[med-svn] [rapmap] 02/03: Update upstream source from tag 'upstream/0.5.0+dfsg'

[Steffen Möller]

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moeller pushed a commit to branch master
in repository rapmap.

commit e25c54f977cc37ed3de003c70e41a7c85c8992f7
Merge: 0f47d9f b8057c0
Author: Steffen Moeller <moeller at debian.org>
Date:   Sun Oct 22 21:12:18 2017 +0200

    Update upstream source from tag 'upstream/0.5.0+dfsg'
    
    Update to upstream version '0.5.0+dfsg'
    with Debian dir 2d16cc0d6994f524da9682a43cb9579718e31480

 .drone.yml                             |    26 +
 .drone.yml.sig                         |     1 +
 .drone/build.sh                        |    20 +
 .drone/copy_build.sh                   |    10 +
 .drone/test_map.sh                     |    27 +
 CMakeLists.txt                         |    41 +-
 README.md                              |    24 +-
 cmake/TestQuasiMap.cmake               |    24 +
 cmake/TestQuasiMapPerfectHash.cmake    |    24 +
 include/IndexHeader.hpp                |    13 +
 include/RapMapConfig.hpp               |     4 +-
 include/RapMapSAIndex.hpp              |     1 +
 include/RapMapUtils.hpp                |     5 +-
 include/SACollector.hpp                |     2 +-
 include/SparseHashSerializer.hpp       |     2 +-
 include/concurrentqueue.h              |     2 +-
 include/kseq.h                         |   218 +-
 include/picosha2.h                     |   359 +
 include/{sparsepp.h => sparsepp/spp.h} |  2787 +--
 include/sparsepp/spp_alloc.h           |   830 +
 include/sparsepp/spp_bitset.h          |   700 +
 include/sparsepp/spp_btree.h           |  2211 ++
 include/sparsepp/spp_config.h          |   760 +
 include/sparsepp/spp_memory.h          |   121 +
 include/sparsepp/spp_smartptr.h        |    56 +
 include/sparsepp/spp_stdint.h          |    16 +
 include/sparsepp/spp_timer.h           |    58 +
 include/sparsepp/spp_traits.h          |   122 +
 include/sparsepp/spp_utils.h           |   441 +
 sample_data/reads_1.fastq              | 40000 +++++++++++++++++++++++++++++++
 sample_data/reads_2.fastq              | 40000 +++++++++++++++++++++++++++++++
 sample_data/transcripts.fasta          |   498 +
 scripts/Dockerfile                     |    22 +
 scripts/make-release.sh                |    22 +-
 src/CMakeLists.txt                     |    12 +-
 src/RapMapSAIndex.cpp                  |     3 +-
 src/RapMapSAIndexer.cpp                |    65 +-
 src/RapMapSAMapper.cpp                 |     6 +-
 38 files changed, 87378 insertions(+), 2155 deletions(-)

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