[med-svn] [salmon] branch upstream updated (65579ce -> 9a33d6a)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sun Feb 7 12:00:29 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream
in repository salmon.
from 65579ce Imported Upstream version 0.4.2+ds1
new 9a33d6a Imported Upstream version 0.6.0+ds1
The 1 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 +
CMakeLists.txt | 172 +-
README.md | 2 +-
cmake/TestSalmon.cmake | 35 -
cmake/TestSalmonFMD.cmake | 33 +
cmake/TestSalmonQuasi.cmake | 24 +
cmake/UnitTests.cmake | 10 +
doc/source/conf.py | 5 +-
doc/source/salmon.rst | 179 +-
external/.gitignore | 28 -
include/AlignmentGroup.hpp | 2 +-
include/AlignmentLibrary.hpp | 70 +-
include/BAMQueue.hpp | 9 +-
include/BAMQueue.tpp | 23 +-
include/BWAMemStaticFuncs.hpp | 120 +
include/BWAUtils.hpp | 34 +
include/BootstrapWriter.hpp | 15 +
include/ClusterForest.hpp | 5 +-
include/CollapsedEMOptimizer.hpp | 11 +
include/CollapsedGibbsSampler.hpp | 5 +-
include/EquivalenceClassBuilder.hpp | 94 +-
include/ForgettingMassCalculator.hpp | 2 +-
include/FragmentLengthDistribution.hpp | 9 +
include/FragmentStartPositionDistribution.hpp | 25 +-
include/GZipWriter.hpp | 52 +
include/IndexVersionInfo.hpp | 11 +
include/KmerIntervalMap.hpp | 131 +
include/LibraryFormat.hpp | 14 +-
include/LightweightAlignmentDefs.hpp | 1470 ++++
include/MultinomialSampler.hpp | 104 +-
include/PCA.hpp | 8 +-
include/PairSequenceParser.hpp | 10 +-
include/ReadExperiment.hpp | 337 +-
include/ReadKmerDist.hpp | 76 +
include/ReadLibrary.hpp | 4 +-
include/ReadPair.hpp | 25 +-
include/SalmonConfig.hpp | 7 +-
include/SalmonIndex.hpp | 321 +
include/SalmonIndexVersionInfo.hpp | 80 +
include/SalmonMath.hpp | 28 +
include/SalmonOpts.hpp | 33 +-
include/{SpinLock.hpp => SalmonSpinLock.hpp} | 6 +-
include/SalmonUtils.hpp | 44 +-
include/Sampler.hpp | 33 +-
include/TextBootstrapWriter.hpp | 101 +
include/Transcript.hpp | 146 +-
include/TranscriptCluster.hpp | 2 +-
include/UnpairedRead.hpp | 10 +
include/UtilityFunctions.hpp | 148 +
include/blockingconcurrentqueue.h | 760 ++
include/concurrentqueue.h | 1121 +--
include/cuckoohash_config.h | 16 -
include/cuckoohash_config.hh | 28 +
include/cuckoohash_map.hh | 2190 +++---
include/cuckoohash_util.h | 23 -
include/cuckoohash_util.hh | 88 +
include/default_hasher.hh | 29 +
include/kseq.h | 235 -
include/posix.h | 344 -
include/tensemble/BaseForest.h | 513 --
include/tensemble/BaseGBM.h | 426 --
include/tensemble/ClassificationCriterion.h | 201 -
include/tensemble/Criterion.h | 163 -
include/tensemble/Estimator.h | 79 -
include/tensemble/EvaluateMetric.h | 83 -
include/tensemble/FeatureData.h | 227 -
include/tensemble/GBMClassifier.h | 400 --
include/tensemble/GBMRegressor.h | 242 -
include/tensemble/LossFunction.h | 350 -
include/tensemble/RandomForestClassifier.h | 269 -
include/tensemble/RandomForestRegressor.h | 279 -
include/tensemble/RandomGenerator.h | 33 -
include/tensemble/ReadData.h | 163 -
include/tensemble/Tree.h | 731 --
include/tensemble/Tree.h.backup.h | 391 -
include/tensemble/TreeClassifier.h | 74 -
include/tensemble/TreeNode.h | 41 -
include/tensemble/TreeRegressor.h | 66 -
include/tensemble/TypeDef.h | 39 -
include/tensemble/cmdline.h | 160 -
include/xxhash.h | 196 +
scripts/cpld.bash | 35 -
scripts/fetchRapMap.sh | 36 +
src/BWAUtils.cpp | 146 +
src/BiasCorrectionDriver.cpp | 52 -
src/BuildSalmonIndex.cpp | 197 +-
src/CMakeLists.txt | 187 +-
src/CollapsedEMOptimizer.cpp | 693 +-
src/CollapsedGibbsSampler.cpp | 229 +-
src/ComputeBiasFeatures.cpp | 225 -
src/FASTAParser.cpp | 38 +-
src/FragmentLengthDistribution.cpp | 23 +-
