[med-svn] [abyss] branch master updated (23461e6 -> b370367)
Andreas Tille
tille at debian.org
Thu Oct 6 04:57:17 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository abyss.
from 23461e6 Upload to unstable
new 95e61ae New upstream version 2.0.1
new 16cfa00 Merge tag 'upstream/2.0.1'
new c81a7a7 New upstream version now licensed under GPL-3
new 083895a Dropped GPL-NC-3+
new 822e1bf Adapt patches
new fc8378a Move package to main
new b370367 cme fix dpkg-control
The 7 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 | 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 ++
Konnector/DBGBloom.h => BloomDBG/RollingBloomDBG.h | 250 ++--
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 +-
debian/changelog | 8 +
debian/control | 7 +-
debian/copyright | 21 +-
debian/patches/privacy-breach.patch | 11 -
debian/patches/series | 1 -
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 +++++
81 files changed, 6833 insertions(+), 985 deletions(-)
create mode 100644 BloomDBG/HashAgnosticCascadingBloom.h
create mode 100644 BloomDBG/LightweightKmer.h
create mode 100644 BloomDBG/Makefile.am
create mode 100644 BloomDBG/MaskedKmer.h
copy Konnector/DBGBloom.h => BloomDBG/RollingBloomDBG.h (57%)
create mode 100644 BloomDBG/RollingHash.h
create mode 100644 BloomDBG/RollingHashIterator.h
create mode 100644 BloomDBG/SpacedSeed.h
create mode 100644 BloomDBG/bloom-dbg.cc
create mode 100644 BloomDBG/bloom-dbg.h
create mode 100644 Dockerfile
rename {Unittest => IntegrationTest}/Konnector/integration-tests.mk (94%)
create mode 100644 Konnector/README.md
delete mode 100644 README.css
create mode 100644 Unittest/BloomDBG/BloomDBGTest.cpp
create mode 100644 Unittest/BloomDBG/HashAgnosticCascadingBloomTest.cpp
create mode 100644 Unittest/BloomDBG/MaskedKmerTest.cpp
create mode 100644 Unittest/BloomDBG/RollingBloomDBGTest.cpp
create mode 100644 Unittest/BloomDBG/RollingHashIteratorTest.cpp
create mode 100644 Unittest/BloomDBG/RollingHashTest.cpp
create mode 100644 Unittest/BloomDBG/SpacedSeedTest.cpp
delete mode 100644 debian/patches/privacy-breach.patch
create mode 100644 lib/bloomfilter/BloomFilter.hpp
create mode 100644 lib/bloomfilter/Makefile.am
create mode 100644 lib/bloomfilter/README.md
create mode 100644 lib/rolling-hash/Makefile.am
create mode 100644 lib/rolling-hash/README.md
create mode 100644 lib/rolling-hash/rolling.h
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