[med-svn] [salmon] 01/02: Merge tag 'upstream/0.6.0+ds1' into experimental
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sun Feb 7 12:00:32 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch experimental
in repository salmon.
commit 61235df0110d025f9f6d89a2b997ef71e5c6e0db
Merge: d5d40a9 9a33d6a
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Sat Jan 30 09:57:31 2016 -0800
Merge tag 'upstream/0.6.0+ds1' into experimental
Upstream version 0.6.0+ds1
.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(-)
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