[med-svn] [ray] branch upstream updated (eb605b7 -> a38ff74)
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 change to branch upstream
in repository ray.
from eb605b7 Imported Upstream version 2.1.0
new a38ff74 Imported Upstream version 2.3.0
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:
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 +
LICENSE.txt => RayPlatform/GPL-3.0.txt | 0
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} | 43 +-
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, 27902 insertions(+), 6297 deletions(-)
mode change 100755 => 100644 Documentation/454.txt
mode change 100755 => 100644 Documentation/AMAZON_EC2.txt
create mode 100644 Documentation/Blue_Gene_Q.txt
mode change 100755 => 100644 Documentation/COMPILERS.txt
mode change 100755 => 100644 Documentation/Illumina.txt
mode change 100755 => 100644 Documentation/IonTorrent.txt
create mode 100644 Documentation/Migration-to-the-Actor-Model.txt
mode change 100755 => 100644 Documentation/PacBio.txt
create mode 100644 Documentation/Ray-Surveyor.md
mode change 100755 => 100644 Documentation/SOLiD.txt
mode change 100755 => 100644 Documentation/VISUAL_STUDIO.txt
create mode 100644 Documentation/index.markdown
create mode 100644 RayPlatform/Documentation/Actor-Model.txt
create mode 100644 RayPlatform/Documentation/DebugMode.txt
create mode 100644 RayPlatform/Documentation/Gates.txt
create mode 100644 RayPlatform/Documentation/MiniRanks.txt
create mode 100644 RayPlatform/Documentation/Torus.txt
copy LICENSE.txt => RayPlatform/GPL-3.0.txt (100%)
create mode 100644 RayPlatform/LICENSE
rename RayPlatform/{README => README.md} (87%)
create mode 100644 RayPlatform/RayPlatform/actors/Actor.cpp
create mode 100644 RayPlatform/RayPlatform/actors/Actor.h
create mode 100644 RayPlatform/RayPlatform/actors/Playground.cpp
create mode 100644 RayPlatform/RayPlatform/actors/Playground.h
rename RayPlatform/{ => RayPlatform}/communication/BufferedData.cpp (92%)
rename RayPlatform/{ => RayPlatform}/communication/BufferedData.h (90%)
create mode 100644 RayPlatform/RayPlatform/communication/Message.cpp
create mode 100644 RayPlatform/RayPlatform/communication/Message.h
create mode 100644 RayPlatform/RayPlatform/communication/MessageQueue.cpp
create mode 100644 RayPlatform/RayPlatform/communication/MessageQueue.h
rename RayPlatform/{ => RayPlatform}/communication/MessageRouter.cpp (78%)
rename RayPlatform/{ => RayPlatform}/communication/MessageRouter.h (86%)
rename RayPlatform/{ => RayPlatform}/communication/MessagesHandler.cpp (53%)
rename RayPlatform/{ => RayPlatform}/communication/MessagesHandler.h (75%)
rename RayPlatform/{ => RayPlatform}/communication/VirtualCommunicator.cpp (93%)
rename RayPlatform/{ => RayPlatform}/communication/VirtualCommunicator.h (95%)
rename RayPlatform/{ => RayPlatform}/communication/mpi_tags.cpp (84%)
copy RayPlatform/{ => RayPlatform}/communication/mpi_tags.h (77%)
rename RayPlatform/{ => RayPlatform}/core/ComputeCore.cpp (72%)
rename RayPlatform/{ => RayPlatform}/core/ComputeCore.h (74%)
copy RayPlatform/{core/slave_modes.h => RayPlatform/core/MiniRank.cpp} (70%)
copy RayPlatform/{scheduling/Worker.h => RayPlatform/core/MiniRank.h} (55%)
rename RayPlatform/{ => RayPlatform}/core/OperatingSystem.cpp (73%)
rename RayPlatform/{ => RayPlatform}/core/OperatingSystem.h (70%)
create mode 100644 RayPlatform/RayPlatform/core/RankProcess.h
rename RayPlatform/{ => RayPlatform}/core/master_modes.cpp (81%)
rename RayPlatform/{ => RayPlatform}/core/master_modes.h (81%)
rename RayPlatform/{ => RayPlatform}/core/slave_modes.cpp (80%)
rename RayPlatform/{ => RayPlatform}/core/slave_modes.h (81%)
