[med-svn] [salmon] branch upstream updated (668d9b7 -> 993416c)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository salmon.

      from  668d9b7   New upstream version 0.7.2+ds1
       new  993416c   New upstream version 0.8.0+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:
 .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(-)
 create mode 100644 .drone.yml
 create mode 100644 .drone.yml.sig
 create mode 100755 .drone/build.sh
 create mode 100755 .drone/copy_build.sh
 create mode 100755 .drone/test_quant.sh
 delete mode 100644 include/PartitionRefiner.hpp
 delete mode 100644 include/PerfectHashIndex.hpp
 delete mode 100644 include/SailfishUtils.hpp
 delete mode 100755 include/btree.h
 delete mode 100755 include/btree_container.h
 delete mode 100755 include/btree_map.h
 delete mode 100755 include/btree_set.h
 delete mode 100644 include/count_main_cmdline.hpp
 delete mode 100644 include/lazy_array.hh
 create mode 100644 include/libcuckoo_lazy_array.hh
 delete mode 100644 include/merge_files.hpp
 create mode 100644 include/pcg_extras.hpp
 create mode 100644 include/pcg_random.hpp
 delete mode 100755 include/safe_btree.h
 delete mode 100755 include/safe_btree_map.h
 delete mode 100755 include/safe_btree_set.h
 create mode 100644 scripts/Dockerfile
 create mode 100644 scripts/test_sim_corr.py
 delete mode 100644 src/JellyfishMerCounter.cpp
 delete mode 100644 src/LookUpTableUtils.cpp
 delete mode 100644 src/SailfishUtils.cpp
 create mode 100644 tests/test_quant.nf

-- 
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