[med-svn] [unanimity] branch upstream updated (d9039ac -> eeb5d26)
Afif Elghraoui
afif at moszumanska.debian.org
Mon Dec 19 06:16:28 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository unanimity.
from d9039ac Imported Upstream version 2.0.2+20160812+ds
new 61ac353 Imported Upstream version 2.0.4+dfsg
new eeb5d26 Imported Upstream version 2.0.4+20161206+dfsg
The 2 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:
.gitignore | 3 +
.gitmodules | 16 +-
CHANGELOG.md | 12 +
CMakeLists.txt | 2 +-
README.md | 4 +-
cmake/uny-compilerflags.cmake | 4 +-
cmake/uny-dependencies.cmake | 28 +-
cmake/uny-gitsha1.cmake | 2 +-
.../ZScoreMath.rst | 187 ++++
.../img/ZScore-HMM-figures.jpeg | Bin 0 -> 105415 bytes
.../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
.../img/pacbioHMM.svg.png | Bin 0 -> 61715 bytes
.../index.rst | 281 +++++-
doc/INSTALL.md | 13 +-
include/pacbio/Version.h.in | 1 +
include/pacbio/ccs/Consensus.h | 112 +--
.../{io/Utility.h => ccs/ConsensusSettings.h} | 71 +-
include/pacbio/consensus/AbstractIntegrator.h | 42 +-
include/pacbio/consensus/AbstractMatrix.h | 19 +-
include/pacbio/consensus/Evaluator.h | 77 +-
.../pacbio/consensus/MatrixViewConvention.h | 27 +-
include/pacbio/consensus/MonoMolecularIntegrator.h | 20 +-
.../pacbio/consensus/MultiMolecularIntegrator.h | 11 +-
include/pacbio/consensus/Mutation.h | 8 +
include/pacbio/consensus/Polish.h | 10 +
include/pacbio/consensus/Template.h | 2 +-
include/pacbio/data/{ReadId.h => PlainOption.h} | 46 +-
include/pacbio/data/Read.h | 4 +
include/pacbio/data/State.h | 6 +-
include/pacbio/denovo/PoaGraph.h | 4 +
include/pacbio/denovo/SparsePoa.h | 4 +-
.../InvalidEvaluatorException.h} | 17 +-
include/pacbio/log/Logging.h | 406 --------
scripts/ci/build.sh | 107 ++
scripts/ci/checkout-submodules.sh | 13 +
scripts/makeChangeLog.py | 31 -
scripts/nightly/build.sh | 42 +
scripts/nightly/checkout-submodules.sh | 13 +
scripts/nightly/test.sh | 20 +
scripts/task_pbccs_ccs | 218 -----
setup.py | 26 +-
src/AbstractIntegrator.cpp | 44 +-
src/CMakeLists.txt | 8 +-
src/Consensus.cpp | 61 --
src/ConsensusSettings.cpp | 317 ++++++
src/Evaluator.cpp | 43 +-
src/EvaluatorImpl.cpp | 55 +-
src/EvaluatorImpl.h | 5 +
src/ModelSelection.cpp | 5 +-
src/Polish.cpp | 56 +-
src/Read.cpp | 6 +-
src/Recursor.h | 201 ++--
src/Sequence.cpp | 2 +-
src/SparsePoa.cpp | 12 +-
src/Template.cpp | 32 +-
src/Timer.cpp | 2 +-
src/Utility.cpp | 6 +-
src/align/AlignConfig.cpp | 2 +-
src/main/ccs.cpp | 324 +++----
.../BasicDenseMatrix.cpp} | 45 +-
.../matrix/BasicDenseMatrix.h | 64 +-
src/matrix/ScaledMatrix.h | 14 +
src/matrix/SparseMatrix.h | 23 +-
src/models/S_P1C1v2_Model.cpp | 2 +-
src/models/S_P2C2_Model.cpp | 395 ++++++++
src/poa/PoaGraph.cpp | 7 +
src/poa/PoaGraphImpl.cpp | 39 +
src/poa/PoaGraphImpl.h | 17 +-
src/poa/PoaGraphTraversals.cpp | 8 +-
swig/CMakeLists.txt | 11 +-
swig/ConsensusCore2.py | 1 +
swig/Matrix.i | 2 +
swig/Mutation.i | 10 +
swig/State.i | 6 +-
tests/CMakeLists.txt | 1 -
tests/cram/100zmws.t | 89 +-
tests/cram/100zmws_byStrand.t | 229 ++---
tests/cram/force.t | 14 +
tests/cram/internal/big.t | 20 +
tests/cram/logfile.t | 14 +
tests/cram/tiny.t | 6 +-
