Created
February 7, 2013 02:27
-
-
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This is a draft patch for dumping scaffolds in a file in less time.
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| diff --git a/code/plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp b/code/plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp | |
| index e9d80f6..7a42732 100644 | |
| --- a/code/plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp | |
| +++ b/code/plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp | |
| @@ -1107,7 +1107,6 @@ void GenomeNeighbourhood::resolveSymbols(ComputeCore*core){ | |
| m_parameters=(Parameters*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/Parameters.ray"); | |
| m_contigLengths=(map<PathHandle,int>*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/ContigLengths.ray"); | |
| - | |
| m_virtualCommunicator=core->getVirtualCommunicator(); | |
| m_core=core; | |
| diff --git a/code/plugin_MachineHelper/MachineHelper.cpp b/code/plugin_MachineHelper/MachineHelper.cpp | |
| index 5e0e6de..c7181ea 100644 | |
| --- a/code/plugin_MachineHelper/MachineHelper.cpp | |
| +++ b/code/plugin_MachineHelper/MachineHelper.cpp | |
| @@ -1191,6 +1191,9 @@ void MachineHelper::registerPlugin(ComputeCore*core){ | |
| RAY_MPI_TAG_GOOD_JOB_SEE_YOU_SOON_REPLY=core->allocateMessageTagHandle(plugin); | |
| core->setMessageTagSymbol(plugin,RAY_MPI_TAG_GOOD_JOB_SEE_YOU_SOON_REPLY,"RAY_MPI_TAG_GOOD_JOB_SEE_YOU_SOON_REPLY"); | |
| + | |
| + core->setObjectSymbol(m_plugin,&(m_ed->m_EXTENSION_contigs),"/RayAssembler/ObjectStore/ContigPaths.ray"); | |
| + core->setObjectSymbol(m_plugin,&(m_ed->m_EXTENSION_identifiers),"/RayAssembler/ObjectStore/ContigNames.ray"); | |
| } | |
| void MachineHelper::resolveSymbols(ComputeCore*core){ | |
| @@ -1358,9 +1361,6 @@ void MachineHelper::resolveSymbols(ComputeCore*core){ | |
| core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_GOOD_JOB_SEE_YOU_SOON, RAY_SLAVE_MODE_DIE); | |
| - core->setObjectSymbol(m_plugin,&(m_ed->m_EXTENSION_contigs),"/RayAssembler/ObjectStore/ContigPaths.ray"); | |
| - core->setObjectSymbol(m_plugin,&(m_ed->m_EXTENSION_identifiers),"/RayAssembler/ObjectStore/ContigNames.ray"); | |
| - | |
| __BindPlugin(MachineHelper); | |
| __BindAdapter(MachineHelper,RAY_MASTER_MODE_LOAD_CONFIG); | |
| diff --git a/code/plugin_MessageProcessor/MessageProcessor.cpp b/code/plugin_MessageProcessor/MessageProcessor.cpp | |
| index b186fd4..d29b112 100644 | |
| --- a/code/plugin_MessageProcessor/MessageProcessor.cpp | |
| +++ b/code/plugin_MessageProcessor/MessageProcessor.cpp | |
| @@ -145,7 +145,6 @@ __CreateMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_SEND_COVERAGE_VALUES_REPL | |
| __CreateMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_READ_SEQUENCE); | |
| __CreateMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_READ_SEQUENCE_REPLY); | |
| __CreateMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_I_FINISHED_SCAFFOLDING); | |
| -__CreateMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_CONTIG_CHUNK); | |
| void MessageProcessor::call_RAY_MPI_TAG_CONTIG_INFO(Message*message){ | |
| MessageUnit*incoming=(MessageUnit*)message->getBuffer(); | |
| @@ -2454,33 +2453,6 @@ void MessageProcessor::call_RAY_MPI_TAG_I_FINISHED_SCAFFOLDING(Message*message){ | |
| } | |
| } | |
| -void MessageProcessor::call_RAY_MPI_TAG_GET_CONTIG_CHUNK(Message*message){ | |
| - MessageUnit*incoming=(MessageUnit*)message->getBuffer(); | |
| - PathHandle contigId=incoming[0]; | |
| - int position=incoming[1]; | |
| - int index=m_fusionData->m_FUSION_identifier_map[contigId]; | |
| - int length=m_ed->m_EXTENSION_contigs[index].size(); | |
| - MessageUnit*messageContent=(MessageUnit*)m_outboxAllocator->allocate(MAXIMUM_MESSAGE_SIZE_IN_BYTES); | |
| - int outputPosition=0; | |
| - int origin=outputPosition; | |
| - outputPosition++; | |
| - int count=0; | |
