[med-svn] [abyss] 02/10: Merge tag 'upstream/1.9.0'

Andreas Tille tille at debian.org
Thu Jul 16 09:42:33 UTC 2015


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tille pushed a commit to branch master
in repository abyss.

commit a01c10502fdb27d9e48dc9c4e5c15b4416b8472e
Merge: 03a15c6 ca88ee1
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jul 14 22:30:09 2015 +0200

    Merge tag 'upstream/1.9.0'
    
    Upstream version 1.9.0

 .travis.yml                                        |   10 +-
 ABYSS/Makefile.am                                  |    9 +-
 ABYSS/{Abyss.cpp => abyss.cc}                      |   58 +-
 AdjList/AdjList.cpp                                |  229 +-
 AdjList/Makefile.am                                |   13 +
 Align/mergepairs.cc                                |    4 +-
 Assembly/AdjacencyAlgorithm.h                      |   50 +
 Assembly/AssembleAlgorithm.h                       |  146 +
 Assembly/AssemblyAlgorithms.cc                     |   20 +
 Assembly/AssemblyAlgorithms.cpp                    | 1049 ----
 Assembly/AssemblyAlgorithms.h                      |  214 +-
 Assembly/BranchGroup.cpp                           |   86 -
 Assembly/BranchGroup.h                             |  105 +-
 Assembly/BranchRecord.cpp                          |   59 -
 Assembly/BranchRecord.h                            |  149 +-
 Assembly/{BranchRecord.h => BranchRecordBase.h}    |   65 +-
 Assembly/BubbleAlgorithm.h                         |  279 ++
 Assembly/CoverageAlgorithm.h                       |  117 +
 Assembly/DBG.h                                     |  913 ++++
 Assembly/DotWriter.cpp                             |   70 -
 Assembly/DotWriter.h                               |  217 +-
 Assembly/ErodeAlgorithm.h                          |  117 +
 Assembly/ISequenceCollection.h                     |   88 -
 Assembly/LoadAlgorithm.h                           |  182 +
 Assembly/Makefile.am                               |   32 +-
 Assembly/{Options.cpp => Options.cc}               |   82 +-
 Assembly/Options.h                                 |    8 +
 {Common => Assembly}/SeqExt.h                      |   36 +-
 Assembly/SequenceCollection.cpp                    |  291 --
 Assembly/SequenceCollection.h                      |  353 +-
 Assembly/SplitAlgorithm.h                          |   97 +
 Assembly/TrimAlgorithm.h                           |  203 +
 Assembly/{KmerData.h => VertexData.h}              |   75 +-
 Bloom/Bloom.h                                      |  162 +-
 Bloom/BloomFilter.h                                |   89 +-
 Bloom/BloomFilterWindow.h                          |   42 +-
 Bloom/CascadingBloomFilter.h                       |   16 +-
 Bloom/CascadingBloomFilterWindow.h                 |   11 +-
 Bloom/bloom.cc                                     |   58 +-
 CITATION.bib                                       |   10 +
 CITATION.md                                        |   39 +
 ChangeLog                                          |   42 +
 Common/BitUtil.h                                   |  107 +
 Common/ContigProperties.h                          |    6 +-
 Common/Estimate.h                                  |    7 +
 Common/Histogram.h                                 |   44 +-
 Common/InsOrderedMap.h                             |   88 +
 Common/Kmer.cpp                                    |   10 +-
 Common/Kmer.h                                      |   25 +-
 Common/KmerSet.h                                   |   47 +
 Common/Makefile.am                                 |    5 +-
 Common/MemUtils.h                                  |    4 +-
 Common/SAM.h                                       |    3 +-
 Common/SeqExt.cpp                                  |   16 -
 Common/Sequence.cpp                                |    4 +-
 Common/Sequence.h                                  |   82 +
 Common/StringUtil.h                                |   78 +-
 Common/VectorUtil.h                                |   35 +
 Common/Warnings.h                                  |    6 -
 DataBase/DB.cc                                     |  208 +
 DataBase/DB.h                                      |  227 +
 DataBase/Makefile.am                               |   11 +
 DataBase/Options.h                                 |   22 +
 DataBase/abyss-db-txt                              |   35 +
 DataBase/db-csv.cc                                 |  124 +
 DataLayer/FastaReader.cpp                          |    4 +-
 DataLayer/FastaReader.h                            |    4 +-
 DataLayer/FastaWriter.h                            |    2 +-
 DataLayer/Makefile.am                              |    9 +-