rename RayPlatform/{ => RayPlatform}/core/statistics.cpp (92%)
rename RayPlatform/{ => RayPlatform}/core/statistics.h (87%)
rename RayPlatform/{ => RayPlatform}/core/types.h (78%)
rename RayPlatform/{ => RayPlatform}/cryptography/crypto.cpp (89%)
rename RayPlatform/{communication/mpi_tags.h => RayPlatform/cryptography/crypto.h} (55%)
create mode 100644 RayPlatform/RayPlatform/files/FileReader.cpp
create mode 100644 RayPlatform/RayPlatform/files/FileReader.h
rename RayPlatform/{ => RayPlatform}/handlers/MasterModeExecutor.cpp (64%)
rename RayPlatform/{ => RayPlatform}/handlers/MasterModeExecutor.h (60%)
create mode 100644 RayPlatform/RayPlatform/handlers/MasterModeHandler.h
rename RayPlatform/{ => RayPlatform}/handlers/MessageTagExecutor.cpp (64%)
rename RayPlatform/{ => RayPlatform}/handlers/MessageTagExecutor.h (59%)
create mode 100644 RayPlatform/RayPlatform/handlers/MessageTagHandler.h
rename RayPlatform/{ => RayPlatform}/handlers/SlaveModeExecutor.cpp (66%)
rename RayPlatform/{ => RayPlatform}/handlers/SlaveModeExecutor.h (60%)
create mode 100644 RayPlatform/RayPlatform/handlers/SlaveModeHandler.h
rename RayPlatform/{ => RayPlatform}/memory/ChunkAllocatorWithDefragmentation.cpp (97%)
rename RayPlatform/{ => RayPlatform}/memory/ChunkAllocatorWithDefragmentation.h (92%)
rename RayPlatform/{ => RayPlatform}/memory/DefragmentationGroup.cpp (98%)
rename RayPlatform/{ => RayPlatform}/memory/DefragmentationGroup.h (96%)
rename RayPlatform/{ => RayPlatform}/memory/DefragmentationLane.cpp (95%)
rename RayPlatform/{ => RayPlatform}/memory/DefragmentationLane.h (93%)
create mode 100644 RayPlatform/RayPlatform/memory/DirtyBuffer.cpp
create mode 100644 RayPlatform/RayPlatform/memory/DirtyBuffer.h
rename RayPlatform/{ => RayPlatform}/memory/MyAllocator.cpp (89%)
rename RayPlatform/{ => RayPlatform}/memory/MyAllocator.h (84%)
rename RayPlatform/{ => RayPlatform}/memory/ReusableMemoryStore.cpp (93%)
rename RayPlatform/{ => RayPlatform}/memory/ReusableMemoryStore.h (89%)
create mode 100644 RayPlatform/RayPlatform/memory/RingAllocator.cpp
rename RayPlatform/{ => RayPlatform}/memory/RingAllocator.h (67%)
rename RayPlatform/{ => RayPlatform}/memory/allocator.cpp (87%)
rename RayPlatform/{ => RayPlatform}/memory/allocator.h (84%)
rename RayPlatform/{ => RayPlatform}/plugins/CorePlugin.cpp (82%)
rename RayPlatform/{ => RayPlatform}/plugins/CorePlugin.h (60%)
rename RayPlatform/{ => RayPlatform}/plugins/RegisteredPlugin.cpp (95%)
rename RayPlatform/{ => RayPlatform}/plugins/RegisteredPlugin.h (94%)
rename RayPlatform/{ => RayPlatform}/profiling/Derivative.cpp (86%)
rename RayPlatform/{ => RayPlatform}/profiling/Derivative.h (86%)
create mode 100644 RayPlatform/RayPlatform/profiling/ProcessStatus.cpp
create mode 100644 RayPlatform/RayPlatform/profiling/ProcessStatus.h
rename RayPlatform/{ => RayPlatform}/profiling/Profiler.cpp (93%)
rename RayPlatform/{ => RayPlatform}/profiling/Profiler.h (94%)
rename RayPlatform/{ => RayPlatform}/profiling/TickLogger.cpp (97%)
rename RayPlatform/{ => RayPlatform}/profiling/TickLogger.h (91%)
rename RayPlatform/{ => RayPlatform}/profiling/TimePrinter.cpp (74%)
rename RayPlatform/{ => RayPlatform}/profiling/TimePrinter.h (80%)
rename RayPlatform/{ => RayPlatform}/routing/ConnectionGraph.cpp (88%)