| - | |
| - while(position<length | |
| - && (outputPosition+KMER_U64_ARRAY_SIZE)<(int)(MAXIMUM_MESSAGE_SIZE_IN_BYTES/sizeof(MessageUnit))){ | |
| - Kmer theKmerObject; | |
| - m_ed->m_EXTENSION_contigs[index].at(position++,&theKmerObject); | |
| - theKmerObject.pack(messageContent,&outputPosition); | |
| - count++; | |
| - } | |
| - messageContent[origin]=count; | |
| - Message aMessage(messageContent, | |
| - m_virtualCommunicator->getElementsPerQuery(RAY_MPI_TAG_GET_CONTIG_CHUNK), | |
| - message->getSource(),RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY, | |
| - m_parameters->getRank()); | |
| - m_outbox->push_back(&aMessage); | |
| -} | |
| - | |
| void MessageProcessor::setScaffolder(Scaffolder*a){ | |
| m_scaffolder=a; | |
| } | |
| @@ -3031,9 +3003,6 @@ void MessageProcessor::registerPlugin(ComputeCore*core){ | |
| core->setMessageTagObjectHandler(plugin,RAY_MPI_TAG_I_FINISHED_SCAFFOLDING, __GetAdapter(MessageProcessor,RAY_MPI_TAG_I_FINISHED_SCAFFOLDING)); | |
| core->setMessageTagSymbol(plugin,RAY_MPI_TAG_I_FINISHED_SCAFFOLDING,"RAY_MPI_TAG_I_FINISHED_SCAFFOLDING"); | |
| - RAY_MPI_TAG_GET_CONTIG_CHUNK=core->allocateMessageTagHandle(plugin); | |
| - core->setMessageTagObjectHandler(plugin,RAY_MPI_TAG_GET_CONTIG_CHUNK, __GetAdapter(MessageProcessor,RAY_MPI_TAG_GET_CONTIG_CHUNK)); | |
| - core->setMessageTagSymbol(plugin,RAY_MPI_TAG_GET_CONTIG_CHUNK,"RAY_MPI_TAG_GET_CONTIG_CHUNK"); | |
| } | |
| @@ -3138,8 +3107,6 @@ void MessageProcessor::resolveSymbols(ComputeCore*core){ | |
| RAY_MPI_TAG_FINISH_FUSIONS=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_FINISH_FUSIONS"); | |
| RAY_MPI_TAG_FINISH_FUSIONS_FINISHED=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_FINISH_FUSIONS_FINISHED"); | |
| RAY_MPI_TAG_FUSION_DONE=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_FUSION_DONE"); | |
| - RAY_MPI_TAG_GET_CONTIG_CHUNK=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_CONTIG_CHUNK"); | |
| - RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY"); | |
| RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION"); | |
| RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION_REPLY"); | |
| RAY_MPI_TAG_GET_COVERAGE_AND_MARK=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_COVERAGE_AND_MARK"); | |
| @@ -3213,8 +3180,6 @@ void MessageProcessor::resolveSymbols(ComputeCore*core){ | |
| core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_AUTOMATIC_DISTANCE_DETECTION, RAY_SLAVE_MODE_AUTOMATIC_DISTANCE_DETECTION); | |
| core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_ASK_LIBRARY_DISTANCES, RAY_SLAVE_MODE_SEND_LIBRARY_DISTANCES); | |
| - | |
| - core->setMessageTagReplyMessageTag(m_plugin, RAY_MPI_TAG_GET_CONTIG_CHUNK, RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY ); | |
| core->setMessageTagReplyMessageTag(m_plugin, RAY_MPI_TAG_REQUEST_VERTEX_READS, RAY_MPI_TAG_REQUEST_VERTEX_READS_REPLY ); | |
| core->setMessageTagReplyMessageTag(m_plugin, RAY_MPI_TAG_GET_READ_MATE, RAY_MPI_TAG_GET_READ_MATE_REPLY ); | |
| core->setMessageTagReplyMessageTag(m_plugin, RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE, RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE_REPLY ); | |
| @@ -3234,7 +3199,6 @@ void MessageProcessor::resolveSymbols(ComputeCore*core){ | |
| core->setMessageTagReplyMessageTag(m_plugin, RAY_MPI_TAG_REQUEST_READ_SEQUENCE, RAY_MPI_TAG_REQUEST_READ_SEQUENCE_REPLY ); | |
| core->setMessageTagReplyMessageTag(m_plugin, RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES, RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES_REPLY ); | |
| - core->setMessageTagSize(m_plugin, RAY_MPI_TAG_GET_CONTIG_CHUNK, MAXIMUM_MESSAGE_SIZE_IN_BYTES/sizeof(MessageUnit) ); | |
| core->setMessageTagSize(m_plugin, RAY_MPI_TAG_REQUEST_VERTEX_READS, max(5,KMER_U64_ARRAY_SIZE+1) ); | |
| core->setMessageTagSize(m_plugin, RAY_MPI_TAG_GET_READ_MATE, 4 ); | |
