[med-svn] [rapmap] branch master updated (4a005ef -> 0dc5b71)

[Andreas Tille]

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tille pushed a change to branch master
in repository rapmap.

      from  4a005ef   ITP + upload to new
       new  5fb69ea   New upstream version 0.4.0+dfsg
       new  ce74074   Merge tag 'upstream/0.4.0+dfsg'
       new  a941d4b   New upstream version
       new  0dc5b71   Adapt patches

The 4 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 +
 debian/changelog                     |    6 +
 debian/patches/use-debian-libs.patch |  165 +-
 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 +-
 41 files changed, 12838 insertions(+), 1216 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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