[med-svn] [ray] 02/03: Merge tag 'upstream/2.3.0'
Sébastien Boisvert
sboisvert-guest at moszumanska.debian.org
Mon Feb 3 19:22:29 UTC 2014
This is an automated email from the git hooks/post-receive script.
sboisvert-guest pushed a commit to branch master
in repository ray.
commit 768eb840f398524a28da0270dfd3a7e6536061f8
Merge: 00482e6 a38ff74
Author: Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca>
Date: Mon Feb 3 14:13:12 2014 -0500
Merge tag 'upstream/2.3.0'
Upstream version 2.3.0
CMakeLists.txt | 293 +--
Documentation/454.txt | 0
Documentation/AMAZON_EC2.txt | 0
Documentation/Blue_Gene_Q.txt | 5 +
Documentation/COMPILERS.txt | 0
Documentation/CodingStyle.txt | 15 +-
Documentation/Distributed-Storage-Engine.txt | 15 +-
Documentation/Illumina.txt | 0
Documentation/IonTorrent.txt | 0
Documentation/Migration-to-the-Actor-Model.txt | 56 +
Documentation/PacBio.txt | 0
Documentation/Profiling.txt | 2 +-
Documentation/RELEASE_PROCEDURE.txt | 12 +-
Documentation/Ray-Surveyor.md | 58 +
Documentation/Releases.txt | 54 +-
Documentation/Routing.txt | 57 +-
Documentation/SOLiD.txt | 0
Documentation/VISUAL_STUDIO.txt | 0
Documentation/Very-Large-Jobs.txt | 5 +-
Documentation/index.markdown | 3 +
MANUAL_PAGE.txt | 78 +-
Makefile | 260 +--
README.md | 54 +-
RayPlatform/Documentation/Actor-Model.txt | 13 +
RayPlatform/Documentation/DebugMode.txt | 18 +
RayPlatform/Documentation/Gates.txt | 41 +
RayPlatform/Documentation/Handlers.txt | 18 +-
RayPlatform/Documentation/MiniRanks.txt | 329 ++++
RayPlatform/Documentation/Torus.txt | 37 +
RayPlatform/Documentation/plugins.txt | 70 +
RayPlatform/GPL-3.0.txt | 6 +
RayPlatform/LICENSE | 3 +
RayPlatform/Makefile | 25 +-
RayPlatform/Makefile.shared-gcc | 3 -
RayPlatform/{README => README.md} | 20 +-
RayPlatform/RayPlatform/actors/Actor.cpp | 114 ++
RayPlatform/RayPlatform/actors/Actor.h | 75 +
RayPlatform/RayPlatform/actors/Playground.cpp | 211 ++
RayPlatform/RayPlatform/actors/Playground.h | 81 +
.../communication/BufferedData.cpp | 17 +-
.../{ => RayPlatform}/communication/BufferedData.h | 13 +-
RayPlatform/RayPlatform/communication/Message.cpp | 389 ++++
RayPlatform/RayPlatform/communication/Message.h | 176 ++
.../RayPlatform/communication/MessageQueue.cpp | 291 +++
.../RayPlatform/communication/MessageQueue.h | 169 ++
.../communication/MessageRouter.cpp | 152 +-
.../communication/MessageRouter.h | 36 +-
.../communication/MessagesHandler.cpp | 832 +++++---
.../communication/MessagesHandler.h | 122 +-
.../communication/VirtualCommunicator.cpp | 58 +-
.../communication/VirtualCommunicator.h | 18 +-
.../{ => RayPlatform}/communication/mpi_tags.cpp | 8 +-
.../{ => RayPlatform}/communication/mpi_tags.h | 10 +-
RayPlatform/{ => RayPlatform}/core/ComputeCore.cpp | 751 +++++--