rename RayPlatform/{ => RayPlatform}/routing/ConnectionGraph.h (79%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementation.cpp (98%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementation.h (93%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationComplete.cpp (88%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationComplete.h (85%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationDeBruijn.cpp (97%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationDeBruijn.h (90%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationExperimental.cpp (97%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationExperimental.h (92%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationGroup.cpp (95%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationGroup.h (87%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationKautz.cpp (97%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationKautz.h (91%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationRandom.cpp (93%)
rename RayPlatform/{ => RayPlatform}/routing/GraphImplementationRandom.h (85%)
rename RayPlatform/{routing/Hypercube.cpp => RayPlatform/routing/Polytope.cpp} (87%)
copy RayPlatform/{routing/Hypercube.h => RayPlatform/routing/Polytope.h} (86%)
create mode 100644 RayPlatform/RayPlatform/routing/Torus.cpp
rename RayPlatform/{routing/Hypercube.h => RayPlatform/routing/Torus.h} (58%)
rename RayPlatform/{ => RayPlatform}/scheduling/SwitchMan.cpp (91%)
rename RayPlatform/{ => RayPlatform}/scheduling/SwitchMan.h (86%)
rename RayPlatform/{ => RayPlatform}/scheduling/TaskCreator.cpp (92%)
rename RayPlatform/{ => RayPlatform}/scheduling/TaskCreator.h (83%)
rename RayPlatform/{ => RayPlatform}/scheduling/VirtualProcessor.cpp (93%)
rename RayPlatform/{ => RayPlatform}/scheduling/VirtualProcessor.h (91%)
rename RayPlatform/{ => RayPlatform}/scheduling/Worker.h (80%)
create mode 100644 RayPlatform/RayPlatform/store/CarriageableItem.h
create mode 100644 RayPlatform/RayPlatform/store/KeyValueStore.cpp
create mode 100644 RayPlatform/RayPlatform/store/KeyValueStore.h
create mode 100644 RayPlatform/RayPlatform/store/KeyValueStoreItem.cpp
create mode 100644 RayPlatform/RayPlatform/store/KeyValueStoreItem.h
create mode 100644 RayPlatform/RayPlatform/store/KeyValueStoreRequest.cpp
create mode 100644 RayPlatform/RayPlatform/store/KeyValueStoreRequest.h
rename RayPlatform/{ => RayPlatform}/structures/MyHashTable.h (98%)
rename RayPlatform/{ => RayPlatform}/structures/MyHashTableGroup.h (98%)
rename RayPlatform/{ => RayPlatform}/structures/MyHashTableIterator.h (91%)
rename RayPlatform/{ => RayPlatform}/structures/MyStack.h (89%)
rename RayPlatform/{ => RayPlatform}/structures/SplayNode.h (92%)
rename RayPlatform/{ => RayPlatform}/structures/SplayTree.h (95%)
rename RayPlatform/{ => RayPlatform}/structures/SplayTreeIterator.h (89%)
rename RayPlatform/{ => RayPlatform}/structures/StaticVector.cpp (79%)
rename RayPlatform/{ => RayPlatform}/structures/StaticVector.h (73%)
delete mode 100644 RayPlatform/communication/Message.cpp
delete mode 100644 RayPlatform/communication/Message.h
delete mode 100644 RayPlatform/git.txt
delete mode 100644 RayPlatform/github.txt
delete mode 100644 RayPlatform/handlers/MasterModeHandler.h
delete mode 100644 RayPlatform/handlers/MessageTagHandler.h
delete mode 100644 RayPlatform/handlers/SlaveModeHandler.h
delete mode 100644 RayPlatform/memory/RingAllocator.cpp
delete mode 100644 RayPlatform/tag.txt
rename code/{plugin_Amos => Amos}/Amos.cpp (86%)
rename code/{plugin_Amos => Amos}/Amos.h (77%)
create mode 100644 code/Amos/Makefile
rename code/{plugin_CoverageGatherer => CoverageGatherer}/CoverageDistribution.cpp (93%)
rename code/{plugin_CoverageGatherer => CoverageGatherer}/CoverageDistribution.h (91%)
rename code/{plugin_CoverageGatherer => CoverageGatherer}/CoverageGatherer.cpp (82%)
rename code/{plugin_CoverageGatherer => CoverageGatherer}/CoverageGatherer.h (79%)
create mode 100644 code/CoverageGatherer/Makefile
rename code/{plugin_EdgePurger => EdgePurger}/EdgePurger.cpp (71%)
rename code/{plugin_EdgePurger => EdgePurger}/EdgePurger.h (76%)
