[med-svn] [salmon] branch master updated (049710b -> 9993249)
Andreas Tille
tille at debian.org
Tue Aug 30 10:12:29 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository salmon.
from 049710b Drop note that we can not set better hardening
new a9ee4aa Use xz compression
adds 9a33d6a Imported Upstream version 0.6.0+ds1
new 8a4ec88 Imported Upstream version 0.7.1+ds1
new c6c13cb Merge tag 'upstream/0.7.1+ds1'
new 0954b5d Try to adapt patches to new upstream version. PLEASE VERIFY!!!
new 0b3e8f3 New upstream version
new 64cc085 Imported Upstream version 0.7.1+ds1
new 18888b1 Merge tag 'upstream/0.7.1+ds1'
new 6a5bda8 Revert commit of patched files
new 9993249 TODO: package https://github.com/COMBINE-lab/RapMap
The 9 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:
.clang-format | 94 +
.gitignore | 3 +
CMakeLists.txt | 195 +-
README.md | 12 +-
cmake/Modules/FindJellyfish.cmake | 26 +
cmake/PostInstall.cmake | 12 +-
cmake/TestSalmon.cmake | 35 -
cmake/TestSalmonFMD.cmake | 33 +
cmake/TestSalmonQuasi.cmake | 24 +
cmake/UnitTests.cmake | 10 +
debian/changelog | 9 +
...007-Remove-unnecessarily-linked-libraries.patch | 34 +-
debian/patches/0008-Remove-salmon_core-lib.patch | 22 +-
...emove-FIND_PACKAGE-for-liblzma-and-libbz2.patch | 109 +-
debian/patches/add_MEM_F_SELF_OVLP.patch | 15 -
debian/patches/cmake-adj | 23 -
debian/patches/cmake-typo-fixes | 72 +-
debian/patches/dependency-fix | 225 +-
debian/patches/disable-version-check | 8 +-
debian/patches/drop-mathjax | 12 -
debian/patches/jellyfish-update | 106 -
debian/patches/reproducible-build | 22 -
debian/patches/series | 5 -
debian/patches/use-system-pkg-config-tbb | 10 +-
debian/rules | 3 -
debian/watch | 2 +-
doc/source/ReadLibraryIllustration.png | Bin 43418 -> 169638 bytes
doc/source/conf.py | 18 +-
doc/source/file_formats.rst | 182 +
doc/source/index.rst | 1 +
doc/source/library_type.rst | 2 +-
doc/source/sailfish.rst | 89 -
doc/source/salmon.rst | 500 +-
docker/Dockerfile | 28 +
docker/build_test.sh | 2 +
external/.gitignore | 28 -
include/AlignmentGroup.hpp | 2 +-
include/AlignmentLibrary.hpp | 167 +-
include/BAMQueue.hpp | 9 +-
include/BAMQueue.tpp | 33 +-
include/BWAMemStaticFuncs.hpp | 120 +
include/BWAUtils.hpp | 34 +
include/BiasParams.hpp | 43 +
include/BootstrapWriter.hpp | 15 +
include/ClusterForest.hpp | 5 +-
include/CollapsedEMOptimizer.hpp | 11 +
include/CollapsedGibbsSampler.hpp | 5 +-
include/DistributionUtils.hpp | 66 +
include/EquivalenceClassBuilder.hpp | 94 +-
include/FASTAParser.hpp | 4 +-
include/FastxParser.hpp | 150 +
include/ForgettingMassCalculator.hpp | 2 +-
include/FragmentLengthDistribution.hpp | 9 +
include/FragmentStartPositionDistribution.hpp | 25 +-
include/GCFragModel.hpp | 181 +
include/GZipWriter.hpp | 57 +
include/IndexVersionInfo.hpp | 11 +
include/KmerContext.hpp | 39 +
include/KmerIntervalMap.hpp | 131 +
include/LibraryFormat.hpp | 84 +-
include/LibraryTypeDetector.hpp | 153 +
include/LightweightAlignmentDefs.hpp | 1497 ++++
include/MultinomialSampler.hpp | 104 +-
include/PCA.hpp | 8 +-
include/PairSequenceParser.hpp | 12 +-
include/ReadExperiment.hpp | 507 +-
include/ReadKmerDist.hpp | 79 +
include/ReadLibrary.hpp | 66 +-
include/ReadPair.hpp | 46 +-
include/SBModel.hpp | 90 +
include/SGSmooth.hpp | 13 +
include/SalmonConfig.hpp | 7 +-
include/SalmonIndex.hpp | 364 +
include/SalmonIndexVersionInfo.hpp | 80 +
include/SalmonMath.hpp | 31 +
include/SalmonOpts.hpp | 73 +-
include/{SpinLock.hpp => SalmonSpinLock.hpp} | 6 +-
include/SalmonUtils.hpp | 110 +-
include/Sampler.hpp | 39 +-
include/SimplePosBias.hpp | 43 +
include/TextBootstrapWriter.hpp | 101 +
include/Transcript.hpp | 402 +-
include/TranscriptCluster.hpp | 5 +-
include/TryableSpinLock.hpp | 25 +
include/UnpairedRead.hpp | 14 +
include/UtilityFunctions.hpp | 160 +
include/blockingconcurrentqueue.h | 981 ++
include/concurrentqueue.h | 1236 ++-
include/cuckoohash_config.h | 16 -
include/cuckoohash_config.hh | 34 +
include/cuckoohash_map.hh | 2652 +++---
include/cuckoohash_util.h | 23 -
include/cuckoohash_util.hh | 177 +
include/default_hasher.hh | 29 +
include/kseq.h | 235 -
include/lazy_array.hh | 119 +
include/make_unique.hpp | 45 +
include/posix.h | 344 -
include/spline.h | 404 +
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/ConvertBootstrapsToTSV.py | 95 +
scripts/compile.sh | 36 +
scripts/cpld.bash | 35 -
scripts/fetchRapMap.sh | 37 +
scripts/make-release.sh | 2 +-
scripts/runner.sh | 24 +
src/BWAUtils.cpp | 146 +
src/BiasCorrectionDriver.cpp | 52 -
src/BuildSalmonIndex.cpp | 237 +-
src/CMakeLists.txt | 239 +-
src/CollapsedEMOptimizer.cpp | 1280 ++-
src/CollapsedGibbsSampler.cpp | 229 +-
src/ComputeBiasFeatures.cpp | 225 -
src/DistributionUtils.cpp | 89 +
src/FASTAParser.cpp | 40 +-
src/FastxParser.cpp | 306 +
src/FragmentLengthDistribution.cpp | 23 +-
src/FragmentStartPositionDistribution.cpp | 128 +-
src/GZipWriter.cpp | 424 +
src/PerformBiasCorrection.cpp | 349 -
src/PerformBiasCorrection_old.cpp | 420 -
src/SBModel.cpp | 295 +
src/SGSmooth.cpp | 555 ++
src/Salmon.cpp | 32 +-
src/SalmonQuantify.cpp | 5174 +++++------
src/SalmonQuantifyAlignments.cpp | 986 +-
src/SalmonUtils.cpp | 3845 +++++---
src/SequenceBiasModel.cpp | 3 +-
src/SimplePosBias.cpp | 78 +
src/TranscriptGroup.cpp | 7 +-
src/cokus.cpp | 196 -
src/merge_files.cc | 149 -
src/posix.cc | 252 -
src/xxhash.c | 915 ++
tests/GCSampleTests.cpp | 61 +
tests/KmerHistTests.cpp | 137 +
tests/LibraryTypeTests.cpp | 166 +
tests/UnitTests.cpp | 13 +
tests/catch.hpp | 9416 ++++++++++++++++++++
160 files changed, 30250 insertions(+), 15170 deletions(-)
create mode 100644 .clang-format
create mode 100644 cmake/Modules/FindJellyfish.cmake
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 debian/patches/add_MEM_F_SELF_OVLP.patch
delete mode 100644 debian/patches/cmake-adj
delete mode 100644 debian/patches/drop-mathjax
delete mode 100644 debian/patches/jellyfish-update
delete mode 100644 debian/patches/reproducible-build
create mode 100644 doc/source/file_formats.rst
delete mode 100644 doc/source/sailfish.rst
create mode 100644 docker/Dockerfile
create mode 100644 docker/build_test.sh
delete mode 100644 external/.gitignore
create mode 100644 include/BWAMemStaticFuncs.hpp
create mode 100644 include/BWAUtils.hpp
create mode 100644 include/BiasParams.hpp
create mode 100644 include/BootstrapWriter.hpp
create mode 100644 include/DistributionUtils.hpp
create mode 100644 include/FastxParser.hpp
create mode 100644 include/GCFragModel.hpp
create mode 100644 include/GZipWriter.hpp
create mode 100644 include/IndexVersionInfo.hpp
create mode 100644 include/KmerContext.hpp
create mode 100644 include/KmerIntervalMap.hpp
create mode 100644 include/LibraryTypeDetector.hpp
create mode 100644 include/LightweightAlignmentDefs.hpp
create mode 100644 include/ReadKmerDist.hpp
create mode 100644 include/SBModel.hpp
create mode 100644 include/SGSmooth.hpp
create mode 100644 include/SalmonIndex.hpp
create mode 100644 include/SalmonIndexVersionInfo.hpp
rename include/{SpinLock.hpp => SalmonSpinLock.hpp} (88%)
create mode 100644 include/SimplePosBias.hpp
create mode 100644 include/TextBootstrapWriter.hpp
create mode 100644 include/TryableSpinLock.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
create mode 100644 include/lazy_array.hh
create mode 100644 include/make_unique.hpp
delete mode 100644 include/posix.h
create mode 100644 include/spline.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
create mode 100644 scripts/ConvertBootstrapsToTSV.py
create mode 100644 scripts/compile.sh
delete mode 100755 scripts/cpld.bash
create mode 100755 scripts/fetchRapMap.sh
create mode 100644 scripts/runner.sh
create mode 100644 src/BWAUtils.cpp
delete mode 100644 src/BiasCorrectionDriver.cpp
delete mode 100644 src/ComputeBiasFeatures.cpp
create mode 100644 src/DistributionUtils.cpp
create mode 100644 src/FastxParser.cpp
create mode 100644 src/GZipWriter.cpp
delete mode 100644 src/PerformBiasCorrection.cpp
delete mode 100644 src/PerformBiasCorrection_old.cpp
create mode 100644 src/SBModel.cpp
create mode 100644 src/SGSmooth.cpp
create mode 100644 src/SimplePosBias.cpp
delete mode 100755 src/cokus.cpp
delete mode 100644 src/merge_files.cc
delete mode 100644 src/posix.cc
create mode 100644 src/xxhash.c
create mode 100644 tests/GCSampleTests.cpp
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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