RayPlatform/{ => RayPlatform}/core/ComputeCore.h | 148 +-
.../core/MiniRank.cpp} | 16 +-
.../Worker.h => RayPlatform/core/MiniRank.h} | 41 +-
.../{ => RayPlatform}/core/OperatingSystem.cpp | 115 +-
.../{ => RayPlatform}/core/OperatingSystem.h | 25 +-
RayPlatform/RayPlatform/core/RankProcess.h | 323 ++++
.../{ => RayPlatform}/core/master_modes.cpp | 8 +-
RayPlatform/{ => RayPlatform}/core/master_modes.h | 8 +-
RayPlatform/{ => RayPlatform}/core/slave_modes.cpp | 9 +-
RayPlatform/{ => RayPlatform}/core/slave_modes.h | 8 +-
RayPlatform/{ => RayPlatform}/core/statistics.cpp | 9 +-
RayPlatform/{ => RayPlatform}/core/statistics.h | 6 +-
RayPlatform/{ => RayPlatform}/core/types.h | 19 +-
.../{ => RayPlatform}/cryptography/crypto.cpp | 32 +-
.../cryptography/crypto.h} | 24 +-
RayPlatform/RayPlatform/files/FileReader.cpp | 179 ++
RayPlatform/RayPlatform/files/FileReader.h | 60 +
.../handlers/MasterModeExecutor.cpp | 36 +-
.../handlers/MasterModeExecutor.h | 28 +-
.../RayPlatform/handlers/MasterModeHandler.h | 106 +
.../handlers/MessageTagExecutor.cpp | 34 +-
.../handlers/MessageTagExecutor.h | 31 +-
.../RayPlatform/handlers/MessageTagHandler.h | 101 +
.../handlers/SlaveModeExecutor.cpp | 33 +-
.../{ => RayPlatform}/handlers/SlaveModeExecutor.h | 30 +-
.../RayPlatform/handlers/SlaveModeHandler.h | 102 +
.../memory/ChunkAllocatorWithDefragmentation.cpp | 11 +-
.../memory/ChunkAllocatorWithDefragmentation.h | 11 +-
.../memory/DefragmentationGroup.cpp | 11 +-
.../memory/DefragmentationGroup.h | 9 +-
.../memory/DefragmentationLane.cpp | 9 +-
.../{ => RayPlatform}/memory/DefragmentationLane.h | 8 +-
RayPlatform/RayPlatform/memory/DirtyBuffer.cpp | 72 +
RayPlatform/RayPlatform/memory/DirtyBuffer.h | 56 +
.../{ => RayPlatform}/memory/MyAllocator.cpp | 27 +-
RayPlatform/{ => RayPlatform}/memory/MyAllocator.h | 15 +-
.../memory/ReusableMemoryStore.cpp | 9 +-
.../{ => RayPlatform}/memory/ReusableMemoryStore.h | 6 +-
RayPlatform/RayPlatform/memory/RingAllocator.cpp | 536 +++++
.../{ => RayPlatform}/memory/RingAllocator.h | 73 +-
RayPlatform/{ => RayPlatform}/memory/allocator.cpp | 13 +-
RayPlatform/{ => RayPlatform}/memory/allocator.h | 6 +-
.../{ => RayPlatform}/plugins/CorePlugin.cpp | 8 +-
RayPlatform/{ => RayPlatform}/plugins/CorePlugin.h | 58 +-
.../{ => RayPlatform}/plugins/RegisteredPlugin.cpp | 15 +-
.../{ => RayPlatform}/plugins/RegisteredPlugin.h | 9 +-
.../{ => RayPlatform}/profiling/Derivative.cpp | 15 +-
.../{ => RayPlatform}/profiling/Derivative.h | 9 +-
.../RayPlatform/profiling/ProcessStatus.cpp | 102 +
RayPlatform/RayPlatform/profiling/ProcessStatus.h | 28 +
.../{ => RayPlatform}/profiling/Profiler.cpp | 14 +-
RayPlatform/{ => RayPlatform}/profiling/Profiler.h | 6 +-