 DataLayer/abyss-tofastq.cc                         |    8 +-
 DataLayer/fac.cc                                   |    6 +-
 DistanceEst/DistanceEst.cpp                        |  111 +-
 DistanceEst/MLE.cpp                                |   64 +-
 DistanceEst/Makefile.am                            |    2 +
 FilterGraph/{FilterGraph.cpp => FilterGraph.cc}    |  286 +-
 FilterGraph/Makefile.am                            |    2 +-
 Graph/AllPathsSearch.h                             |    1 -
 Graph/AsqgIO.h                                     |   24 +-
 Graph/BidirectionalBFSVisitor.h                    |   48 +-
 Graph/ConstrainedBidiBFSVisitor.h                  |   14 +-
 Graph/ConstrainedSearch.h                          |    8 +-
 Graph/ContigGraph.h                                |    2 +-
 Graph/ContigGraphAlgorithms.h                      |   14 +-
 Graph/DirectedGraph.h                              |    9 +-
 Graph/ExtendPath.h                                 |  296 ++
 Graph/{AsqgIO.h => GfaIO.h}                        |  118 +-
 Graph/GraphAlgorithms.h                            |   25 +-
 Graph/GraphIO.h                                    |   21 +-
 Graph/GraphUtil.h                                  |   52 +-
 Graph/HashGraph.h                                  |   24 +-
 Graph/Makefile.am                                  |    2 +
 Graph/Options.h                                    |    2 +-
 Graph/Path.h                                       |    6 +-
 Graph/SAMIO.h                                      |    2 +-
 Graph/todot.cc                                     |   19 +-
 IntegrationTest/DIDA/alignment-test.mk             |   84 +
 IntegrationTest/DIDA/assembly-test.mk              |   83 +
 IntegrationTest/DIDA/compare-fastx                 |   14 +
 IntegrationTest/DIDA/compare-sam                   |  110 +
 Konnector/DBGBloom.h                               |    4 +-
 Konnector/DBGBloomAlgorithms.h                     |  122 +-
 Konnector/konnector.cc                             |  683 ++-
 Konnector/konnector.h                              |  485 +-
 LogKmerCount/logcounter.cc                         |    4 +-
 Makefile.am                                        |   31 +-
 Map/Makefile.am                                    |    4 +-
 Map/index.cc                                       |   18 +-
 Map/map.cc                                         |  109 +-
 Map/overlap.cc                                     |    4 +-
 MergePaths/Makefile.am                             |    6 +
 MergePaths/MergeContigs.cpp                        |   84 +-
 MergePaths/MergePaths.cpp                          |   74 +-
 MergePaths/PathConsensus.cpp                       |   77 +-
 Overlap/Overlap.cpp                                |   15 +-
 PairedDBG/BranchRecord.h                           |   43 +
 PairedDBG/Dinuc.h                                  |  167 +
 PairedDBG/KmerPair.cc                              |    4 +
 PairedDBG/KmerPair.h                               |  229 +
 PairedDBG/Makefile.am                              |   26 +
 PairedDBG/PairedDBGAlgorithms.h                    |   42 +
 PairedDBG/SequenceCollection.h                     |   24 +
 PairedDBG/abyss-paired-dbg.cc                      |    1 +
 Parallel/CommLayer.cpp                             |    4 +-
 Parallel/Makefile.am                               |   20 +-
 Parallel/MessageBuffer.cpp                         |   16 +-
 Parallel/MessageBuffer.h                           |   22 +-
 Parallel/Messages.h                                |   45 +-
 Parallel/NetworkSequenceCollection.cpp             |  171 +-
 Parallel/NetworkSequenceCollection.h               |  118 +-
 Parallel/SequenceCollection.h                      |   10 +
 Parallel/parallelAbyss.cpp                         |   37 +-
 ParseAligns/Makefile.am                            |    2 +
 ParseAligns/abyss-fixmate.cc                       |   98 +-
 PathOverlap/Makefile.am                            |    2 +
 PathOverlap/PathOverlap.cpp                        |   58 +-
 PopBubbles/PopBubbles.cpp                          |   38 +-
 README.md                                          |  111 +-
 Scaffold/Makefile.am                               |    2 +
 Scaffold/drawgraph.cc                              |   89 +-
 Scaffold/junction.cc                               |    2 +-
 Scaffold/scaffold.cc                               |  152 +-
 Sealer/Makefile.am                                 |   29 +
 Sealer/README.md                                   |  171 +
 Sealer/sealer.cc                                   | 1025 ++++