rename code/{plugin_EdgePurger => EdgePurger}/EdgePurgerWorker.cpp (95%)
rename code/{plugin_EdgePurger => EdgePurger}/EdgePurgerWorker.h (82%)
create mode 100644 code/EdgePurger/Makefile
create mode 100644 code/Example/Example.cpp
create mode 100644 code/Example/Example.h
create mode 100644 code/Example/Makefile
rename code/{plugin_FusionData => FusionData}/FusionData.cpp (91%)
rename code/{plugin_FusionData => FusionData}/FusionData.h (83%)
create mode 100644 code/FusionData/Makefile
rename code/{plugin_FusionTaskCreator => FusionTaskCreator}/FusionTaskCreator.cpp (93%)
rename code/{plugin_FusionTaskCreator => FusionTaskCreator}/FusionTaskCreator.h (70%)
rename code/{plugin_FusionTaskCreator => FusionTaskCreator}/FusionWorker.cpp (92%)
rename code/{plugin_FusionTaskCreator => FusionTaskCreator}/FusionWorker.h (81%)
create mode 100644 code/FusionTaskCreator/Makefile
rename code/{plugin_GeneOntology => GeneOntology}/GeneOntology.cpp (98%)
rename code/{plugin_GeneOntology => GeneOntology}/GeneOntology.h (83%)
rename code/{plugin_GeneOntology => GeneOntology}/KeyEncoder.cpp (96%)
rename code/{plugin_GeneOntology => GeneOntology}/KeyEncoder.h (89%)
create mode 100644 code/GeneOntology/Makefile
rename code/{plugin_GeneOntology => GeneOntology}/types.h (100%)
rename code/{plugin_GenomeNeighbourhood => GenomeNeighbourhood}/GenomeNeighbourhood.cpp (96%)
rename code/{plugin_GenomeNeighbourhood => GenomeNeighbourhood}/GenomeNeighbourhood.h (81%)
create mode 100644 code/GenomeNeighbourhood/Makefile
rename code/{plugin_GenomeNeighbourhood => GenomeNeighbourhood}/Neighbour.cpp (95%)
rename code/{plugin_GenomeNeighbourhood => GenomeNeighbourhood}/Neighbour.h (93%)
rename code/{plugin_GenomeNeighbourhood => GenomeNeighbourhood}/NeighbourPair.cpp (93%)
rename code/{plugin_GenomeNeighbourhood => GenomeNeighbourhood}/NeighbourPair.h (94%)
rename code/{plugin_JoinerTaskCreator => JoinerTaskCreator}/JoinerTaskCreator.cpp (92%)
rename code/{plugin_JoinerTaskCreator => JoinerTaskCreator}/JoinerTaskCreator.h (72%)
rename code/{plugin_JoinerTaskCreator => JoinerTaskCreator}/JoinerWorker.cpp (83%)
rename code/{plugin_JoinerTaskCreator => JoinerTaskCreator}/JoinerWorker.h (84%)
create mode 100644 code/JoinerTaskCreator/Makefile
rename code/{plugin_KmerAcademyBuilder => KmerAcademyBuilder}/BloomFilter.cpp (93%)
rename code/{plugin_KmerAcademyBuilder => KmerAcademyBuilder}/BloomFilter.h (94%)
rename code/{plugin_KmerAcademyBuilder => KmerAcademyBuilder}/Kmer.cpp (67%)
rename code/{plugin_KmerAcademyBuilder => KmerAcademyBuilder}/Kmer.h (57%)
rename code/{plugin_KmerAcademyBuilder => KmerAcademyBuilder}/KmerAcademyBuilder.cpp (91%)
rename code/{plugin_KmerAcademyBuilder => KmerAcademyBuilder}/KmerAcademyBuilder.h (77%)
create mode 100644 code/KmerAcademyBuilder/Makefile
rename code/{plugin_Library => Library}/Library.cpp (83%)
rename code/{plugin_Library => Library}/Library.h (73%)
rename code/{plugin_Library => Library}/LibraryPeakFinder.cpp (97%)
rename code/{plugin_Library => Library}/LibraryPeakFinder.h (95%)
rename code/{plugin_Library => Library}/LibraryWorker.cpp (92%)
rename code/{plugin_Library => Library}/LibraryWorker.h (84%)
create mode 100644 code/Library/Makefile
rename code/{plugin_MachineHelper => MachineHelper}/MachineHelper.cpp (78%)
rename code/{plugin_MachineHelper => MachineHelper}/MachineHelper.h (61%)
create mode 100644 code/MachineHelper/Makefile
delete mode 100644 code/Makefile
create mode 100644 code/MessageProcessor/Makefile
rename code/{plugin_MessageProcessor => MessageProcessor}/MessageProcessor.cpp (88%)
rename code/{plugin_MessageProcessor => MessageProcessor}/MessageProcessor.h (51%)