.../{ => RayPlatform}/profiling/TickLogger.cpp | 10 +-
.../{ => RayPlatform}/profiling/TickLogger.h | 8 +-
.../{ => RayPlatform}/profiling/TimePrinter.cpp | 39 +-
.../{ => RayPlatform}/profiling/TimePrinter.h | 17 +-
.../{ => RayPlatform}/routing/ConnectionGraph.cpp | 55 +-
.../{ => RayPlatform}/routing/ConnectionGraph.h | 38 +-
.../routing/GraphImplementation.cpp | 9 +-
.../routing/GraphImplementation.h | 8 +-
.../routing/GraphImplementationComplete.cpp | 8 +-
.../routing/GraphImplementationComplete.h | 8 +-
.../routing/GraphImplementationDeBruijn.cpp | 9 +-
.../routing/GraphImplementationDeBruijn.h | 9 +-
.../routing/GraphImplementationExperimental.cpp | 9 +-
.../routing/GraphImplementationExperimental.h | 9 +-
.../routing/GraphImplementationGroup.cpp | 9 +-
.../routing/GraphImplementationGroup.h | 8 +-
.../routing/GraphImplementationKautz.cpp | 9 +-
.../routing/GraphImplementationKautz.h | 9 +-
.../routing/GraphImplementationRandom.cpp | 9 +-
.../routing/GraphImplementationRandom.h | 8 +-
.../routing/Polytope.cpp} | 69 +-
.../Hypercube.h => RayPlatform/routing/Polytope.h} | 21 +-
RayPlatform/RayPlatform/routing/Torus.cpp | 558 ++++++
.../Hypercube.h => RayPlatform/routing/Torus.h} | 77 +-
.../{ => RayPlatform}/scheduling/SwitchMan.cpp | 39 +-
.../{ => RayPlatform}/scheduling/SwitchMan.h | 28 +-
.../{ => RayPlatform}/scheduling/TaskCreator.cpp | 9 +-
.../{ => RayPlatform}/scheduling/TaskCreator.h | 12 +-
.../scheduling/VirtualProcessor.cpp | 18 +-
.../scheduling/VirtualProcessor.h | 13 +-
RayPlatform/{ => RayPlatform}/scheduling/Worker.h | 11 +-
RayPlatform/RayPlatform/store/CarriageableItem.h | 61 +
RayPlatform/RayPlatform/store/KeyValueStore.cpp | 604 ++++++
RayPlatform/RayPlatform/store/KeyValueStore.h | 177 ++
.../RayPlatform/store/KeyValueStoreItem.cpp | 105 +
RayPlatform/RayPlatform/store/KeyValueStoreItem.h | 50 +
.../RayPlatform/store/KeyValueStoreRequest.cpp | 66 +
.../RayPlatform/store/KeyValueStoreRequest.h | 54 +
.../{ => RayPlatform}/structures/MyHashTable.h | 18 +-
.../structures/MyHashTableGroup.h | 9 +-
.../structures/MyHashTableIterator.h | 9 +-
RayPlatform/{ => RayPlatform}/structures/MyStack.h | 8 +-
.../{ => RayPlatform}/structures/SplayNode.h | 8 +-
.../{ => RayPlatform}/structures/SplayTree.h | 20 +-
.../structures/SplayTreeIterator.h | 26 +-
.../{ => RayPlatform}/structures/StaticVector.cpp | 17 +-
.../{ => RayPlatform}/structures/StaticVector.h | 16 +-
RayPlatform/common.mk | 120 +-
RayPlatform/communication/Message.cpp | 85 -
RayPlatform/communication/Message.h | 92 -
RayPlatform/git.txt | 1 -
RayPlatform/github.txt | 1 -
RayPlatform/handlers/MasterModeHandler.h | 42 -
RayPlatform/handlers/MessageTagHandler.h | 46 -
