[med-svn] [abyss] 02/07: Merge tag 'upstream/2.0.1'

[Andreas Tille]

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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(-)

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