create mode 100644 code/Mock/Makefile
create mode 100644 code/Mock/Mock.cpp
rename RayPlatform/cryptography/crypto.h => code/Mock/Mock.h (66%)
rename code/{application_core => Mock}/Parameters.cpp (86%)
rename code/{application_core => Mock}/Parameters.h (91%)
rename code/{application_core => Mock}/common_functions.cpp (71%)
rename code/{application_core => Mock}/common_functions.h (73%)
rename code/{application_core => Mock}/constants.h (62%)
create mode 100644 code/NetworkTest/Makefile
rename code/{plugin_NetworkTest => NetworkTest}/NetworkTest.cpp (86%)
rename code/{plugin_NetworkTest => NetworkTest}/NetworkTest.h (79%)
create mode 100644 code/Partitioner/Makefile
rename code/{plugin_Partitioner => Partitioner}/Partitioner.cpp (84%)
rename code/{plugin_Partitioner => Partitioner}/Partitioner.h (77%)
create mode 100644 code/PathEvaluator/Makefile
create mode 100644 code/PathEvaluator/PathEvaluator.cpp
create mode 100644 code/PathEvaluator/PathEvaluator.h
create mode 100644 code/Scaffolder/Makefile
rename code/{plugin_Scaffolder => Scaffolder}/Scaffolder.cpp (75%)
rename code/{plugin_Scaffolder => Scaffolder}/Scaffolder.h (71%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingAlgorithm.cpp (94%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingAlgorithm.h (86%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingEdge.cpp (97%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingEdge.h (92%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingLink.cpp (92%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingLink.h (95%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingVertex.cpp (92%)
rename code/{plugin_Scaffolder => Scaffolder}/ScaffoldingVertex.h (85%)
rename code/{plugin_Scaffolder => Scaffolder}/SummarizedLink.cpp (92%)
rename code/{plugin_Scaffolder => Scaffolder}/SummarizedLink.h (89%)
rename code/{plugin_Searcher => Searcher}/ColorSet.cpp (99%)
rename code/{plugin_Searcher => Searcher}/ColorSet.h (99%)
rename code/{plugin_Searcher => Searcher}/ColoredPeakFinder.cpp (97%)
rename code/{plugin_Searcher => Searcher}/ColoredPeakFinder.h (96%)
rename code/{plugin_Searcher => Searcher}/ContigHit.cpp (96%)
rename code/{plugin_Searcher => Searcher}/ContigHit.h (90%)
rename code/{plugin_Searcher => Searcher}/ContigSearchEntry.cpp (97%)
rename code/{plugin_Searcher => Searcher}/ContigSearchEntry.h (91%)
rename code/{plugin_Searcher => Searcher}/DistributionWriter.cpp (96%)
rename code/{plugin_Searcher => Searcher}/DistributionWriter.h (94%)
create mode 100644 code/Searcher/Makefile
rename code/{plugin_Searcher => Searcher}/QualityCaller.cpp (97%)
rename code/{plugin_Searcher => Searcher}/QualityCaller.h (94%)
rename code/{plugin_Searcher => Searcher}/SearchDirectory.cpp (96%)
rename code/{plugin_Searcher => Searcher}/SearchDirectory.h (93%)
rename code/{plugin_Searcher => Searcher}/Searcher.cpp (98%)
rename code/{plugin_Searcher => Searcher}/Searcher.h (76%)
rename code/{plugin_Searcher => Searcher}/VirtualKmerColor.cpp (97%)
rename code/{plugin_Searcher => Searcher}/VirtualKmerColor.h (95%)
rename code/{plugin_SeedExtender => SeedExtender}/BubbleData.h (86%)
rename code/{plugin_SeedExtender => SeedExtender}/BubbleTool.cpp (97%)
rename code/{plugin_SeedExtender => SeedExtender}/BubbleTool.h (87%)
rename code/{plugin_SeedExtender => SeedExtender}/Chooser.cpp (94%)
rename code/{plugin_SeedExtender => SeedExtender}/Chooser.h (88%)
rename code/{plugin_SeedExtender => SeedExtender}/DepthFirstSearchData.cpp (95%)
rename code/{plugin_SeedExtender => SeedExtender}/DepthFirstSearchData.h (88%)
rename code/{plugin_SeedExtender => SeedExtender}/Direction.cpp (85%)