RayPlatform/handlers/SlaveModeHandler.h | 42 -
RayPlatform/memory/RingAllocator.cpp | 222 ---
RayPlatform/tag.txt | 1 -
code/{plugin_Amos => Amos}/Amos.cpp | 59 +-
code/{plugin_Amos => Amos}/Amos.h | 27 +-
code/Amos/Makefile | 3 +
.../CoverageDistribution.cpp | 10 +-
.../CoverageDistribution.h | 8 +-
.../CoverageGatherer.cpp | 148 +-
.../CoverageGatherer.h | 20 +-
code/CoverageGatherer/Makefile | 4 +
.../EdgePurger.cpp | 109 +-
.../{plugin_EdgePurger => EdgePurger}/EdgePurger.h | 37 +-
.../EdgePurgerWorker.cpp | 8 +-
.../EdgePurgerWorker.h | 20 +-
code/EdgePurger/Makefile | 4 +
code/Example/Example.cpp | 273 +++
code/Example/Example.h | 117 ++
code/Example/Makefile | 3 +
.../FusionData.cpp | 95 +-
.../{plugin_FusionData => FusionData}/FusionData.h | 35 +-
code/FusionData/Makefile | 3 +
.../FusionTaskCreator.cpp | 27 +-
.../FusionTaskCreator.h | 43 +-
.../FusionWorker.cpp | 31 +-
.../FusionWorker.h | 20 +-
code/FusionTaskCreator/Makefile | 4 +
.../GeneOntology.cpp | 41 +-
.../GeneOntology.h | 38 +-
.../KeyEncoder.cpp | 11 +-
.../KeyEncoder.h | 8 +-
code/GeneOntology/Makefile | 4 +
code/{plugin_GeneOntology => GeneOntology}/types.h | 0
.../GenomeNeighbourhood.cpp | 53 +-
.../GenomeNeighbourhood.h | 33 +-
code/GenomeNeighbourhood/Makefile | 5 +
.../Neighbour.cpp | 2 +-
.../Neighbour.h | 5 +-
.../NeighbourPair.cpp | 5 +-
.../NeighbourPair.h | 5 +-
.../JoinerTaskCreator.cpp | 32 +-
.../JoinerTaskCreator.h | 39 +-
.../JoinerWorker.cpp | 169 +-
.../JoinerWorker.h | 22 +-
code/JoinerTaskCreator/Makefile | 4 +
.../BloomFilter.cpp | 20 +-
.../BloomFilter.h | 5 +-
.../Kmer.cpp | 188 +-
.../Kmer.h | 94 +-
.../KmerAcademyBuilder.cpp | 48 +-
.../KmerAcademyBuilder.h | 32 +-
code/KmerAcademyBuilder/Makefile | 5 +
code/{plugin_Library => Library}/Library.cpp | 182 +-
code/{plugin_Library => Library}/Library.h | 46 +-
.../LibraryPeakFinder.cpp | 8 +-
.../LibraryPeakFinder.h | 2 +-
code/{plugin_Library => Library}/LibraryWorker.cpp | 22 +-
code/{plugin_Library => Library}/LibraryWorker.h | 18 +-
code/Library/Makefile | 5 +
.../MachineHelper.cpp | 720 ++++---
.../MachineHelper.h | 179 +-
code/MachineHelper/Makefile | 3 +
code/Makefile | 35 -
code/MessageProcessor/Makefile | 3 +
.../MessageProcessor.cpp | 782 ++++----
.../MessageProcessor.h | 307 ++-
code/Mock/Makefile | 5 +
code/Mock/Mock.cpp | 47 +
.../cryptography/crypto.h => code/Mock/Mock.h | 25 +-
code/{application_core => Mock}/Parameters.cpp | 447 ++++-
code/{application_core => Mock}/Parameters.h | 42 +-
.../common_functions.cpp | 110 +-
code/{application_core => Mock}/common_functions.h | 37 +-
code/{application_core => Mock}/constants.h | 82 +-
code/NetworkTest/Makefile | 3 +
.../NetworkTest.cpp | 108 +-
.../NetworkTest.h | 33 +-
code/Partitioner/Makefile | 3 +
