[med-svn] [salmon] 02/07: Merge tag 'upstream/0.8.0+ds1'

[Andreas Tille]

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tille pushed a commit to branch master
in repository salmon.

commit ab1af01017d7ceb917666790896ba6ffaf249d09
Merge: 393bd0a 993416c
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jan 24 09:45:37 2017 +0100

    Merge tag 'upstream/0.8.0+ds1'
    
    Upstream version 0.8.0+ds1

 .drone.yml                             |   26 +
 .drone.yml.sig                         |    1 +
 .drone/build.sh                        |   19 +
 .drone/copy_build.sh                   |   10 +
 .drone/test_quant.sh                   |   27 +
 CMakeLists.txt                         |  162 +-
 doc/source/salmon.rst                  |    8 +-
 include/AlignmentLibrary.hpp           |   96 +
 include/CollapsedGibbsSampler.hpp      |   11 +-
 include/EquivalenceClassBuilder.hpp    |    2 +-
 include/FragmentLengthDistribution.hpp |   11 +-
 include/GCFragModel.hpp                |  334 +--
 include/GZipWriter.hpp                 |    7 +-
 include/PartitionRefiner.hpp           |   42 -
 include/PerfectHashIndex.hpp           |  174 --
 include/ReadExperiment.hpp             |  132 +-
 include/ReadPair.hpp                   |    7 +-
 include/SailfishUtils.hpp              |  153 --
 include/SalmonConfig.hpp               |    9 +-
 include/SalmonIndex.hpp                |    9 +-
 include/SalmonOpts.hpp                 |   29 +-
 include/SalmonUtils.hpp                |    6 +-
 include/Sampler.hpp                    |   86 +-
 include/SimplePosBias.hpp              |    6 +
 include/Transcript.hpp                 |  101 +-
 include/TranscriptGeneMap.hpp          |   16 +-
 include/UnpairedRead.hpp               |    2 +-
 include/btree.h                        | 2394 ---------------------
 include/btree_container.h              |  350 ----
 include/btree_map.h                    |  130 --
 include/btree_set.h                    |  121 --
 include/concurrentqueue.h              |    4 +-
 include/count_main_cmdline.hpp         |  711 -------
 include/cuckoohash_config.hh           |   14 +-
 include/cuckoohash_map.hh              | 3572 ++++++++++++++++++--------------
 include/cuckoohash_util.hh             |   81 +-
 include/lazy_array.hh                  |  119 --
 include/libcuckoo_lazy_array.hh        |  202 ++
 include/merge_files.hpp                |   30 -
 include/pcg_extras.hpp                 |  638 ++++++
 include/pcg_random.hpp                 | 1756 ++++++++++++++++
 include/safe_btree.h                   |  395 ----
 include/safe_btree_map.h               |   89 -
 include/safe_btree_set.h               |   88 -
 scripts/ConvertBootstrapsToTSV.py      |    9 +-
 scripts/Dockerfile                     |   34 +
 scripts/fetchRapMap.sh                 |    4 +-
 scripts/make-release.sh                |    3 +
 scripts/test_sim_corr.py               |   48 +
 src/BuildSalmonIndex.cpp               |   14 +-
 src/CMakeLists.txt                     |   40 +-
 src/CollapsedEMOptimizer.cpp           |  227 +-
 src/CollapsedGibbsSampler.cpp          |  774 +++++--
 src/FASTAParser.cpp                    |   38 +-
 src/FragmentLengthDistribution.cpp     |   51 +-
 src/GZipWriter.cpp                     |  158 +-
 src/JellyfishMerCounter.cpp            |  379 ----
 src/LookUpTableUtils.cpp               |  255 ---
 src/SailfishUtils.cpp                  |  699 -------
 src/Salmon.cpp                         |  123 +-
 src/SalmonQuantify.cpp                 |  382 +++-
 src/SalmonQuantifyAlignments.cpp       |  213 +-
 src/SalmonUtils.cpp                    |  347 +++-
 src/SimplePosBias.cpp                  |   20 +-
 tests/test_quant.nf                    |   71 +
 65 files changed, 7508 insertions(+), 8561 deletions(-)

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