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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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