.../Partitioner.cpp | 118 +-
.../Partitioner.h | 30 +-
code/PathEvaluator/Makefile | 3 +
code/PathEvaluator/PathEvaluator.cpp | 113 ++
code/PathEvaluator/PathEvaluator.h | 68 +
code/Scaffolder/Makefile | 8 +
.../Scaffolder.cpp | 562 +++++-
.../{plugin_Scaffolder => Scaffolder}/Scaffolder.h | 98 +-
.../ScaffoldingAlgorithm.cpp | 28 +-
.../ScaffoldingAlgorithm.h | 13 +-
.../ScaffoldingEdge.cpp | 5 +-
.../ScaffoldingEdge.h | 8 +-
.../ScaffoldingLink.cpp | 4 +-
.../ScaffoldingLink.h | 2 +-
.../ScaffoldingVertex.cpp | 5 +-
.../ScaffoldingVertex.h | 10 +-
.../SummarizedLink.cpp | 8 +-
.../SummarizedLink.h | 9 +-
code/{plugin_Searcher => Searcher}/ColorSet.cpp | 5 +-
code/{plugin_Searcher => Searcher}/ColorSet.h | 2 +-
.../ColoredPeakFinder.cpp | 8 +-
.../ColoredPeakFinder.h | 2 +-
code/{plugin_Searcher => Searcher}/ContigHit.cpp | 2 +-
code/{plugin_Searcher => Searcher}/ContigHit.h | 8 +-
.../ContigSearchEntry.cpp | 2 +-
.../ContigSearchEntry.h | 6 +-
.../DistributionWriter.cpp | 7 +-
.../DistributionWriter.h | 5 +-
code/Searcher/Makefile | 11 +
.../QualityCaller.cpp | 5 +-
code/{plugin_Searcher => Searcher}/QualityCaller.h | 6 +-
.../SearchDirectory.cpp | 29 +-
.../SearchDirectory.h | 9 +-
code/{plugin_Searcher => Searcher}/Searcher.cpp | 97 +-
code/{plugin_Searcher => Searcher}/Searcher.h | 99 +-
.../VirtualKmerColor.cpp | 5 +-
.../VirtualKmerColor.h | 5 +-
.../BubbleData.h | 15 +-
.../BubbleTool.cpp | 8 +-
.../BubbleTool.h | 11 +-
.../Chooser.cpp | 7 +-
.../Chooser.h | 7 +-
.../DepthFirstSearchData.cpp | 24 +-
.../DepthFirstSearchData.h | 18 +-
.../Direction.cpp | 13 +-
.../Direction.h | 10 +-
.../ExtensionData.cpp | 44 +-
.../ExtensionData.h | 42 +-
.../ExtensionElement.cpp | 37 +-
.../ExtensionElement.h | 24 +-
code/SeedExtender/Makefile | 14 +
.../NovaEngine.cpp | 5 +-
.../NovaEngine.h | 5 +-
.../OpenAssemblerChooser.cpp | 6 +-
.../OpenAssemblerChooser.h | 6 +-
.../ReadFetcher.cpp | 15 +-
.../ReadFetcher.h | 14 +-
.../SeedExtender.cpp | 464 +++--
.../SeedExtender.h | 108 +-
.../TipWatchdog.cpp | 4 +-
.../TipWatchdog.h | 8 +-
.../VertexMessenger.cpp | 25 +-
.../VertexMessenger.h | 15 +-
code/SeedingData/GraphPath.cpp | 743 +++++++
code/SeedingData/GraphPath.h | 154 ++
code/SeedingData/Makefile | 9 +
code/SeedingData/PathHandle.cpp | 128 ++
code/SeedingData/PathHandle.h | 69 +
.../SeedWorker.cpp | 286 ++-
.../SeedWorker.h | 62 +-
.../SeedingData.cpp | 330 ++--
.../SeedingData.h | 56 +-
.../DynamicVector.h | 7 +-
.../IndexerWorker.cpp | 14 +-
.../IndexerWorker.h | 19 +-
code/SequencesIndexer/Makefile | 9 +
.../PairedRead.cpp | 18 +-
.../PairedRead.h | 12 +-
.../ReadAnnotation.cpp | 20 +-
.../ReadAnnotation.h | 10 +-
.../SequencesIndexer.cpp | 38 +-
.../SequencesIndexer.h | 39 +-
