[med-svn] [salmon] branch upstream updated (9a33d6a -> 64cc085)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository salmon.

      from  9a33d6a   Imported Upstream version 0.6.0+ds1
       new  8a4ec88   Imported Upstream version 0.7.1+ds1
       new  64cc085   Imported Upstream version 0.7.1+ds1

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:
 .clang-format                          |   94 +
 CMakeLists.txt                         |   55 +-
 README.md                              |   10 +-
 cmake/Modules/FindJellyfish.cmake      |   26 +
 cmake/PostInstall.cmake                |   12 +-
 doc/source/ReadLibraryIllustration.png |  Bin 43418 -> 169638 bytes
 doc/source/conf.py                     |   17 +-
 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                  |  373 ++-
 docker/Dockerfile                      |   28 +
 docker/build_test.sh                   |    2 +
 include/AlignmentLibrary.hpp           |  121 +-
 include/BAMQueue.tpp                   |   10 +-
 include/BiasParams.hpp                 |   43 +
 include/DistributionUtils.hpp          |   66 +
 include/FASTAParser.hpp                |    4 +-
 include/FastxParser.hpp                |  150 ++
 include/GCFragModel.hpp                |  181 ++
 include/GZipWriter.hpp                 |    5 +
 include/KmerContext.hpp                |   39 +
 include/LibraryFormat.hpp              |   70 +
 include/LibraryTypeDetector.hpp        |  153 ++
 include/LightweightAlignmentDefs.hpp   |   43 +-
 include/PairSequenceParser.hpp         |    2 +-
 include/ReadExperiment.hpp             |  276 ++-
 include/ReadKmerDist.hpp               |   89 +-
 include/ReadLibrary.hpp                |   62 +-
 include/ReadPair.hpp                   |   23 +-
 include/SBModel.hpp                    |   90 +
 include/SGSmooth.hpp                   |   13 +
 include/SalmonConfig.hpp               |    6 +-
 include/SalmonIndex.hpp                |  105 +-
 include/SalmonIndexVersionInfo.hpp     |    2 +-
 include/SalmonMath.hpp                 |    3 +
 include/SalmonOpts.hpp                 |   40 +
 include/SalmonUtils.hpp                |   82 +-
 include/Sampler.hpp                    |    8 +-
 include/SimplePosBias.hpp              |   43 +
 include/Transcript.hpp                 |  352 ++-
 include/TranscriptCluster.hpp          |    3 -
 include/TryableSpinLock.hpp            |   25 +
 include/UnpairedRead.hpp               |    4 +
 include/UtilityFunctions.hpp           |   68 +-
 include/blockingconcurrentqueue.h      |  639 +++--
 include/concurrentqueue.h              |  131 +-
 include/cuckoohash_config.hh           |    6 +
 include/cuckoohash_map.hh              | 1056 +++++----
 include/cuckoohash_util.hh             |  103 +-
 include/lazy_array.hh                  |  119 +
 include/make_unique.hpp                |   45 +
 include/spline.h                       |  404 ++++
 scripts/ConvertBootstrapsToTSV.py      |   95 +
 scripts/compile.sh                     |   36 +
 scripts/fetchRapMap.sh                 |    5 +-
 scripts/make-release.sh                |    2 +-
 scripts/runner.sh                      |   24 +
 src/BuildSalmonIndex.cpp               |   44 +-
 src/CMakeLists.txt                     |  126 +-
 src/CollapsedEMOptimizer.cpp           | 1697 +++++++-------
 src/CollapsedGibbsSampler.cpp          |    2 +-
 src/DistributionUtils.cpp              |   89 +
 src/FASTAParser.cpp                    |   16 +-
 src/FastxParser.cpp                    |  306 +++
 src/GZipWriter.cpp                     |  181 +-
 src/SBModel.cpp                        |  295 +++
 src/SGSmooth.cpp                       |  555 +++++
 src/Salmon.cpp                         |   30 +-
 src/SalmonQuantify.cpp                 | 3711 ++++++++++++++++-------------
 src/SalmonQuantifyAlignments.cpp       |  428 +++-
 src/SalmonUtils.cpp                    | 3969 +++++++++++++++++++++-----------
 src/SequenceBiasModel.cpp              |    3 +-
 src/SimplePosBias.cpp                  |   78 +
 src/merge_files.cc                     |  149 --
 tests/GCSampleTests.cpp                |   61 +
 tests/KmerHistTests.cpp                |   74 +-
 tests/UnitTests.cpp                    |    4 +-
 79 files changed, 12416 insertions(+), 5139 deletions(-)
 create mode 100644 .clang-format
 create mode 100644 cmake/Modules/FindJellyfish.cmake
 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
 create mode 100644 include/BiasParams.hpp
 create mode 100644 include/DistributionUtils.hpp
 create mode 100644 include/FastxParser.hpp
 create mode 100644 include/GCFragModel.hpp
 create mode 100644 include/KmerContext.hpp
 create mode 100644 include/LibraryTypeDetector.hpp
 create mode 100644 include/SBModel.hpp
 create mode 100644 include/SGSmooth.hpp
 create mode 100644 include/SimplePosBias.hpp
 create mode 100644 include/TryableSpinLock.hpp
 create mode 100644 include/lazy_array.hh
 create mode 100644 include/make_unique.hpp
 create mode 100644 include/spline.h
 create mode 100644 scripts/ConvertBootstrapsToTSV.py
 create mode 100644 scripts/compile.sh
 create mode 100644 scripts/runner.sh
 create mode 100644 src/DistributionUtils.cpp
 create mode 100644 src/FastxParser.cpp
 create mode 100644 src/SBModel.cpp
 create mode 100644 src/SGSmooth.cpp
 create mode 100644 src/SimplePosBias.cpp
 delete mode 100644 src/merge_files.cc
 create mode 100644 tests/GCSampleTests.cpp

-- 
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