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tille pushed a commit to branch master
in repository rapmap.
commit ce74074ed6422541de1046ed5fdf3b407799bf45
Merge: 4a005ef 5fb69ea
Author: Andreas Tille <ti...@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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