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/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#include "LibraryWorker.h"
#include <code/Mock/constants.h>
#include <code/SeedingData/SeedingData.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <RayPlatform/communication/Message.h>
#include <map>
#include <assert.h>
using namespace std;
bool LibraryWorker::isDone(){
return m_done;
}
void LibraryWorker::constructor(WorkerHandle id,SeedingData*seedingData,VirtualCommunicator*virtualCommunicator,RingAllocator*outboxAllocator,Parameters*parameters,
StaticVector*inbox,StaticVector*outbox, map<int,map<int,int> >*libraryDistances,int*detectedDistances,MyAllocator*allocator,
MessageTag RAY_MPI_TAG_GET_READ_MATE,
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS
){
this->RAY_MPI_TAG_GET_READ_MATE=RAY_MPI_TAG_GET_READ_MATE;
this->RAY_MPI_TAG_REQUEST_VERTEX_READS=RAY_MPI_TAG_REQUEST_VERTEX_READS;
m_done=false;
m_parameters=parameters;
m_SEEDING_i=id;
m_seedingData=seedingData;
m_virtualCommunicator=virtualCommunicator;
m_outboxAllocator=outboxAllocator;
m_EXTENSION_currentPosition=0;
m_EXTENSION_reads_requested=false;
m_EXTENSION_hasPairedReadRequested=false;
m_EXTENSION_edgeIterator=0;
m_inbox=inbox;
m_outbox=outbox;
m_libraryDistances=libraryDistances;
m_detectedDistances=detectedDistances;
m_allocator=allocator;
m_database.constructor();
}
void LibraryWorker::work(){
if(m_done){
return;
}
#ifdef CONFIG_ASSERT
assert(m_SEEDING_i<m_seedingData->m_SEEDING_seeds.size());
#endif
if(m_EXTENSION_currentPosition==(int)m_seedingData->m_SEEDING_seeds[m_SEEDING_i].size()){
while(m_database.size()>0){
SplayNode<ReadHandle,LibraryElement>*node=m_database.getRoot();
ReadHandle key=node->getKey();
m_database.remove(key,true,m_allocator);
}
m_done=true;
}else{
if(!m_EXTENSION_reads_requested){
m_EXTENSION_reads_requested=true;
#ifdef CONFIG_ASSERT
assert(m_seedingData!=NULL);
assert(m_EXTENSION_currentPosition<(int)m_seedingData->m_SEEDING_seeds[m_SEEDING_i].size());
#endif
Kmer theKmerObject;
m_seedingData->m_SEEDING_seeds[m_SEEDING_i].at(m_EXTENSION_currentPosition,&theKmerObject);
Kmer*vertex=&theKmerObject;
m_readFetcher.constructor(vertex,m_outboxAllocator,m_inbox,m_outbox,m_parameters,m_virtualCommunicator,
m_SEEDING_i,RAY_MPI_TAG_REQUEST_VERTEX_READS);
#ifdef CONFIG_ASSERT
assert(!m_readFetcher.isDone());
#endif
m_EXTENSION_edgeIterator=0;// iterate over reads
m_EXTENSION_hasPairedReadRequested=false;
}else if(!m_readFetcher.isDone()){
m_readFetcher.work();
}else{
if(m_EXTENSION_edgeIterator<(int)m_readFetcher.getResult()->size()){
ReadAnnotation annotation=m_readFetcher.getResult()->at(m_EXTENSION_edgeIterator);
int rightRead=annotation.getReadIndex();
if(!m_EXTENSION_hasPairedReadRequested){
MessageUnit*message=(MessageUnit*)(m_outboxAllocator)->allocate(1*sizeof(MessageUnit));
message[0]=rightRead;
#ifdef CONFIG_ASSERT
assert(m_parameters!=NULL);
if(!(annotation.getRank()<m_parameters->getSize())){
cout<<"Error rank="<<annotation.getRank()<<" size="<<m_parameters->getSize()<<endl;
}
assert(annotation.getRank()<m_parameters->getSize());
#endif
Message aMessage(message,1,annotation.getRank(),RAY_MPI_TAG_GET_READ_MATE,m_parameters->getRank());
m_virtualCommunicator->pushMessage(m_SEEDING_i,&aMessage);
m_EXTENSION_hasPairedReadRequested=true;
}else if(m_virtualCommunicator->isMessageProcessed(m_SEEDING_i)){
vector<MessageUnit> buffer;
m_virtualCommunicator->getMessageResponseElements(m_SEEDING_i,&buffer);
#ifdef CONFIG_ASSERT
assert((int)buffer.size()==4);
#endif
/** this is a sentinel value */
/** data: readLength, rank, id, library */
if((int)buffer[1] != MAX_NUMBER_OF_MPI_PROCESSES){
int library=buffer[3];
int readLength=buffer[0];
bool isAutomatic=m_parameters->isAutomatic(library);
if(isAutomatic){
PathHandle uniqueReadIdentifier=getPathUniqueId(buffer[1],buffer[2]);
SplayNode<ReadHandle,LibraryElement>*node=m_database.find(uniqueReadIdentifier.getValue(),false);
if(node!=NULL){
LibraryElement*element=node->getValue();
int rightStrandPosition=annotation.getPositionOnStrand();
Strand rightStrand=annotation.getStrand();
Strand leftStrand=element->m_readStrand;
int leftStrandPosition=element->m_strandPosition;
if(( leftStrand=='F' && rightStrand=='R' )
||( leftStrand=='R' && rightStrand=='F' )){// make sure the orientation is OK
int p1=element->m_readPosition;
int p2=m_EXTENSION_currentPosition;
int d=p2-p1+readLength+leftStrandPosition-rightStrandPosition;
(*m_libraryDistances)[library][d]++;
(*m_detectedDistances)++;
}
}
}
}
m_EXTENSION_edgeIterator++;
m_EXTENSION_hasPairedReadRequested=false;
}
}else{
for(int i=0;i<(int)m_readFetcher.getResult()->size();i++){
ReadHandle uniqueId=m_readFetcher.getResult()->at(i).getUniqueId();
int position=m_EXTENSION_currentPosition;
Strand strand=m_readFetcher.getResult()->at(i).getStrand();
int strandPosition=m_readFetcher.getResult()->at(i).getPositionOnStrand();
// read, position, strand
bool flag;
SplayNode<ReadHandle,LibraryElement>*node=m_database.insert(uniqueId,m_allocator,&flag);
LibraryElement*element=node->getValue();
element->m_readPosition=position;
element->m_readStrand=strand;
element->m_strandPosition=strandPosition;
}
m_EXTENSION_currentPosition++;
m_EXTENSION_reads_requested=false;
}
}
}
}
WorkerHandle LibraryWorker::getWorkerIdentifier(){
return m_SEEDING_i;
}
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