rename code/{plugin_SeedExtender => SeedExtender}/Direction.h (87%)
rename code/{plugin_SeedExtender => SeedExtender}/ExtensionData.cpp (82%)
rename code/{plugin_SeedExtender => SeedExtender}/ExtensionData.h (81%)
rename code/{plugin_SeedExtender => SeedExtender}/ExtensionElement.cpp (78%)
rename code/{plugin_SeedExtender => SeedExtender}/ExtensionElement.h (79%)
create mode 100644 code/SeedExtender/Makefile
rename code/{plugin_SeedExtender => SeedExtender}/NovaEngine.cpp (98%)
rename code/{plugin_SeedExtender => SeedExtender}/NovaEngine.h (92%)
rename code/{plugin_SeedExtender => SeedExtender}/OpenAssemblerChooser.cpp (98%)
rename code/{plugin_SeedExtender => SeedExtender}/OpenAssemblerChooser.h (91%)
rename code/{plugin_SeedExtender => SeedExtender}/ReadFetcher.cpp (93%)
rename code/{plugin_SeedExtender => SeedExtender}/ReadFetcher.h (85%)
rename code/{plugin_SeedExtender => SeedExtender}/SeedExtender.cpp (90%)
rename code/{plugin_SeedExtender => SeedExtender}/SeedExtender.h (73%)
rename code/{plugin_SeedExtender => SeedExtender}/TipWatchdog.cpp (96%)
rename code/{plugin_SeedExtender => SeedExtender}/TipWatchdog.h (82%)
rename code/{plugin_SeedExtender => SeedExtender}/VertexMessenger.cpp (92%)
rename code/{plugin_SeedExtender => SeedExtender}/VertexMessenger.h (88%)
create mode 100644 code/SeedingData/GraphPath.cpp
create mode 100644 code/SeedingData/GraphPath.h
create mode 100644 code/SeedingData/Makefile
create mode 100644 code/SeedingData/PathHandle.cpp
create mode 100644 code/SeedingData/PathHandle.h
rename code/{plugin_SeedingData => SeedingData}/SeedWorker.cpp (65%)
rename code/{plugin_SeedingData => SeedingData}/SeedWorker.h (70%)
rename code/{plugin_SeedingData => SeedingData}/SeedingData.cpp (60%)
rename code/{plugin_SeedingData => SeedingData}/SeedingData.h (74%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/DynamicVector.h (93%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/IndexerWorker.cpp (97%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/IndexerWorker.h (86%)
create mode 100644 code/SequencesIndexer/Makefile
rename code/{plugin_SequencesIndexer => SequencesIndexer}/PairedRead.cpp (81%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/PairedRead.h (85%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/ReadAnnotation.cpp (85%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/ReadAnnotation.h (87%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/SequencesIndexer.cpp (95%)
rename code/{plugin_SequencesIndexer => SequencesIndexer}/SequencesIndexer.h (75%)
rename code/{plugin_SequencesLoader => SequencesLoader}/ArrayOfReads.cpp (96%)
rename code/{plugin_SequencesLoader => SequencesLoader}/ArrayOfReads.h (90%)
create mode 100644 code/SequencesLoader/BufferedReader.cpp
create mode 100644 code/SequencesLoader/BufferedReader.h
rename code/{plugin_SequencesLoader => SequencesLoader}/BzReader.cpp (93%)
rename code/{plugin_SequencesLoader => SequencesLoader}/BzReader.h (88%)
rename code/{plugin_SequencesLoader => SequencesLoader}/ColorSpaceDecoder.cpp (76%)
rename code/{plugin_SequencesLoader => SequencesLoader}/ColorSpaceDecoder.h (81%)
rename code/{plugin_SequencesLoader => SequencesLoader}/ColorSpaceLoader.cpp (79%)
copy code/{plugin_SequencesLoader => SequencesLoader}/ColorSpaceLoader.h (71%)
create mode 100644 code/SequencesLoader/ExportLoader.cpp
rename code/{plugin_SequencesLoader/FastqLoader.h => SequencesLoader/ExportLoader.h} (55%)
create mode 100644 code/SequencesLoader/FastaBz2Loader.cpp
rename code/{plugin_SequencesLoader/FastqGzLoader.h => SequencesLoader/FastaBz2Loader.h} (60%)
create mode 100644 code/SequencesLoader/FastaGzLoader.cpp
