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from 9ed5cb4 Upload to unstable new 3b71a25 Switch from legacy version to version 2.x at GibHub new ff0272f New upstream version 2.0.7 new 319dd30 Updated version 2.0.7 from 'upstream/2.0.7' new 331ffe9 Build system is changed so old patches are useless new 3df5410 Needs packaging of https://github.com/GATB/gatb-core The 5 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: .gitignore | 1 + .gitmodules | 3 + Bank.cpp | 1087 ----- Bank.h | 200 - Bloom.cpp | 474 -- Bloom.h | 248 - CMakeLists.txt | 119 + Debloom.cpp | 466 -- Debloom.h | 45 - GraphOutput.cpp | 380 -- GraphOutput.h | 204 - Hash16.cpp | 404 -- Hash16.h | 95 - Hashing.cpp | 42 - Hashing.h | 31 - INSTALL | 20 + Kmer.cpp | 373 -- Kmer.h | 84 - LICENSE | 1175 +++-- LargeInt.cpp | 277 -- LargeInt.h | 48 - LinearCounter.cpp | 47 - LinearCounter.h | 29 - Minia.cpp | 351 -- MultiConsumer.cpp | 144 - MultiConsumer.h | 86 - OAHash.cpp | 212 - OAHash.h | 77 - Pool.cpp | 156 - Pool.h | 92 - README | 18 - README.md | 38 + Set.cpp | 305 -- Set.h | 158 - SortingCount.cpp | 847 ---- SortingCount.h | 27 - Terminator.cpp | 410 -- Terminator.h | 79 - Traversal.cpp | 955 ---- Traversal.h | 168 - Utils.cpp | 647 --- Utils.h | 103 - debian/changelog | 9 + debian/control | 4 +- debian/patches/add_hardening | 34 - debian/patches/series | 1 - debian/watch | 4 +- doc/CMakeLists.txt | 13 + doc/manual.tex | 142 + lut.h | 272 -- makefile | 76 - manual/manual.pdf | Bin 1155669 -> 0 bytes manual/manual.tex | 124 - rvalues.h | 131 - simple_test.sh | 20 - src/Minia.cpp | 296 ++ src/Minia.hpp | 61 + src/NodeSelector.cpp | 244 + src/NodeSelector.hpp | 125 + src/main.cpp | 50 + test/read50x_ref10K_e001.fasta | 10000 --------------------------------------- test/result10K.fasta | 2 - ttmath/ttmath.h | 2849 ----------- ttmath/ttmathbig.h | 6061 ------------------------ ttmath/ttmathint.h | 1924 -------- ttmath/ttmathmisc.h | 250 - ttmath/ttmathobjects.h | 809 ---- ttmath/ttmathparser.h | 2765 ----------- ttmath/ttmaththreads.h | 250 - ttmath/ttmathtypes.h | 667 --- ttmath/ttmathuint.h | 4062 ---------------- ttmath/ttmathuint_noasm.h | 1017 ---- ttmath/ttmathuint_x86.h | 1602 ------- ttmath/ttmathuint_x86_64.h | 1146 ----- 74 files changed, 1787 insertions(+), 43948 deletions(-) create mode 100644 .gitignore create mode 100644 .gitmodules delete mode 100644 Bank.cpp delete mode 100644 Bank.h delete mode 100644 Bloom.cpp delete mode 100644 Bloom.h create mode 100644 CMakeLists.txt delete mode 100644 Debloom.cpp delete mode 100644 Debloom.h delete mode 100644 GraphOutput.cpp delete mode 100644 GraphOutput.h delete mode 100644 Hash16.cpp delete mode 100644 Hash16.h delete mode 100644 Hashing.cpp delete mode 100644 Hashing.h create mode 100644 INSTALL delete mode 100644 Kmer.cpp delete mode 100644 Kmer.h delete mode 100644 LargeInt.cpp delete mode 100644 LargeInt.h delete mode 100644 LinearCounter.cpp delete mode 100644 LinearCounter.h delete mode 100644 Minia.cpp delete mode 100644 MultiConsumer.cpp delete mode 100644 MultiConsumer.h delete mode 100644 OAHash.cpp delete mode 100644 OAHash.h delete mode 100644 Pool.cpp delete mode 100644 Pool.h delete mode 100644 README create mode 100644 README.md delete mode 100644 Set.cpp delete mode 100644 Set.h delete mode 100644 SortingCount.cpp delete mode 100644 SortingCount.h delete mode 100644 Terminator.cpp delete mode 100644 Terminator.h delete mode 100644 Traversal.cpp delete mode 100644 Traversal.h delete mode 100644 Utils.cpp delete mode 100644 Utils.h delete mode 100644 debian/patches/add_hardening delete mode 100644 debian/patches/series create mode 100644 doc/CMakeLists.txt create mode 100644 doc/manual.tex delete mode 100644 lut.h delete mode 100644 makefile delete mode 100644 manual/manual.pdf delete mode 100644 manual/manual.tex delete mode 100644 rvalues.h delete mode 100644 simple_test.sh create mode 100644 src/Minia.cpp create mode 100644 src/Minia.hpp create mode 100644 src/NodeSelector.cpp create mode 100644 src/NodeSelector.hpp create mode 100644 src/main.cpp delete mode 100644 test/read50x_ref10K_e001.fasta delete mode 100644 test/result10K.fasta delete mode 100644 ttmath/ttmath.h delete mode 100644 ttmath/ttmathbig.h delete mode 100644 ttmath/ttmathint.h delete mode 100644 ttmath/ttmathmisc.h delete mode 100644 ttmath/ttmathobjects.h delete mode 100644 ttmath/ttmathparser.h delete mode 100644 ttmath/ttmaththreads.h delete mode 100644 ttmath/ttmathtypes.h delete mode 100644 ttmath/ttmathuint.h delete mode 100644 ttmath/ttmathuint_noasm.h delete mode 100644 ttmath/ttmathuint_x86.h delete mode 100644 ttmath/ttmathuint_x86_64.h -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/minia.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