[med-svn] [unanimity] 04/04: Merge tag 'upstream/2.0.4+20161206+dfsg'
Afif Elghraoui
afif at moszumanska.debian.org
Mon Dec 19 06:16:09 UTC 2016
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afif pushed a commit to branch master
in repository unanimity.
commit 17cc0f4201170a80cb88e951a1ec9ba9c78d8317
Merge: 6e8f934 eeb5d26
Author: Afif Elghraoui <afif at debian.org>
Date: Sun Dec 18 01:15:25 2016 -0800
Merge tag 'upstream/2.0.4+20161206+dfsg'
Upstream version 2.0.4+20161206+dfsg
.gitignore | 3 +
.gitmodules | 4 -
CMakeLists.txt | 2 +-
cmake/uny-compilerflags.cmake | 4 +-
cmake/uny-dependencies.cmake | 32 +-
cmake/uny-gitsha1.cmake | 2 +-
.../ZScoreMath.rst | 354 +++----
.../img/ZScore-HMM-figures.jpeg | Bin 0 -> 105415 bytes
.../{ => img}/pacbioHMM.svg.png | Bin
include/pacbio/Version.h.in | 1 +
include/pacbio/ccs/Consensus.h | 25 +-
include/pacbio/ccs/ConsensusSettings.h | 3 +-
include/pacbio/consensus/AbstractIntegrator.h | 24 +-
include/pacbio/consensus/Evaluator.h | 11 +-
include/pacbio/consensus/MonoMolecularIntegrator.h | 5 +
include/pacbio/data/State.h | 6 +-
include/pacbio/denovo/PoaGraph.h | 2 +
include/pacbio/denovo/SparsePoa.h | 2 +-
.../InvalidEvaluatorException.h} | 28 +-
include/pacbio/log/Logging.h | 406 --------
build.sh => scripts/ci/build.sh | 12 +-
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 +
setup.py | 26 +-
src/AbstractIntegrator.cpp | 42 +-
src/CMakeLists.txt | 4 -
src/ConsensusSettings.cpp | 59 +-
src/Evaluator.cpp | 25 +-
src/Polish.cpp | 56 +-
src/SparsePoa.cpp | 5 +-
src/Template.cpp | 32 +-
src/Utility.cpp | 7 +-
src/main/ccs.cpp | 146 +--
src/models/S_P1C1v2_Model.cpp | 2 +-
src/models/S_P2C2_Model.cpp | 395 ++++++++
src/poa/PoaGraph.cpp | 2 +
src/poa/PoaGraphImpl.cpp | 22 +
src/poa/PoaGraphImpl.h | 16 +-
src/poa/PoaGraphTraversals.cpp | 8 +-
swig/CMakeLists.txt | 11 +-
swig/ConsensusCore2.py | 1 +
tests/cram/100zmws.t | 64 +-
tests/cram/100zmws_byStrand.t | 134 +--
tests/cram/force.t | 14 +
tests/cram/internal/big.t | 20 +
tests/cram/logfile.t | 14 +
tests/cram/tiny.t | 4 +-
tests/cram/tiny_noPolish.t | 33 +
tests/data/params/SP2C2.json | 1026 ++++++++++++++++++++
tests/python/test_tool_contract.py | 2 +-
tests/unit/TestLoadModels.cpp | 27 +-
tests/unit/TestPoaConsensus.cpp | 45 +-
tests/unit/TestTemplate.cpp | 2 +-
56 files changed, 2293 insertions(+), 996 deletions(-)
--
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