| core->setMessageTagSize(m_plugin, RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE, KMER_U64_ARRAY_SIZE ); | |
| @@ -3355,6 +3319,5 @@ void MessageProcessor::resolveSymbols(ComputeCore*core){ | |
| __BindAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_READ_SEQUENCE); | |
| __BindAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_READ_SEQUENCE_REPLY); | |
| __BindAdapter(MessageProcessor,RAY_MPI_TAG_I_FINISHED_SCAFFOLDING); | |
| - __BindAdapter(MessageProcessor,RAY_MPI_TAG_GET_CONTIG_CHUNK); | |
| } | |
| diff --git a/code/plugin_MessageProcessor/MessageProcessor.h b/code/plugin_MessageProcessor/MessageProcessor.h | |
| index cb4fac3..cc0356c 100644 | |
| --- a/code/plugin_MessageProcessor/MessageProcessor.h | |
| +++ b/code/plugin_MessageProcessor/MessageProcessor.h | |
| @@ -1,6 +1,6 @@ | |
| /* | |
| - Ray | |
| - Copyright (C) 2010, 2011, 2012 Sébastien Boisvert | |
| + Ray -- Parallel genome assemblies for parallel DNA sequencing | |
| + Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert | |
| http://DeNovoAssembler.SourceForge.Net/ | |
| @@ -19,8 +19,8 @@ | |
| */ | |
| -#ifndef _MessageProcessor | |
| -#define _MessageProcessor | |
| +#ifndef _MessageProcessor_h | |
| +#define _MessageProcessor_h | |
| #include <code/plugin_SeedExtender/OpenAssemblerChooser.h> | |
| #include <code/plugin_SeedExtender/SeedExtender.h> | |
| @@ -157,13 +157,13 @@ __DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_SEND_COVERAGE_VALUES_REP | |
| __DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_READ_SEQUENCE); | |
| __DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_READ_SEQUENCE_REPLY); | |
| __DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_I_FINISHED_SCAFFOLDING); | |
| -__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_CONTIG_CHUNK); | |
| /** | |
| * MessageProcessor receives all the messages of a MPI rank | |
| * Message objects may also be checked using the Message inbox (m_inbox) | |
| * | |
| * Sometimes, a message will generate a reply (_REPLY) | |
| + * | |
| * \author Sébastien Boisvert | |
| */ | |
| class MessageProcessor : public CorePlugin { | |
| @@ -270,7 +270,6 @@ class MessageProcessor : public CorePlugin { | |
| __AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_READ_SEQUENCE); | |
| __AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_READ_SEQUENCE_REPLY); | |
| __AddAdapter(MessageProcessor,RAY_MPI_TAG_I_FINISHED_SCAFFOLDING); | |
| - __AddAdapter(MessageProcessor,RAY_MPI_TAG_GET_CONTIG_CHUNK); | |
| uint64_t m_bloomBits; | |
| @@ -342,8 +341,6 @@ class MessageProcessor : public CorePlugin { | |
| MessageTag RAY_MPI_TAG_FINISH_FUSIONS; | |
| MessageTag RAY_MPI_TAG_FINISH_FUSIONS_FINISHED; | |
| MessageTag RAY_MPI_TAG_FUSION_DONE; | |
| - MessageTag RAY_MPI_TAG_GET_CONTIG_CHUNK; | |
| - MessageTag RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY; | |
| MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION; | |
| MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION_REPLY; | |
| MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_MARK; | |
| @@ -680,12 +677,9 @@ SequencesIndexer*m_si | |
| void call_RAY_MPI_TAG_REQUEST_READ_SEQUENCE(Message*message); | |
| void call_RAY_MPI_TAG_REQUEST_READ_SEQUENCE_REPLY(Message*message); | |
| void call_RAY_MPI_TAG_I_FINISHED_SCAFFOLDING(Message*message); | |
| - void call_RAY_MPI_TAG_GET_CONTIG_CHUNK(Message*message); | |
| void registerPlugin(ComputeCore*core); | |
| void resolveSymbols(ComputeCore*core); | |
| }; | |
| #endif | |
| - | |
| - | |
| diff --git a/code/plugin_Scaffolder/Scaffolder.cpp b/code/plugin_Scaffolder/Scaffolder.cpp | |
| index 82d4a84..92c780d 100644 | |
| --- a/code/plugin_Scaffolder/Scaffolder.cpp | |
| +++ b/code/plugin_Scaffolder/Scaffolder.cpp | |
| @@ -1,5 +1,5 @@ | |
| /* | |
| - Ray | |
| + Ray -- Parallel genome assemblies for parallel DNA sequencing | |
| Copyright (C) 2011, 2012, 2013 Sébastien Boisvert | |
