[med-svn] [minia] branch master updated (6d8f7b6 -> 3aa0f54)
Andreas Tille
tille at debian.org
Fri Dec 1 09:06:58 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository minia.
from 6d8f7b6 Upload to unstable
adds 3b71a25 Switch from legacy version to version 2.x at GibHub
adds ff0272f New upstream version 2.0.7
adds 319dd30 Updated version 2.0.7 from 'upstream/2.0.7'
adds 331ffe9 Build system is changed so old patches are useless
adds 3df5410 Needs packaging of https://github.com/GATB/gatb-core
new 2dc0368 Merge branch 'minia2'
new 3aa0f54 Packaging of gatb-core in progress
The 2 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 | 10 +
debian/control | 4 +-
debian/patches/add_hardening | 34 -
debian/patches/series | 1 -
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 -----
73 files changed, 1786 insertions(+), 43946 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
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