[med-svn] [abyss] 02/07: Merge tag 'upstream/2.0.1'
Andreas Tille
tille at debian.org
Thu Oct 6 04:57:21 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository abyss.
commit 16cfa0050c4855d6ffe4f84356181c2a812eee66
Merge: 23461e6 95e61ae
Author: Andreas Tille <tille at debian.org>
Date: Thu Oct 6 06:40:38 2016 +0200
Merge tag 'upstream/2.0.1'
Upstream version 2.0.1
.gitignore | 12 +-
Assembly/Options.cc | 8 +-
Bloom/Bloom.h | 10 +-
Bloom/BloomFilter.h | 21 +-
Bloom/BloomFilterWindow.h | 21 +-
Bloom/CascadingBloomFilter.h | 9 +-
Bloom/CascadingBloomFilterWindow.h | 14 +-
Bloom/ConcurrentBloomFilter.h | 10 +-
Bloom/bloom.cc | 470 ++++++-
BloomDBG/HashAgnosticCascadingBloom.h | 145 +++
BloomDBG/LightweightKmer.h | 96 ++
BloomDBG/Makefile.am | 23 +
BloomDBG/MaskedKmer.h | 121 ++
BloomDBG/RollingBloomDBG.h | 486 ++++++++
BloomDBG/RollingHash.h | 289 +++++
BloomDBG/RollingHashIterator.h | 234 ++++
BloomDBG/SpacedSeed.h | 79 ++
BloomDBG/bloom-dbg.cc | 345 ++++++
BloomDBG/bloom-dbg.h | 1276 ++++++++++++++++++++
COPYRIGHT | 84 +-
ChangeLog | 57 +
Common/Kmer.h | 8 +-
Common/Sequence.h | 9 +-
DataBase/Makefile.am | 3 +
DataBase/db-csv.cc | 3 +-
DataLayer/fac.cc | 27 +-
Dockerfile | 20 +
Graph/BreadthFirstSearch.h | 3 +
Graph/ExtendPath.h | 482 ++++++--
Graph/Path.h | 13 +
.../Konnector/integration-tests.mk | 24 +-
Konnector/DBGBloomAlgorithms.h | 11 +-
Konnector/README.md | 176 +++
Konnector/konnector.cc | 690 +++++++----
Konnector/konnector.h | 239 +++-
LICENSE | 22 +-
LogKmerCount/CountingBloomFilter.h | 4 +-
LogKmerCount/plc.h | 6 +-
Makefile.am | 15 +-
ParseAligns/abyss-fixmate.cc | 1 -
README.css | 39 -
README.md | 156 +--
Scaffold/drawgraph.cc | 2 +-
Scaffold/scaffold.cc | 21 +-
Sealer/Makefile.am | 2 +-
Sealer/README.md | 16 +-
Sealer/sealer.cc | 92 +-
SimpleGraph/SimpleGraph.cpp | 2 +-
Unittest/BloomDBG/BloomDBGTest.cpp | 155 +++
.../BloomDBG/HashAgnosticCascadingBloomTest.cpp | 46 +
Unittest/BloomDBG/MaskedKmerTest.cpp | 26 +
Unittest/BloomDBG/RollingBloomDBGTest.cpp | 275 +++++
Unittest/BloomDBG/RollingHashIteratorTest.cpp | 116 ++
Unittest/BloomDBG/RollingHashTest.cpp | 195 +++
Unittest/BloomDBG/SpacedSeedTest.cpp | 26 +
Unittest/Graph/ExtendPathTest.cpp | 98 +-
Unittest/Makefile.am | 191 +--
bin/abyss-adjtodot.pl | 2 +-
bin/abyss-cstont | 2 +-
bin/abyss-dida | 2 +-
bin/abyss-fac.pl | 2 +-
bin/abyss-fatoagp | 23 +-
bin/abyss-joindist | 2 +-
bin/abyss-pe | 123 +-
bin/abyss-samtoafg | 2 +-
configure.ac | 29 +-
doc/ABYSS.1 | 2 +-
doc/abyss-pe.1 | 19 +-
doc/abyss-tofastq.1 | 2 +-
doc/flowchart.graffle | 2 +-
lib/bloomfilter/BloomFilter.hpp | 446 +++++++
lib/bloomfilter/Makefile.am | 1 +
lib/bloomfilter/README.md | 4 +
lib/rolling-hash/Makefile.am | 1 +
lib/rolling-hash/README.md | 2 +
lib/rolling-hash/rolling.h | 316 +++++
76 files changed, 7156 insertions(+), 850 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/abyss.git
More information about the debian-med-commit
mailing list