| http://DeNovoAssembler.SourceForge.Net/ | |
| @@ -49,6 +49,9 @@ __CreatePlugin(Scaffolder); | |
| __CreateMasterModeAdapter(Scaffolder,RAY_MASTER_MODE_WRITE_SCAFFOLDS); | |
| __CreateSlaveModeAdapter(Scaffolder,RAY_SLAVE_MODE_SCAFFOLDER); | |
| +__CreateMessageTagAdapter(Scaffolder,RAY_MPI_TAG_GET_CONTIG_CHUNK); | |
| +__CreateMessageTagAdapter(Scaffolder,RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK); | |
| + | |
| void Scaffolder::addMasterLink(SummarizedLink*a){ | |
| m_masterLinks.push_back(*a); | |
| } | |
| @@ -1423,6 +1426,84 @@ Case 16. (allowed) | |
| } | |
| void Scaffolder::getContigSequence(PathHandle id){ | |
| + int mode=0; | |
| + int CODE_PATH_VANILLA_KMERS=mode++; | |
| + int CODE_PATH_PACKED_REGION=mode++; | |
| + | |
| + int configuredCodePath=CODE_PATH_VANILLA_KMERS; | |
| + | |
| + if(configuredCodePath==CODE_PATH_VANILLA_KMERS) | |
| + getContigSequenceFromKmers(id); | |
| + else if(configuredCodePath==CODE_PATH_PACKED_REGION){ | |
| + getContigSequenceFromPackedObjects(id); | |
| + } | |
| +} | |
| + | |
| +void Scaffolder::getContigSequenceFromPackedObjects(PathHandle id){ | |
| + | |
| + if(!m_hasContigSequence_Initialised){ | |
| + m_hasContigSequence_Initialised=true; | |
| + m_rankIdForContig=getRankFromPathUniqueId(id); | |
| + m_theLengthInNucleotides=m_contigLengths[id]; | |
| + m_position=0; | |
| + m_requestedContigChunk=false; | |
| + m_contigPathBuffer.str(""); | |
| + } | |
| + | |
| + if(m_position<m_theLengthInNucleotides){ | |
| + if(!m_requestedContigChunk){ | |
| + MessageUnit*message=(MessageUnit*)m_outboxAllocator->allocate(MAXIMUM_MESSAGE_SIZE_IN_BYTES); | |
| + | |
| + int bufferPosition=0; | |
| + message[bufferPosition++]=id; | |
| + message[bufferPosition++]=m_position; | |
| + Message aMessage(message,bufferPosition, | |
| + m_rankIdForContig,RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK,m_parameters->getRank()); | |
| + m_virtualCommunicator->pushMessage(m_workerId,&aMessage); | |
| + | |
| + m_requestedContigChunk=true; | |
| + | |
| + }else if(m_virtualCommunicator->isMessageProcessed(m_workerId)){ | |
| + | |
| + vector<MessageUnit> data; | |
| + m_virtualCommunicator->getMessageResponseElements(m_workerId,&data); | |
| + /* the position in the message buffer */ | |
| + int position=0; | |
| + /* the first element is the number of nucleotides */ | |
| + int count=data[position++]; | |
| + int iterator=0; | |
| + while(iterator<count){ | |
| + int elementIndex=(iterator*2 ) / (sizeof(MessageUnit)*BITS_PER_BYTE); | |
| + int offset=(iterator*2) % (sizeof(MessageUnit)*BITS_PER_BYTE); | |
| + | |
| + #ifdef ASSERT | |
| + assert(sizeof(MessageUnit)==sizeof(uint64_t)); | |
| + #endif | |
| + | |
| + uint64_t value=data[position+elementIndex]; | |
| + | |
| + value <<= ( sizeof(MessageUnit) - BITS_PER_NUCLEOTIDE - offset); | |
| + value>>= (sizeof(MessageUnit) - BITS_PER_NUCLEOTIDE ); | |
| + | |
| + char nucleotide=codeToChar(value,m_parameters->getColorSpaceMode()); | |
| + | |
| + m_contigPathBuffer<<nucleotide; | |
| + } | |
| + m_position+=count; | |
| + m_requestedContigChunk=false; | |
| + } | |
| + }else{ | |
| + m_contigSequence=m_contigPathBuffer.str(); | |
| + m_hasContigSequence=true; | |
| + | |
| + #ifdef ASSERT | |
| + assert((int)m_contigSequence.length()==m_theLengthInNucleotides); | |
| + #endif | |
| + } | |
| +} | |
| + | |
| +void Scaffolder::getContigSequenceFromKmers(PathHandle id){ | |
| + | |
| if(!m_hasContigSequence_Initialised){ | |
| m_hasContigSequence_Initialised=true; | |
| m_rankIdForContig=getRankFromPathUniqueId(id); | |
| @@ -1526,6 +1607,7 @@ void Scaffolder::call_RAY_MASTER_MODE_WRITE_SCAFFOLDS(){ | |
| m_positionOnScaffold++; | |
| /* | |
| + * | |
| * Only add a new line if there is something more to add. | |
| */ | |
| if(m_positionOnScaffold%columns==0 && contigPosition < length){ | |