 SimpleGraph/Makefile.am                            |    2 +
 SimpleGraph/SimpleGraph.cpp                        |   84 +-
 Unittest/Common/BitUtilTest.cpp                    |  230 +
 Unittest/Common/StringUtilTest.cpp                 |   30 +-
 Unittest/DBG/LoadAlgorithmTest.cpp                 |   43 +
 Unittest/Graph/AllPathsSearchTest.cpp              |    1 -
 Unittest/Graph/BidirectionalBFSTest.cpp            |   31 +-
 Unittest/Graph/ConstrainedBidiBFSVisitorTest.cpp   |    1 -
 Unittest/Graph/ExtendPathTest.cpp                  |  345 ++
 Unittest/Konnector/BloomFilter.cc                  |   41 +-
 Unittest/Konnector/DBGBloomAlgorithmsTest.cpp      |   77 +-
 Unittest/Konnector/DBGBloomTest.cpp                |    2 +-
 Unittest/Konnector/integration-tests.mk            |    8 +-
 Unittest/Makefile.am                               |  213 +-
 Unittest/PairedDBG/BranchRecordTest.cpp            |   58 +
 Unittest/PairedDBG/DinucTest.cc                    |   82 +
 Unittest/PairedDBG/KmerPairTest.cc                 |   96 +
 Unittest/PairedDBG/LoadAlgorithmTest.cpp           |   53 +
 Unittest/PairedDBG/test.fa                         |    2 +
 Unittest/PairedDBG/test.png                        |  Bin 0 -> 156866 bytes
 Unittest/PairedDBG/test.svg                        |  859 ++++
 bin/Makefile.am                                    |   14 +-
 bin/abyss-dida                                     |  107 +
 bin/abyss-fac.pl                                   |    4 +-
 bin/abyss-fatoagp                                  |    2 +
 bin/abyss-nompi                                    |    6 +
 bin/abyss-pe                                       |  254 +-
 circle.yml                                         |   11 +
 configure.ac                                       |  110 +-
 doc/ABYSS.1                                        |    4 +-
 doc/abyss-pe.1                                     |   55 +-
 doc/abyss-tofastq.1                                |    4 +-
 doc/flowchart.graffle                              |    2 +-
 lib/gtest-1.7.0/CHANGES                            |  157 +
 lib/gtest-1.7.0/CONTRIBUTORS                       |   37 +
 lib/gtest-1.7.0/LICENSE                            |   28 +
 lib/gtest-1.7.0/Makefile.am                        |   42 +
 lib/gtest-1.7.0/README                             |  435 ++
 lib/gtest-1.7.0/include/gtest/gtest-death-test.h   |  294 ++
 lib/gtest-1.7.0/include/gtest/gtest-message.h      |  250 +
 lib/gtest-1.7.0/include/gtest/gtest-param-test.h   | 1421 ++++++
 .../include/gtest/gtest-param-test.h.pump          |  487 ++
 lib/gtest-1.7.0/include/gtest/gtest-printers.h     |  855 ++++
 lib/gtest-1.7.0/include/gtest/gtest-spi.h          |  232 +
 lib/gtest-1.7.0/include/gtest/gtest-test-part.h    |  179 +
 lib/gtest-1.7.0/include/gtest/gtest-typed-test.h   |  259 +
 lib/gtest-1.7.0/include/gtest/gtest.h              | 2291 +++++++++
 lib/gtest-1.7.0/include/gtest/gtest_pred_impl.h    |  358 ++
 lib/gtest-1.7.0/include/gtest/gtest_prod.h         |   58 +
 .../gtest/internal/gtest-death-test-internal.h     |  319 ++
 .../include/gtest/internal/gtest-filepath.h        |  206 +
 .../include/gtest/internal/gtest-internal.h        | 1158 +++++
 .../include/gtest/internal/gtest-linked_ptr.h      |  233 +
 .../gtest/internal/gtest-param-util-generated.h    | 5143 ++++++++++++++++++++
 .../internal/gtest-param-util-generated.h.pump     |  301 ++
 .../include/gtest/internal/gtest-param-util.h      |  619 +++
 .../include/gtest/internal/gtest-port.h            | 1947 ++++++++
 .../include/gtest/internal/gtest-string.h          |  167 +
 .../include/gtest/internal/gtest-tuple.h           | 1012 ++++
 .../include/gtest/internal/gtest-tuple.h.pump      |  339 ++
 .../include/gtest/internal/gtest-type-util.h       | 3331 +++++++++++++
 .../include/gtest/internal/gtest-type-util.h.pump  |  297 ++
 lib/gtest-1.7.0/src/gtest-all.cc                   |   48 +
 lib/gtest-1.7.0/src/gtest-death-test.cc            | 1344 +++++
 lib/gtest-1.7.0/src/gtest-filepath.cc              |  382 ++
 lib/gtest-1.7.0/src/gtest-internal-inl.h           | 1218 +++++
 lib/gtest-1.7.0/src/gtest-port.cc                  |  805 +++
 lib/gtest-1.7.0/src/gtest-printers.cc              |  363 ++
 lib/gtest-1.7.0/src/gtest-test-part.cc             |  110 +
 lib/gtest-1.7.0/src/gtest-typed-test.cc            |  110 +
 lib/gtest-1.7.0/src/gtest.cc                       | 5015 +++++++++++++++++++
 lib/gtest-1.7.0/src/gtest_main.cc                  |   38 +
 m4/m4_ax_pthread.m4                                |  332 ++
 217 files changed, 44455 insertions(+), 3639 deletions(-)

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