[med-svn] [salmon] branch master updated (7e3465a -> 723622f)

[Sascha Steinbiss]

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

satta pushed a change to branch master
in repository salmon.

      from  7e3465a   update d/copyright for embedded RapMap source
       new  668d9b7   New upstream version 0.7.2+ds1
       new  0360e1c   Merge tag 'upstream/0.7.2+ds1'
       new  5ea5fb8   new upstream version
       new  9af2d25   new upstream version
       new  b36d1b0   remove unnecessary build-dep on rapmap
       new  e86b7e7   bump Standards-Version
       new  371eeb4   add patch header
       new  150bee8   drop obsolete override
       new  e7df800   adjust d/changelog
       new  1577dd2   enable bindnow hardening
       new  723622f   add patch header

The 11 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 +-
 debian/changelog                                |  12 +-
 debian/control                                  |   5 +-
 debian/lintian-overrides                        |   1 -
 debian/patches/add_MEM_F_SELF_OVLP.patch        |   4 +-
 debian/patches/cmake-typo-fixes                 |   2 +-
 debian/patches/dependency-fix                   |  28 +-
 debian/patches/disable-version-check            |   2 +-
 debian/patches/fix-unittest.patch               |   4 +-
 debian/patches/use_debian_packaged_rapmap.patch |  14 +-
 debian/rapmap/BooPHF.hpp                        |  24 +-
 debian/rapmap/PairAlignmentFormatter.hpp        |  29 ++
 debian/rapmap/RapMapSAIndex.hpp                 |   4 +-
 debian/rapmap/RapMapSAIndexer.cpp               |  66 +--
 debian/rapmap/RapMapUtils.cpp                   | 584 ++++++++++++++++++++++++
 debian/rapmap/RapMapUtils.hpp                   |  33 +-
 debian/rapmap/SingleAlignmentFormatter.hpp      |  22 +
 debian/rules                                    |  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 ++++-
 40 files changed, 1769 insertions(+), 220 deletions(-)
 delete mode 100644 debian/lintian-overrides
 create mode 100644 debian/rapmap/PairAlignmentFormatter.hpp
 create mode 100644 debian/rapmap/RapMapUtils.cpp
 create mode 100644 debian/rapmap/SingleAlignmentFormatter.hpp
 create mode 100644 scripts/build_docker_binary.sh

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