[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
This is an automated email from the git hooks/post-receive script.
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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