| @@ -1591,6 +1673,86 @@ void Scaffolder::setTimePrinter(TimePrinter*a){ | |
| m_timePrinter=a; | |
| } | |
| +void Scaffolder::call_RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK(Message*message){ | |
| +// TODO: this returns a part of a region, in 2-bit encoding | |
| + | |
| + MessageUnit*incoming=(MessageUnit*)message->getBuffer(); | |
| + int thePosition=0; | |
| + PathHandle contigId=incoming[thePosition++]; | |
| + int position=incoming[thePosition++]; | |
| + | |
| +#ifdef ASSERT | |
| + assert(m_contigNameIndex->count(contigId)>0); | |
| +#endif | |
| + | |
| + int index=(*m_contigNameIndex)[contigId]; | |
| + int length=(*m_contigs)[index].size(); | |
| + MessageUnit*messageContent=(MessageUnit*)m_outboxAllocator->allocate(MAXIMUM_MESSAGE_SIZE_IN_BYTES); | |
| + int outputPosition=0; | |
| + int origin=outputPosition; | |
| + outputPosition++; | |
| + int count=0; | |
| + | |
| + while(position<length | |
| + && (outputPosition+KMER_U64_ARRAY_SIZE)<(int)(MAXIMUM_MESSAGE_SIZE_IN_BYTES/sizeof(MessageUnit))){ | |
| + Kmer theKmerObject; | |
| + | |
| +#ifdef ASSERT | |
| + assert(index<(int)m_contigs->size()); | |
| +#endif | |
| + | |
| + (*m_contigs)[index].at(position++,&theKmerObject); | |
| + theKmerObject.pack(messageContent,&outputPosition); | |
| + count++; | |
| + } | |
| + messageContent[origin]=count; | |
| + Message aMessage(messageContent, | |
| + m_virtualCommunicator->getElementsPerQuery(RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK), | |
| + message->getSource(),RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK_REPLY, | |
| + m_parameters->getRank()); | |
| + m_outbox->push_back(&aMessage); | |
| +} | |
| + | |
| +void Scaffolder::call_RAY_MPI_TAG_GET_CONTIG_CHUNK(Message*message){ | |
| + MessageUnit*incoming=(MessageUnit*)message->getBuffer(); | |
| + int thePosition=0; | |
| + PathHandle contigId=incoming[thePosition++]; | |
| + int position=incoming[thePosition++]; | |
| + | |
| +#ifdef ASSERT | |
| + assert(m_contigNameIndex->count(contigId)>0); | |
| +#endif | |
| + | |
| + int index=(*m_contigNameIndex)[contigId]; | |
| + int length=(*m_contigs)[index].size(); | |
| + MessageUnit*messageContent=(MessageUnit*)m_outboxAllocator->allocate(MAXIMUM_MESSAGE_SIZE_IN_BYTES); | |
| + int outputPosition=0; | |
| + int origin=outputPosition; | |
| + outputPosition++; | |
| + int count=0; | |
| + | |
| + while(position<length | |
| + && (outputPosition+KMER_U64_ARRAY_SIZE)<(int)(MAXIMUM_MESSAGE_SIZE_IN_BYTES/sizeof(MessageUnit))){ | |
| + Kmer theKmerObject; | |
| + | |
| +#ifdef ASSERT | |
| + assert(index<(int)m_contigs->size()); | |
| +#endif | |
| + (*m_contigs)[index].at(position++,&theKmerObject); | |
| + theKmerObject.pack(messageContent,&outputPosition); | |
| + count++; | |
| + } | |
| + | |
| + messageContent[origin]=count; | |
| + Message aMessage(messageContent, | |
| + m_virtualCommunicator->getElementsPerQuery(RAY_MPI_TAG_GET_CONTIG_CHUNK), | |
| + message->getSource(),RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY, | |
| + m_parameters->getRank()); | |
| + m_outbox->push_back(&aMessage); | |
| +} | |
| + | |
| + | |
| + | |
| void Scaffolder::registerPlugin(ComputeCore*core){ | |
| PluginHandle plugin=core->allocatePluginHandle(); | |
| @@ -1614,6 +1776,19 @@ void Scaffolder::registerPlugin(ComputeCore*core){ | |
| RAY_MPI_TAG_START_SCAFFOLDER=core->allocateMessageTagHandle(plugin); | |
| core->setMessageTagSymbol(plugin,RAY_MPI_TAG_START_SCAFFOLDER,"RAY_MPI_TAG_START_SCAFFOLDER"); | |
| + | |
| + RAY_MPI_TAG_GET_CONTIG_CHUNK=core->allocateMessageTagHandle(plugin); | |
| + core->setMessageTagObjectHandler(plugin,RAY_MPI_TAG_GET_CONTIG_CHUNK, __GetAdapter(Scaffolder,RAY_MPI_TAG_GET_CONTIG_CHUNK)); | |
| + core->setMessageTagSymbol(plugin,RAY_MPI_TAG_GET_CONTIG_CHUNK,"RAY_MPI_TAG_GET_CONTIG_CHUNK"); | |
| + | |
| + RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK=core->allocateMessageTagHandle(plugin); | |
| + core->setMessageTagObjectHandler(plugin,RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK, __GetAdapter(Scaffolder,RAY_MPI_TAG_GET_CONTIG_CHUNK)); | |
| + core->setMessageTagSymbol(plugin,RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK,"RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK"); | |
| + | |
| + RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY=core->allocateMessageTagHandle(plugin); | |
| + core->setMessageTagSymbol(plugin,RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY,"RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY"); | |
| + RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK_REPLY=core->allocateMessageTagHandle(plugin); | |
| + core->setMessageTagSymbol(plugin,RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK_REPLY,"RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK_REPLY"); | |
| } | |
| void Scaffolder::resolveSymbols(ComputeCore*core){ | |
| @@ -1626,6 +1801,7 @@ void Scaffolder::resolveSymbols(ComputeCore*core){ | |
| RAY_MPI_TAG_CONTIG_INFO=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_CONTIG_INFO"); | |
| RAY_MPI_TAG_GET_CONTIG_CHUNK=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_CONTIG_CHUNK"); | |
| + RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK"); | |
| RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION"); | |
| RAY_MPI_TAG_GET_PATH_LENGTH=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_PATH_LENGTH"); | |
| RAY_MPI_TAG_GET_READ_MARKERS=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_READ_MARKERS"); | |
| @@ -1640,12 +1816,33 @@ void Scaffolder::resolveSymbols(ComputeCore*core){ | |
| RAY_MPI_TAG_SCAFFOLDING_LINKS_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_SCAFFOLDING_LINKS_REPLY"); | |
| RAY_MPI_TAG_START_SCAFFOLDER=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_START_SCAFFOLDER"); | |
| + RAY_MPI_TAG_GET_CONTIG_CHUNK=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_CONTIG_CHUNK"); | |
| + RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY"); | |
| + RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK"); | |
| + RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK_REPLY"); | |
| + | |
| core->setMessageTagToSlaveModeSwitch(m_plugin, RAY_MPI_TAG_START_SCAFFOLDER, RAY_SLAVE_MODE_SCAFFOLDER ); | |
| core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_WRITE_SCAFFOLDS, RAY_MASTER_MODE_COUNT_SEARCH_ELEMENTS); | |
| +// the two message tags below won't multiplex very well during the transit | |
| +// in the virtual messaging layer of Ray Platform | |
| + | |
| + core->setMessageTagReplyMessageTag(m_plugin, RAY_MPI_TAG_GET_CONTIG_CHUNK, RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY ); | |
| + core->setMessageTagSize(m_plugin, RAY_MPI_TAG_GET_CONTIG_CHUNK, MAXIMUM_MESSAGE_SIZE_IN_BYTES/sizeof(MessageUnit) ); | |
| + core->setMessageTagReplyMessageTag(m_plugin, RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK, RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK_REPLY ); | |
| + core->setMessageTagSize(m_plugin, RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK, MAXIMUM_MESSAGE_SIZE_IN_BYTES/sizeof(MessageUnit) ); | |
| + | |
| __BindPlugin(Scaffolder); | |
| __BindAdapter(Scaffolder,RAY_MASTER_MODE_WRITE_SCAFFOLDS); | |
| __BindAdapter(Scaffolder,RAY_SLAVE_MODE_SCAFFOLDER); | |
| + __BindAdapter(MessageProcessor,RAY_MPI_TAG_GET_CONTIG_CHUNK); | |
| + __BindAdapter(MessageProcessor,RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK); | |
| + | |
| +#if 0 | |
| + m_contigs=(vector<GraphPath>*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/ContigPaths.ray"); | |
| +#endif | |
| + | |
| + m_contigNameIndex=(map<PathHandle,int>*)core->getObjectFromSymbol(m_plugin, "/RayAssembler/ObjectStore/ContigNameIndex.ray"); | |
| } | |
| diff --git a/code/plugin_Scaffolder/Scaffolder.h b/code/plugin_Scaffolder/Scaffolder.h | |
| index 8701abc..c8e4e16 100644 | |
| --- a/code/plugin_Scaffolder/Scaffolder.h | |
| +++ b/code/plugin_Scaffolder/Scaffolder.h | |
| @@ -1,5 +1,5 @@ | |
| /* | |
| - Ray | |
| + Ray -- Parallel genome assemblies for parallel DNA sequencing | |
| Copyright (C) 2011, 2012, 2013 Sébastien Boisvert | |
| http://DeNovoAssembler.SourceForge.Net/ | |
| @@ -19,8 +19,8 @@ | |
| */ | |
| -#ifndef _Scaffolder | |
| -#define _Scaffolder | |
| +#ifndef _Scaffolder_h | |
| +#define _Scaffolder_h | |
| #include "ScaffoldingLink.h" | |
| #include "SummarizedLink.h" | |
| @@ -47,6 +47,8 @@ __DeclarePlugin(Scaffolder); | |
| __DeclareMasterModeAdapter(Scaffolder,RAY_MASTER_MODE_WRITE_SCAFFOLDS); | |
| __DeclareSlaveModeAdapter(Scaffolder,RAY_SLAVE_MODE_SCAFFOLDER); | |
| +__DeclareMessageTagAdapter(Scaffolder,RAY_MPI_TAG_GET_CONTIG_CHUNK); | |
| +__DeclareMessageTagAdapter(Scaffolder,RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK); | |
| /** | |
| * Scaffolder class, it uses MPI through the virtual communicator. | |
| @@ -57,6 +59,8 @@ class Scaffolder : public CorePlugin{ | |
| __AddAdapter(Scaffolder,RAY_MASTER_MODE_WRITE_SCAFFOLDS); | |
| __AddAdapter(Scaffolder,RAY_SLAVE_MODE_SCAFFOLDER); | |
| + __AddAdapter(Scaffolder,RAY_MPI_TAG_GET_CONTIG_CHUNK); | |
| + __AddAdapter(Scaffolder,RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK); | |
| ostringstream m_operationBuffer; | |
| @@ -66,6 +70,9 @@ class Scaffolder : public CorePlugin{ | |
| MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS; | |
| MessageTag RAY_MPI_TAG_CONTIG_INFO; | |
| MessageTag RAY_MPI_TAG_GET_CONTIG_CHUNK; | |
| + MessageTag RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY; | |
| + MessageTag RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK; | |
| + MessageTag RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK_REPLY; | |
| MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION; | |
| MessageTag RAY_MPI_TAG_GET_PATH_LENGTH; | |
| MessageTag RAY_MPI_TAG_GET_READ_MARKERS; | |
| @@ -188,10 +195,15 @@ class Scaffolder : public CorePlugin{ | |
| RingAllocator*m_outboxAllocator; | |
| bool m_ready; | |
| - /** | |
| +/** | |
| * gets a contig sequence by receiving several MPI messages | |
| */ | |
| + | |
| + map<PathHandle,int>*m_contigNameIndex; | |
| + | |
| void getContigSequence(PathHandle id); | |
| + void getContigSequenceFromKmers(PathHandle id); | |
| + void getContigSequenceFromPackedObjects(PathHandle id); | |
| void processContig(); | |
| void processContigPosition(); | |
| void processVertex(Kmer*vertex); | |
| @@ -211,26 +223,38 @@ class Scaffolder : public CorePlugin{ | |
| void getCoverageOfBlockOfLife(); | |
| Rank m_rank; | |
| + | |
| +/* | |
| + * Variables for fetching remote paths. | |
| + */ | |
| + | |
| + int m_theLengthInNucleotides; | |
| + ostringstream m_contigPathBuffer; | |
| public: | |
| bool m_initialised; | |
| - /** | |
| +/** | |
| * Number of ranks that have finished scaffolding | |
| */ | |
| int m_numberOfRanksFinished; | |
| - | |
| - /** | |
| +/** | |
| * Constructor of the scaffolder | |
| */ | |
| void constructor(StaticVector*outbox,StaticVector*inbox,RingAllocator*outboxAllocator,Parameters*parameters, | |
| VirtualCommunicator*vc,SwitchMan*switchMan); | |
| - void call_RAY_SLAVE_MODE_SCAFFOLDER(); | |
| void setContigPaths(vector<PathHandle>*names,vector<GraphPath>*paths); | |
| void addMasterLink(SummarizedLink*link); | |
| void solve(); | |
| void addMasterContig(PathHandle name,int length); | |
| + | |
| void call_RAY_MASTER_MODE_WRITE_SCAFFOLDS(); | |
| + | |
| + void call_RAY_SLAVE_MODE_SCAFFOLDER(); | |
| + | |
| + void call_RAY_MPI_TAG_GET_CONTIG_CHUNK(Message*message); | |
| + void call_RAY_MPI_TAG_GET_CONTIG_PACKED_CHUNK(Message*message); | |
| + | |
| void printFinalMessage(); | |
| void setTimePrinter(TimePrinter*a); | |
| @@ -240,4 +264,3 @@ public: | |
| }; | |