copy code/{plugin_SequencesLoader/ColorSpaceLoader.h => SequencesLoader/FastaGzLoader.h} (59%)
rename code/{plugin_SequencesLoader => SequencesLoader}/FastaLoader.cpp (89%)
rename code/{plugin_SequencesLoader => SequencesLoader}/FastaLoader.h (69%)
create mode 100644 code/SequencesLoader/FastaLoaderForReads.cpp
copy code/{plugin_SequencesLoader/ColorSpaceLoader.h => SequencesLoader/FastaLoaderForReads.h} (63%)
rename code/{plugin_SequencesLoader => SequencesLoader}/FastqBz2Loader.cpp (62%)
rename code/{plugin_SequencesLoader => SequencesLoader}/FastqBz2Loader.h (58%)
create mode 100644 code/SequencesLoader/FastqGzLoader.cpp
create mode 100644 code/SequencesLoader/FastqGzLoader.h
create mode 100644 code/SequencesLoader/FastqLoader.cpp
rename code/{plugin_SequencesLoader/ColorSpaceLoader.h => SequencesLoader/FastqLoader.h} (59%)
create mode 100644 code/SequencesLoader/Loader.cpp
rename code/{plugin_SequencesLoader => SequencesLoader}/Loader.h (55%)
create mode 100644 code/SequencesLoader/LoaderFactory.cpp
create mode 100644 code/SequencesLoader/LoaderFactory.h
create mode 100644 code/SequencesLoader/LoaderInterface.cpp
copy code/{plugin_PhylogenyViewer/GenomeToTaxonLoader.h => SequencesLoader/LoaderInterface.h} (50%)
create mode 100644 code/SequencesLoader/Makefile
rename code/{plugin_SequencesLoader => SequencesLoader}/Read.cpp (85%)
rename code/{plugin_SequencesLoader => SequencesLoader}/Read.h (85%)
create mode 100644 code/SequencesLoader/ReadHandle.cpp
create mode 100644 code/SequencesLoader/ReadHandle.h
create mode 100644 code/SequencesLoader/SequenceFileDetector.cpp
create mode 100644 code/SequencesLoader/SequenceFileDetector.h
rename code/{plugin_SequencesLoader => SequencesLoader}/SequencesLoader.cpp (70%)
rename code/{plugin_SequencesLoader => SequencesLoader}/SequencesLoader.h (62%)
rename code/{plugin_SequencesLoader => SequencesLoader}/SffLoader.cpp (88%)
rename code/{plugin_SequencesLoader => SequencesLoader}/SffLoader.h (70%)
create mode 100644 code/SpuriousSeedAnnihilator/AnnihilationWorker.cpp
create mode 100644 code/SpuriousSeedAnnihilator/AnnihilationWorker.h
create mode 100644 code/SpuriousSeedAnnihilator/AnnotationFetcher.cpp
create mode 100644 code/SpuriousSeedAnnihilator/AnnotationFetcher.h
create mode 100644 code/SpuriousSeedAnnihilator/AttributeFetcher.cpp
create mode 100644 code/SpuriousSeedAnnihilator/AttributeFetcher.h
create mode 100644 code/SpuriousSeedAnnihilator/GossipAssetManager.cpp
create mode 100644 code/SpuriousSeedAnnihilator/GossipAssetManager.h
create mode 100644 code/SpuriousSeedAnnihilator/GraphExplorer.cpp
create mode 100644 code/SpuriousSeedAnnihilator/GraphExplorer.h
create mode 100644 code/SpuriousSeedAnnihilator/GraphSearchResult.cpp
create mode 100644 code/SpuriousSeedAnnihilator/GraphSearchResult.h
create mode 100644 code/SpuriousSeedAnnihilator/Makefile
create mode 100644 code/SpuriousSeedAnnihilator/NanoMerger.cpp
create mode 100644 code/SpuriousSeedAnnihilator/NanoMerger.h
create mode 100644 code/SpuriousSeedAnnihilator/SeedFilteringWorkflow.cpp
create mode 100644 code/SpuriousSeedAnnihilator/SeedFilteringWorkflow.h
create mode 100644 code/SpuriousSeedAnnihilator/SeedGossipSolver.cpp
create mode 100644 code/SpuriousSeedAnnihilator/SeedGossipSolver.h
create mode 100644 code/SpuriousSeedAnnihilator/SeedMergingWorkflow.cpp
create mode 100644 code/SpuriousSeedAnnihilator/SeedMergingWorkflow.h
create mode 100644 code/SpuriousSeedAnnihilator/SpuriousSeedAnnihilator.cpp
create mode 100644 code/SpuriousSeedAnnihilator/SpuriousSeedAnnihilator.h
create mode 100644 code/Surveyor/CoalescenceManager.cpp
create mode 100644 code/Surveyor/CoalescenceManager.h
create mode 100644 code/Surveyor/ExperimentVertex.cpp
