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commit bb8c8c1c60d60ecdbaa32c200fab28a947984914 Merge: 4a39c87 4d0299d Author: Afif Elghraoui <[email protected]> Date: Sun Jul 3 16:25:31 2016 -0700 Merge tag 'upstream/0.12.0' Upstream version 0.12.0 CMakeLists.txt | 2 +- README.md | 2 +- circle.yml | 8 +- include/pacbio/consensus/Coverage.h | 3 +- include/pacbio/consensus/Evaluator.h | 34 ++ include/pacbio/consensus/Exceptions.h | 34 ++ include/pacbio/consensus/Integrator.h | 35 ++ include/pacbio/consensus/ModelConfig.h | 39 +- include/pacbio/consensus/Mutation.h | 34 ++ include/pacbio/consensus/Polish.h | 46 ++- include/pacbio/consensus/Read.h | 37 ++ include/pacbio/consensus/Sequence.h | 36 ++ include/pacbio/consensus/Template.h | 75 +++- include/pacbio/consensus/Version.h.in | 37 ++ include/pacbio/consensus/align/AffineAlignment.h | 2 +- include/pacbio/consensus/align/AlignConfig.h | 2 +- include/pacbio/consensus/align/LinearAlignment.h | 2 +- include/pacbio/consensus/align/PairwiseAlignment.h | 2 +- include/pacbio/consensus/poa/PoaConsensus.h | 2 +- include/pacbio/consensus/poa/PoaGraph.h | 2 +- include/pacbio/consensus/poa/RangeFinder.h | 35 ++ setup.py | 135 +++++-- src/Coverage.cpp | 2 +- src/Evaluator.cpp | 40 +- src/EvaluatorImpl.cpp | 40 +- src/EvaluatorImpl.h | 41 +- src/Integrator.cpp | 66 +++- src/ModelConfig.cpp | 34 ++ src/ModelFactory.cpp | 34 ++ src/ModelFactory.h | 34 ++ src/Mutation.cpp | 34 ++ src/Polish.cpp | 159 ++++++-- src/Read.cpp | 49 +++ src/Recursor.cpp | 34 ++ src/Recursor.h | 25 +- src/Sequence.cpp | 34 ++ src/Template.cpp | 65 +++- src/align/AffineAlignment.cpp | 2 +- src/align/AlignConfig.cpp | 8 +- src/align/LinearAlignment.cpp | 2 +- src/align/PairwiseAlignment.cpp | 2 +- src/matrix/ScaledMatrix.cpp | 34 ++ src/matrix/ScaledMatrix.h | 55 ++- src/matrix/SparseMatrix.cpp | 2 +- src/matrix/SparseMatrix.h | 2 +- src/matrix/SparseVector.h | 2 +- src/models/P6C4NoCovModel.cpp | 76 +++- src/models/SP1C1BetaNoCovModel.cpp | 174 --------- src/models/SP1C1PwModel.cpp | 301 --------------- src/models/S_P1C1Beta_Model.cpp | 239 ++++++++++++ src/models/S_P1C1v1_Model.cpp | 423 +++++++++++++++++++++ src/models/S_P1C1v2_Model.cpp | 422 ++++++++++++++++++++ src/poa/PoaConsensus.cpp | 2 +- src/poa/PoaGraph.cpp | 2 +- src/poa/PoaGraphImpl.cpp | 34 ++ src/poa/PoaGraphImpl.h | 34 ++ src/poa/PoaGraphTraversals.cpp | 2 +- src/poa/RangeFinder.cpp | 34 ++ src/poa/VectorL.h | 34 ++ swig/ConsensusCore2.i.in | 12 + tests/Mutations.cpp | 34 ++ tests/Mutations.h | 36 ++ tests/RandomDNA.cpp | 43 ++- tests/RandomDNA.h | 36 ++ tests/TestIntegrator.cpp | 136 ++++--- tests/TestTemplate.cpp | 14 + 66 files changed, 2778 insertions(+), 714 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/consensuscore2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
