This is an automated email from the git hooks/post-receive script. 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rapmap.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit