[med-svn] [rapmap] branch upstream updated (b8d1725 -> 5fb69ea)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository rapmap.

      from  b8d1725   Imported Upstream version 0.3.0+dfsg
       new  5fb69ea   New upstream version 0.4.0+dfsg

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                       |   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(-)
 create mode 100644 License.md
 create mode 100644 include/FastxParser.hpp
 create mode 100644 include/FrugalBooMap.hpp
 create mode 100644 include/SparseHashSerializer.hpp
 create mode 100644 include/concurrentqueue.h
 create mode 100644 include/sparsepp.h
 create mode 100755 scripts/RunRapMap.sh
 create mode 100644 scripts/add-header.sh
 create mode 100644 src/FastxParser.cpp

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