7817b26f997c0c202a4b495 Merge: d9039ac 61ac353 Author: Afif Elghraoui <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
