[med-svn] [rapmap] 02/04: Merge tag 'upstream/0.4.0+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository rapmap.

commit ce74074ed6422541de1046ed5fdf3b407799bf45
Merge: 4a005ef 5fb69ea
Author: Andreas Tille <tille at debian.org>
Date:   Sat Oct 15 15:33:42 2016 +0200

    Merge tag 'upstream/0.4.0+dfsg'
    
    Upstream version 0.4.0+dfsg

 CMakeLists.txt                       |   58 +-
 License.md                           |  676 ++++
 README.md                            |   60 +
 include/BooMap.hpp                   |   60 +-
 include/BooPHF.hpp                   |   26 +-
 include/FastxParser.hpp              |  150 +
 include/FrugalBooMap.hpp             |  323 ++
 include/HitManager.hpp               |   22 +
 include/IndexHeader.hpp              |   21 +
 include/JFRaw.hpp                    |   21 +
 include/PairAlignmentFormatter.hpp   |   21 +
 include/RapMapConfig.hpp             |   27 +-
 include/RapMapFileSystem.hpp         |   21 +
 include/RapMapIndex.hpp              |   21 +
 include/RapMapSAIndex.hpp            |   25 +-
 include/RapMapUtils.hpp              |  144 +-
 include/SACollector.hpp              | 1283 ++++----
 include/SASearcher.hpp               |   21 +
 include/ScopedTimer.hpp              |   30 +-
 include/SingleAlignmentFormatter.hpp |   21 +
 include/SparseHashSerializer.hpp     |   51 +
 include/SpinLock.hpp                 |   21 +
 include/concurrentqueue.h            | 3621 ++++++++++++++++++++++
 include/sparsepp.h                   | 5622 ++++++++++++++++++++++++++++++++++
 scripts/RunRapMap.sh                 |   29 +
 scripts/add-header.sh                |   33 +
 scripts/compile.sh                   |    2 +-
 src/CMakeLists.txt                   |   50 +-
 src/FastxParser.cpp                  |  306 ++
 src/HitManager.cpp                   |   55 +-
 src/RapMap.cpp                       |   21 +
 src/RapMapFileSystem.cpp             |   21 +
 src/RapMapIndex.cpp                  |   21 +
 src/RapMapIndexer.cpp                |   58 +-
 src/RapMapMapper.cpp                 |  105 +-
 src/RapMapSAIndex.cpp                |  112 +-
 src/RapMapSAIndexer.cpp              |  177 +-
 src/RapMapSAMapper.cpp               |  371 ++-
 src/RapMapUtils.cpp                  |  176 +-
 39 files changed, 12822 insertions(+), 1061 deletions(-)

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