tests/cram/tiny_noPolish.t | 33 +
tests/data/params/SP2C2.json | 1026 ++++++++++++++++++++
tests/python/test_tool_contract.py | 4 +-
tests/unit/TestConsensus.cpp | 10 +-
tests/unit/TestIntegrator.cpp | 9 +-
tests/unit/TestLoadModels.cpp | 31 +-
tests/unit/TestPoaConsensus.cpp | 45 +-
tests/unit/TestPolish.cpp | 2 +-
tests/unit/TestTemplate.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
113 files changed, 5702 insertions(+), 2776 deletions(-)
create mode 100644 doc/ConsensusCore2-DesignAndImplementation/ZScoreMath.rst
create mode 100644 doc/ConsensusCore2-DesignAndImplementation/img/ZScore-HMM-figures.jpeg
create mode 100644 doc/ConsensusCore2-DesignAndImplementation/img/consensus-modalities.pdf
create mode 100644 doc/ConsensusCore2-DesignAndImplementation/img/consensus-modalities.png
create mode 100644 doc/ConsensusCore2-DesignAndImplementation/img/hmms.pdf
create mode 100644 doc/ConsensusCore2-DesignAndImplementation/img/hmms.png
create mode 100644 doc/ConsensusCore2-DesignAndImplementation/img/pacbioHMM.svg.png
copy include/pacbio/{io/Utility.h => ccs/ConsensusSettings.h} (55%)
copy src/Recursor.cpp => include/pacbio/consensus/MatrixViewConvention.h (79%)
copy include/pacbio/data/{ReadId.h => PlainOption.h} (70%)
copy include/pacbio/{data/StrandType.h => exception/InvalidEvaluatorException.h} (87%)
delete mode 100644 include/pacbio/log/Logging.h
create mode 100755 scripts/ci/build.sh
create mode 100755 scripts/ci/checkout-submodules.sh
delete mode 100644 scripts/makeChangeLog.py
create mode 100755 scripts/nightly/build.sh
create mode 100755 scripts/nightly/checkout-submodules.sh
create mode 100755 scripts/nightly/test.sh
delete mode 100755 scripts/task_pbccs_ccs
delete mode 100644 src/Consensus.cpp
create mode 100644 src/ConsensusSettings.cpp
copy src/{EasyReadScorer.cpp => matrix/BasicDenseMatrix.cpp} (68%)
copy include/pacbio/consensus/EasyReadScorer.h => src/matrix/BasicDenseMatrix.h (57%)
create mode 100644 src/models/S_P2C2_Model.cpp
create mode 100644 swig/ConsensusCore2.py
create mode 100644 tests/cram/force.t
create mode 100644 tests/cram/internal/big.t
create mode 100644 tests/cram/logfile.t
create mode 100644 tests/cram/tiny_noPolish.t
create mode 100644 tests/data/params/SP2C2.json
create mode 100644 third-party/cram-0.7/cram/__init__.py
create mode 100644 third-party/cram-0.7/cram/__main__.py
create mode 100644 third-party/cram-0.7/cram/_cli.py
create mode 100644 third-party/cram-0.7/cram/_diff.py
create mode 100644 third-party/cram-0.7/cram/_encoding.py
create mode 100644 third-party/cram-0.7/cram/_main.py
create mode 100644 third-party/cram-0.7/cram/_process.py
create mode 100644 third-party/cram-0.7/cram/_run.py
create mode 100644 third-party/cram-0.7/cram/_test.py
create mode 100644 third-party/cram-0.7/cram/_xunit.py
create mode 100755 third-party/cram-0.7/scripts/cram
delete mode 100755 tools/Darwin/clang-format
delete mode 100755 tools/Linux/clang-format
delete mode 100755 tools/check-formatting
delete mode 100755 tools/format-all
delete mode 100755 tools/git-clang-format
delete mode 100644 tools/win32/clang-format.exe
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