.../ArrayOfReads.cpp | 7 +-
.../ArrayOfReads.h | 6 +-
code/SequencesLoader/BufferedReader.cpp | 206 ++
code/SequencesLoader/BufferedReader.h | 66 +
.../BzReader.cpp | 17 +-
.../BzReader.h | 8 +-
.../ColorSpaceDecoder.cpp | 39 +-
.../ColorSpaceDecoder.h | 8 +-
.../ColorSpaceLoader.cpp | 36 +-
.../ColorSpaceLoader.h | 26 +-
code/SequencesLoader/ExportLoader.cpp | 108 ++
.../ExportLoader.h} | 45 +-
code/SequencesLoader/FastaBz2Loader.cpp | 51 +
.../FastaBz2Loader.h} | 37 +-
code/SequencesLoader/FastaGzLoader.cpp | 53 +
.../FastaGzLoader.h} | 42 +-
.../FastaLoader.cpp | 10 +-
.../FastaLoader.h | 23 +-
code/SequencesLoader/FastaLoaderForReads.cpp | 49 +
.../FastaLoaderForReads.h} | 41 +-
.../FastqBz2Loader.cpp | 44 +-
.../FastqBz2Loader.h | 36 +-
code/SequencesLoader/FastqGzLoader.cpp | 305 +++
code/SequencesLoader/FastqGzLoader.h | 75 +
code/SequencesLoader/FastqLoader.cpp | 134 ++
.../FastqLoader.h} | 46 +-
code/SequencesLoader/Loader.cpp | 154 ++
.../Loader.h | 64 +-
code/SequencesLoader/LoaderFactory.cpp | 50 +
code/SequencesLoader/LoaderFactory.h | 77 +
code/SequencesLoader/LoaderInterface.cpp | 54 +
.../LoaderInterface.h} | 41 +-
code/SequencesLoader/Makefile | 25 +
.../Read.cpp | 52 +-
.../Read.h | 18 +-
code/SequencesLoader/ReadHandle.cpp | 100 +
code/SequencesLoader/ReadHandle.h | 58 +
code/SequencesLoader/SequenceFileDetector.cpp | 380 ++++
code/SequencesLoader/SequenceFileDetector.h | 59 +
.../SequencesLoader.cpp | 185 +-
.../SequencesLoader.h | 41 +-
.../SffLoader.cpp | 35 +-
.../SffLoader.h | 29 +-
.../SpuriousSeedAnnihilator/AnnihilationWorker.cpp | 614 ++++++
code/SpuriousSeedAnnihilator/AnnihilationWorker.h | 141 ++
code/SpuriousSeedAnnihilator/AnnotationFetcher.cpp | 154 ++
code/SpuriousSeedAnnihilator/AnnotationFetcher.h | 70 +
code/SpuriousSeedAnnihilator/AttributeFetcher.cpp | 98 +
code/SpuriousSeedAnnihilator/AttributeFetcher.h | 107 +
.../SpuriousSeedAnnihilator/GossipAssetManager.cpp | 433 +++++
code/SpuriousSeedAnnihilator/GossipAssetManager.h | 73 +
code/SpuriousSeedAnnihilator/GraphExplorer.cpp | 491 +++++
code/SpuriousSeedAnnihilator/GraphExplorer.h | 112 ++
code/SpuriousSeedAnnihilator/GraphSearchResult.cpp | 267 +++
code/SpuriousSeedAnnihilator/GraphSearchResult.h | 89 +
code/SpuriousSeedAnnihilator/Makefile | 13 +
code/SpuriousSeedAnnihilator/NanoMerger.cpp | 167 ++
code/SpuriousSeedAnnihilator/NanoMerger.h | 136 ++
.../SeedFilteringWorkflow.cpp | 138 ++
.../SeedFilteringWorkflow.h | 94 +
code/SpuriousSeedAnnihilator/SeedGossipSolver.cpp | 371 ++++
code/SpuriousSeedAnnihilator/SeedGossipSolver.h | 64 +
.../SeedMergingWorkflow.cpp | 169 ++
code/SpuriousSeedAnnihilator/SeedMergingWorkflow.h | 103 +
.../SpuriousSeedAnnihilator.cpp | 2042 ++++++++++++++++++++