src/FragmentStartPositionDistribution.cpp | 128 +-
src/GZipWriter.cpp | 253 +
src/PerformBiasCorrection.cpp | 349 -
src/PerformBiasCorrection_old.cpp | 420 --
src/Salmon.cpp | 2 +-
src/SalmonQuantify.cpp | 3229 +++------
src/SalmonQuantifyAlignments.cpp | 608 +-
src/SalmonUtils.cpp | 600 +-
src/SequenceBiasModel.cpp | 2 +-
src/TranscriptGroup.cpp | 7 +-
src/cokus.cpp | 196 -
src/posix.cc | 252 -
src/xxhash.c | 915 +++
tests/KmerHistTests.cpp | 115 +
tests/LibraryTypeTests.cpp | 166 +
tests/UnitTests.cpp | 11 +
tests/catch.hpp | 9416 +++++++++++++++++++++++++
109 files changed, 20314 insertions(+), 12292 deletions(-)
delete mode 100644 cmake/TestSalmon.cmake
create mode 100644 cmake/TestSalmonFMD.cmake
create mode 100644 cmake/TestSalmonQuasi.cmake
create mode 100644 cmake/UnitTests.cmake
delete mode 100644 external/.gitignore
create mode 100644 include/BWAMemStaticFuncs.hpp
create mode 100644 include/BWAUtils.hpp
create mode 100644 include/BootstrapWriter.hpp
create mode 100644 include/GZipWriter.hpp
create mode 100644 include/IndexVersionInfo.hpp
create mode 100644 include/KmerIntervalMap.hpp
create mode 100644 include/LightweightAlignmentDefs.hpp
create mode 100644 include/ReadKmerDist.hpp
create mode 100644 include/SalmonIndex.hpp
create mode 100644 include/SalmonIndexVersionInfo.hpp
rename include/{SpinLock.hpp => SalmonSpinLock.hpp} (88%)
create mode 100644 include/TextBootstrapWriter.hpp
create mode 100644 include/UtilityFunctions.hpp
create mode 100644 include/blockingconcurrentqueue.h
delete mode 100644 include/cuckoohash_config.h
create mode 100644 include/cuckoohash_config.hh
delete mode 100644 include/cuckoohash_util.h
create mode 100644 include/cuckoohash_util.hh
create mode 100644 include/default_hasher.hh
delete mode 100644 include/kseq.h
delete mode 100644 include/posix.h
delete mode 100644 include/tensemble/BaseForest.h
delete mode 100644 include/tensemble/BaseGBM.h
delete mode 100644 include/tensemble/ClassificationCriterion.h
delete mode 100644 include/tensemble/Criterion.h
delete mode 100644 include/tensemble/Estimator.h
delete mode 100644 include/tensemble/EvaluateMetric.h
delete mode 100644 include/tensemble/FeatureData.h
delete mode 100644 include/tensemble/GBMClassifier.h
delete mode 100644 include/tensemble/GBMRegressor.h
delete mode 100644 include/tensemble/LossFunction.h
delete mode 100644 include/tensemble/RandomForestClassifier.h
delete mode 100644 include/tensemble/RandomForestRegressor.h
delete mode 100644 include/tensemble/RandomGenerator.h
delete mode 100644 include/tensemble/ReadData.h
delete mode 100644 include/tensemble/Tree.h
delete mode 100644 include/tensemble/Tree.h.backup.h
delete mode 100644 include/tensemble/TreeClassifier.h
delete mode 100644 include/tensemble/TreeNode.h
delete mode 100644 include/tensemble/TreeRegressor.h
delete mode 100644 include/tensemble/TypeDef.h
delete mode 100644 include/tensemble/cmdline.h
create mode 100644 include/xxhash.h
delete mode 100755 scripts/cpld.bash
create mode 100755 scripts/fetchRapMap.sh
create mode 100644 src/BWAUtils.cpp
delete mode 100644 src/BiasCorrectionDriver.cpp
delete mode 100644 src/ComputeBiasFeatures.cpp
create mode 100644 src/GZipWriter.cpp
delete mode 100644 src/PerformBiasCorrection.cpp
delete mode 100644 src/PerformBiasCorrection_old.cpp
delete mode 100755 src/cokus.cpp
delete mode 100644 src/posix.cc
create mode 100644 src/xxhash.c
create mode 100644 tests/KmerHistTests.cpp
create mode 100644 tests/LibraryTypeTests.cpp
create mode 100644 tests/UnitTests.cpp
create mode 100644 tests/catch.hpp
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