| #endif | |
| - | |
| diff --git a/code/plugin_SeedExtender/SeedExtender.cpp b/code/plugin_SeedExtender/SeedExtender.cpp | |
| index d1111a8..6fff453 100644 | |
| --- a/code/plugin_SeedExtender/SeedExtender.cpp | |
| +++ b/code/plugin_SeedExtender/SeedExtender.cpp | |
| @@ -1,5 +1,5 @@ | |
| /* | |
| - Ray | |
| + Ray -- Parallel genome assemblies for parallel DNA sequencing | |
| Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert | |
| http://DeNovoAssembler.SourceForge.Net/ | |
| @@ -2668,9 +2668,6 @@ void SeedExtender::registerPlugin(ComputeCore*core){ | |
| RAY_MPI_TAG_CONTIG_INFO_REPLY=core->allocateMessageTagHandle(plugin); | |
| core->setMessageTagSymbol(plugin,RAY_MPI_TAG_CONTIG_INFO_REPLY,"RAY_MPI_TAG_CONTIG_INFO_REPLY"); | |
| - RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY=core->allocateMessageTagHandle(plugin); | |
| - core->setMessageTagSymbol(plugin,RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY,"RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY"); | |
| - | |
| m_switchMan=core->getSwitchMan(); | |
| RAY_MPI_TAG_ASK_IS_ASSEMBLED=core->allocateMessageTagHandle(plugin); | |
| @@ -2681,7 +2678,7 @@ void SeedExtender::registerPlugin(ComputeCore*core){ | |
| core->setMessageTagObjectHandler(plugin,RAY_MPI_TAG_ASK_IS_ASSEMBLED_REPLY, __GetAdapter(SeedExtender,RAY_MPI_TAG_ASK_IS_ASSEMBLED_REPLY)); | |
| core->setMessageTagSymbol(plugin,RAY_MPI_TAG_ASK_IS_ASSEMBLED_REPLY,"RAY_MPI_TAG_ASK_IS_ASSEMBLED_REPLY"); | |
| - | |
| + core->setObjectSymbol(m_plugin,&(m_fusionData->m_FUSION_identifier_map),"/RayAssembler/ObjectStore/ContigNameIndex.ray"); | |
| } | |
| void SeedExtender::resolveSymbols(ComputeCore*core){ | |
| @@ -2701,8 +2698,6 @@ void SeedExtender::resolveSymbols(ComputeCore*core){ | |
| RAY_MPI_TAG_VERTEX_READS_FROM_LIST_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_VERTEX_READS_FROM_LIST_REPLY"); | |
| RAY_MPI_TAG_VERTEX_READS_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_VERTEX_READS_REPLY"); | |
| RAY_MPI_TAG_CONTIG_INFO_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_CONTIG_INFO_REPLY"); | |
| - RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY"); | |
| - | |
| RAY_MPI_TAG_ASK_IS_ASSEMBLED=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_ASK_IS_ASSEMBLED"); | |
| RAY_MPI_TAG_ASK_IS_ASSEMBLED_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_ASK_IS_ASSEMBLED_REPLY"); | |
| @@ -2713,5 +2708,4 @@ void SeedExtender::resolveSymbols(ComputeCore*core){ | |
| __BindAdapter(SeedExtender,RAY_MPI_TAG_ADD_GRAPH_PATH); | |
| __BindAdapter(SeedExtender,RAY_MPI_TAG_ASK_IS_ASSEMBLED); /**/ | |
| __BindAdapter(SeedExtender,RAY_MPI_TAG_ASK_IS_ASSEMBLED_REPLY); /**/ | |
| - | |
| } | |
| diff --git a/code/plugin_SeedExtender/SeedExtender.h b/code/plugin_SeedExtender/SeedExtender.h | |
| index 27b2257..45ec60a 100644 | |
| --- a/code/plugin_SeedExtender/SeedExtender.h | |
| +++ b/code/plugin_SeedExtender/SeedExtender.h | |
| @@ -1,6 +1,6 @@ | |
| /* | |
| - Ray | |
| - Copyright (C) 2010, 2011, 2012 Sébastien Boisvert | |
| + Ray -- Parallel genome assemblies for parallel DNA sequencing | |
| + Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert | |
| http://DeNovoAssembler.SourceForge.Net/ | |
| @@ -84,11 +84,9 @@ class SeedExtender: public CorePlugin { | |
| void configureTheBeautifulHotSkippingTechnology(); | |
| - | |
| Rank m_rank; | |
| MessageTag RAY_MPI_TAG_CONTIG_INFO_REPLY; | |
| - MessageTag RAY_MPI_TAG_GET_CONTIG_CHUNK_REPLY; | |
| MessageTag RAY_MPI_TAG_ASK_IS_ASSEMBLED; | |
| MessageTag RAY_MPI_TAG_ASK_IS_ASSEMBLED_REPLY; | |
| @@ -108,8 +106,6 @@ class SeedExtender: public CorePlugin { | |
| SlaveMode RAY_SLAVE_MODE_EXTENSION; | |
| SlaveMode RAY_SLAVE_MODE_DO_NOTHING; | |
| - | |
| - | |
| // all these parameters are not attributes. | |
| vector<GraphPath>*m_seeds; | |
| Kmer*m_currentVertex; |
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