[med-svn] [salmon] branch upstream updated (64cc085 -> 668d9b7)

[Sascha Steinbiss]

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satta pushed a change to branch upstream
in repository salmon.

      from  64cc085   Imported Upstream version 0.7.1+ds1
       new  668d9b7   New upstream version 0.7.2+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:
 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(-)
 create mode 100644 scripts/build_docker_binary.sh

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