create mode 100644 code/Surveyor/ExperimentVertex.h
create mode 100644 code/Surveyor/GenomeGraphReader.cpp
create mode 100644 code/Surveyor/GenomeGraphReader.h
create mode 100644 code/Surveyor/Makefile
create mode 100644 code/Surveyor/MatrixOwner.cpp
create mode 100644 code/Surveyor/MatrixOwner.h
create mode 100644 code/Surveyor/Mother.cpp
create mode 100644 code/Surveyor/Mother.h
create mode 100644 code/Surveyor/StoreKeeper.cpp
create mode 100644 code/Surveyor/StoreKeeper.h
rename code/{plugin_PhylogenyViewer => TaxonomyViewer}/GenomeToTaxonLoader.cpp (94%)
rename code/{plugin_PhylogenyViewer => TaxonomyViewer}/GenomeToTaxonLoader.h (91%)
create mode 100644 code/TaxonomyViewer/Makefile
rename code/{plugin_PhylogenyViewer => TaxonomyViewer}/TaxonNameLoader.cpp (95%)
rename code/{plugin_PhylogenyViewer => TaxonomyViewer}/TaxonNameLoader.h (91%)
rename code/{plugin_PhylogenyViewer/PhylogeneticTreeLoader.cpp => TaxonomyViewer/TaxonomicTreeLoader.cpp} (83%)
rename code/{plugin_PhylogenyViewer/PhylogeneticTreeLoader.h => TaxonomyViewer/TaxonomicTreeLoader.h} (83%)
rename code/{plugin_PhylogenyViewer/PhylogenyViewer.cpp => TaxonomyViewer/TaxonomyViewer.cpp} (91%)
rename code/{plugin_PhylogenyViewer/PhylogenyViewer.h => TaxonomyViewer/TaxonomyViewer.h} (83%)
rename code/{plugin_PhylogenyViewer => TaxonomyViewer}/types.h (100%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/GridTable.cpp (83%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/GridTable.h (86%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/GridTableIterator.cpp (88%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/GridTableIterator.h (82%)
create mode 100644 code/VerticesExtractor/Makefile
rename code/{plugin_VerticesExtractor => VerticesExtractor}/Vertex.cpp (74%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/Vertex.h (73%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/VerticesExtractor.cpp (86%)
rename code/{plugin_VerticesExtractor => VerticesExtractor}/VerticesExtractor.h (76%)
delete mode 100644 code/plugin_Amos/Makefile
delete mode 100644 code/plugin_CoverageGatherer/Makefile
delete mode 100644 code/plugin_EdgePurger/Makefile
delete mode 100644 code/plugin_FusionData/Makefile
delete mode 100644 code/plugin_FusionTaskCreator/Makefile
delete mode 100644 code/plugin_GeneOntology/Makefile
delete mode 100644 code/plugin_GenomeNeighbourhood/Makefile
delete mode 100644 code/plugin_JoinerTaskCreator/Makefile
delete mode 100644 code/plugin_KmerAcademyBuilder/Makefile
delete mode 100644 code/plugin_Library/Makefile
delete mode 100644 code/plugin_MachineHelper/Makefile
delete mode 100644 code/plugin_MessageProcessor/Makefile
delete mode 100644 code/plugin_NetworkTest/Makefile
delete mode 100644 code/plugin_Partitioner/Makefile
delete mode 100644 code/plugin_PhylogenyViewer/Makefile
delete mode 100644 code/plugin_Scaffolder/Makefile
delete mode 100644 code/plugin_Searcher/Makefile
delete mode 100644 code/plugin_SeedExtender/Makefile
delete mode 100644 code/plugin_SeedingData/AssemblySeed.cpp
delete mode 100644 code/plugin_SeedingData/AssemblySeed.h
delete mode 100644 code/plugin_SeedingData/Makefile
delete mode 100644 code/plugin_SequencesIndexer/Makefile
delete mode 100644 code/plugin_SequencesLoader/FastqGzLoader.cpp
delete mode 100644 code/plugin_SequencesLoader/FastqLoader.cpp
delete mode 100644 code/plugin_SequencesLoader/Loader.cpp
delete mode 100644 code/plugin_SequencesLoader/Makefile
delete mode 100644 code/plugin_VerticesExtractor/Makefile
delete mode 100644 git.txt
delete mode 100644 github.txt
delete mode 100755 scripts/install.sh
delete mode 100644 tag.txt
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