.../SpuriousSeedAnnihilator.h | 363 ++++
code/Surveyor/CoalescenceManager.cpp | 425 ++++
code/Surveyor/CoalescenceManager.h | 82 +
code/Surveyor/ExperimentVertex.cpp | 49 +
code/Surveyor/ExperimentVertex.h | 58 +
code/Surveyor/GenomeGraphReader.cpp | 251 +++
code/Surveyor/GenomeGraphReader.h | 75 +
code/Surveyor/Makefile | 8 +
code/Surveyor/MatrixOwner.cpp | 232 +++
code/Surveyor/MatrixOwner.h | 68 +
code/Surveyor/Mother.cpp | 482 +++++
code/Surveyor/Mother.h | 118 ++
code/Surveyor/StoreKeeper.cpp | 460 +++++
code/Surveyor/StoreKeeper.h | 99 +
.../GenomeToTaxonLoader.cpp | 4 +-
.../GenomeToTaxonLoader.h | 8 +-
code/TaxonomyViewer/Makefile | 6 +
.../TaxonNameLoader.cpp | 4 +-
.../TaxonNameLoader.h | 7 +-
.../TaxonomicTreeLoader.cpp} | 10 +-
.../TaxonomicTreeLoader.h} | 13 +-
.../TaxonomyViewer.cpp} | 117 +-
.../TaxonomyViewer.h} | 52 +-
.../types.h | 0
.../GridTable.cpp | 43 +-
.../GridTable.h | 16 +-
.../GridTableIterator.cpp | 10 +-
.../GridTableIterator.h | 12 +-
code/VerticesExtractor/Makefile | 9 +
.../Vertex.cpp | 128 +-
.../Vertex.h | 97 +-
.../VerticesExtractor.cpp | 94 +-
.../VerticesExtractor.h | 39 +-
code/application_core/Machine.cpp | 444 +++--
code/application_core/Machine.h | 164 +-
code/application_core/Makefile | 5 +-
code/application_core/ray_main.cpp | 16 +-
code/plugin_Amos/Makefile | 7 -
code/plugin_CoverageGatherer/Makefile | 8 -
code/plugin_EdgePurger/Makefile | 8 -
code/plugin_FusionData/Makefile | 5 -
code/plugin_FusionTaskCreator/Makefile | 6 -
code/plugin_GeneOntology/Makefile | 6 -
code/plugin_GenomeNeighbourhood/Makefile | 11 -
code/plugin_JoinerTaskCreator/Makefile | 8 -
code/plugin_KmerAcademyBuilder/Makefile | 8 -
code/plugin_Library/Makefile | 8 -
code/plugin_MachineHelper/Makefile | 7 -
code/plugin_MessageProcessor/Makefile | 7 -
code/plugin_NetworkTest/Makefile | 7 -
code/plugin_Partitioner/Makefile | 6 -
code/plugin_PhylogenyViewer/Makefile | 8 -
code/plugin_Scaffolder/Makefile | 13 -
code/plugin_Searcher/Makefile | 13 -
code/plugin_SeedExtender/Makefile | 14 -
code/plugin_SeedingData/AssemblySeed.cpp | 160 --
code/plugin_SeedingData/AssemblySeed.h | 66 -
code/plugin_SeedingData/Makefile | 8 -
code/plugin_SequencesIndexer/Makefile | 9 -
code/plugin_SequencesLoader/FastqGzLoader.cpp | 81 -
code/plugin_SequencesLoader/FastqLoader.cpp | 76 -
code/plugin_SequencesLoader/Loader.cpp | 207 --
code/plugin_SequencesLoader/Makefile | 13 -
code/plugin_VerticesExtractor/Makefile | 9 -
git.txt | 1 -
github.txt | 1 -
scripts/Build-Link-Time-Optimization.sh | 10 +-
scripts/ShipProduct.sh | 34 +-
scripts/install.sh | 33 -
tag.txt | 1 -
455 files changed, 27908 insertions(+), 6295 deletions(-)
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