[med-svn] [salmon] 02/11: Merge tag 'upstream/0.7.2+ds1'

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository salmon.

commit 0360e1cf94a0f65763240a5dc498f30afc3485c3
Merge: 7e3465a 668d9b7
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sat Sep 10 11:46:58 2016 +0000

    Merge tag 'upstream/0.7.2+ds1'
    
    Upstream version 0.7.2+ds1

 CMakeLists.txt                   |  18 +-
 doc/source/conf.py               |   4 +-
 doc/source/file_formats.rst      |  18 ++
 doc/source/salmon.rst            |  43 +++++
 include/AlignmentLibrary.hpp     |  20 ++
 include/LibraryFormat.hpp        |  21 +-
 include/LibraryTypeDetector.hpp  |   2 +
 include/ReadExperiment.hpp       |  30 ---
 include/SalmonConfig.hpp         |   4 +-
 include/SalmonOpts.hpp           |   9 +
 include/SalmonUtils.hpp          |   3 +
 include/atomicops.h              | 402 ++++++++++++++++++++++++++++++++++++++-
 include/concurrentqueue.h        |   2 +-
 include/readerwriterqueue.h      | 207 ++++++++++++++++++--
 scripts/build_docker_binary.sh   |   5 +
 scripts/fetchRapMap.sh           |   7 +-
 src/BuildSalmonIndex.cpp         |   4 +-
 src/CMakeLists.txt               |   2 +-
 src/GZipWriter.cpp               |  16 +-
 src/Salmon.cpp                   |   2 -
 src/SalmonQuantify.cpp           | 137 +++++++++++--
 src/SalmonQuantifyAlignments.cpp |  75 ++++++--
 src/SalmonUtils.cpp              | 106 ++++++++++-
 23 files changed, 1009 insertions(+), 128 deletions(-)

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