[med-svn] [abyss] branch upstream updated (ca88ee1 -> 95e61ae)
Andreas Tille
tille at debian.org
Thu Oct 6 04:57:39 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository abyss.
from ca88ee1 Imported Upstream version 1.9.0
new 95e61ae New upstream version 2.0.1
The 1 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 +-
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, 6821 insertions(+), 949 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
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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