[med-svn] [salmon] branch master updated (6605466 -> 4b16494)

[Sascha Steinbiss]

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satta pushed a change to branch master
in repository salmon.

      from  6605466   use Debian's libdivsufsort and libsparsehash
       new  cf2b888   add patch again
       new  4b16494   fix building

The 2 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
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Summary of changes:
 debian/control                                     |    3 +
 ...007-Remove-unnecessarily-linked-libraries.patch |    8 +-
 debian/patches/0008-Remove-salmon_core-lib.patch   |   19 +-
 ...emove-FIND_PACKAGE-for-liblzma-and-libbz2.patch |    2 +-
 debian/patches/add_MEM_F_SELF_OVLP.patch           |   23 +
 debian/patches/cmake-typo-fixes                    |    2 +-
 debian/patches/dependency-fix                      |   51 +-
 debian/patches/series                              |    1 +
 debian/patches/use_debian_packaged_rapmap.patch    |   28 +
 debian/rapmap/BooMap.hpp                           |  193 ++
 debian/rapmap/BooPHF.hpp                           | 1221 ++++++++
 debian/rapmap/HitManager.cpp                       |  700 +++++
 debian/rapmap/HitManager.hpp                       |  109 +
 debian/rapmap/IndexHeader.hpp                      |   77 +
 debian/rapmap/JFRaw.hpp                            |   30 +
 debian/rapmap/RapMapConfig.hpp                     |   14 +
 debian/rapmap/RapMapFileSystem.cpp                 |   37 +
 debian/rapmap/RapMapFileSystem.hpp                 |   15 +
 debian/rapmap/RapMapIndex.hpp                      |   52 +
 debian/rapmap/RapMapSAIndex.cpp                    |  177 ++
 debian/rapmap/RapMapSAIndex.hpp                    |   63 +
 debian/rapmap/RapMapSAIndexer.cpp                  |  731 +++++
 debian/rapmap/RapMapUtils.hpp                      |  825 +++++
 debian/rapmap/SACollector.hpp                      |  580 ++++
 debian/rapmap/SASearcher.hpp                       |  631 ++++
 debian/rapmap/ScopedTimer.hpp                      |   22 +
 .../rapmap/SpinLock.hpp                            |    8 +-
 debian/rapmap/bit_array.c                          | 3160 ++++++++++++++++++++
 debian/rapmap/bit_array.h                          |  552 ++++
 debian/rapmap/bit_macros.h                         |  205 ++
 debian/rapmap/kseq.h                               |  235 ++
 debian/rapmap/macros.h                             |   59 +
 debian/rapmap/rank9b.cpp                           |   67 +
 debian/rapmap/rank9b.h                             |   42 +
 debian/rules                                       |   39 +
 35 files changed, 9960 insertions(+), 21 deletions(-)
 create mode 100644 debian/patches/add_MEM_F_SELF_OVLP.patch
 create mode 100644 debian/rapmap/BooMap.hpp
 create mode 100644 debian/rapmap/BooPHF.hpp
 create mode 100644 debian/rapmap/HitManager.cpp
 create mode 100644 debian/rapmap/HitManager.hpp
 create mode 100644 debian/rapmap/IndexHeader.hpp
 create mode 100644 debian/rapmap/JFRaw.hpp
 create mode 100644 debian/rapmap/RapMapConfig.hpp
 create mode 100644 debian/rapmap/RapMapFileSystem.cpp
 create mode 100644 debian/rapmap/RapMapFileSystem.hpp
 create mode 100644 debian/rapmap/RapMapIndex.hpp
 create mode 100644 debian/rapmap/RapMapSAIndex.cpp
 create mode 100644 debian/rapmap/RapMapSAIndex.hpp
 create mode 100644 debian/rapmap/RapMapSAIndexer.cpp
 create mode 100644 debian/rapmap/RapMapUtils.hpp
 create mode 100644 debian/rapmap/SACollector.hpp
 create mode 100644 debian/rapmap/SASearcher.hpp
 create mode 100644 debian/rapmap/ScopedTimer.hpp
 copy include/TryableSpinLock.hpp => debian/rapmap/SpinLock.hpp (83%)
 create mode 100644 debian/rapmap/bit_array.c
 create mode 100644 debian/rapmap/bit_array.h
 create mode 100644 debian/rapmap/bit_macros.h
 create mode 100644 debian/rapmap/kseq.h
 create mode 100644 debian/rapmap/macros.h
 create mode 100644 debian/rapmap/rank9b.cpp
 create mode 100644 debian/rapmap/rank9b.h

-- 
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