void ColorSpaceLoader::load(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator){
char bufferForLine[1024];
int loadedSequences=0;
while(m_loaded<m_size&& loadedSequences<maxToLoad){
fgets(bufferForLine,4096,m_f);
if(bufferForLine[0]=='#'){
continue;// skip csfasta comment
}
// read two lines
if(bufferForLine[0]=='>'){
fgets(bufferForLine,4096,m_f);
for(int j=0;j<(int)strlen(bufferForLine);j++){
if(bufferForLine[j]==DOUBLE_ENCODING_A_COLOR){
bufferForLine[j]='A';
}else if(bufferForLine[j]==DOUBLE_ENCODING_T_COLOR){
bufferForLine[j]='T';
}else if(bufferForLine[j]==DOUBLE_ENCODING_C_COLOR){
bufferForLine[j]='C';
}else if(bufferForLine[j]==DOUBLE_ENCODING_G_COLOR){
bufferForLine[j]='G';
}
}
Read t;
// remove the leading T & first color
t.constructor(bufferForLine+2,seqMyAllocator,true);
reads->push_back(&t);
loadedSequences++;
m_loaded++;
}
}
if(m_loaded==m_size){
fclose(m_f);
}
}
void FastqLoader::loadWithPeriod(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator,int period){
char buffer[RAY_MAXIMUM_READ_LENGTH];
int rotatingVariable=0;
int loadedSequences=0;
while(loadedSequences<maxToLoad && NULL!=fgets(buffer,RAY_MAXIMUM_READ_LENGTH,m_f)){
if(rotatingVariable==1){
Read t;
t.constructor(buffer,seqMyAllocator,true);
reads->push_back(&t);
}
rotatingVariable++;
// a period is reached for each read.
if(rotatingVariable==period){
rotatingVariable=0;
loadedSequences++;
m_loaded++;
}
}
if(m_loaded==m_size){
fclose(m_f);
}
}
/** load sequences */
int FastaLoader::load(string file,ArrayOfReads*reads,MyAllocator*seqMyAllocator){
string id;
ostringstream sequence;
string buffer;
ifstream f(file.c_str());
while(!f.eof()){
buffer="";
f>>buffer;
if(buffer=="")
continue;
if(buffer[0]=='>'){
char bufferForLine[1024];
f.getline(bufferForLine,1024);
if(id!=""){
string sequenceStr=sequence.str();
Read t;
t.constructor(sequenceStr.c_str(),seqMyAllocator,true);
reads->push_back(&t);
}
id=buffer;
sequence.str("");
}else{
sequence<< buffer;
}
}
string sequenceStr=sequence.str();
ostringstream quality;
for(int i=0;i<(int)sequenceStr.length();i++){
quality<< "F";
}
Read t;
t.constructor(sequenceStr.c_str(),seqMyAllocator,true);
reads->push_back(&t);
f.close();
return EXIT_SUCCESS;
}
void ColorSpaceLoader::load(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator){
char bufferForLine[RAY_MAXIMUM_READ_LENGTH];
int loadedSequences=0;
while(m_loaded<m_size&& loadedSequences<maxToLoad){
if(NULL==fgets(bufferForLine,RAY_MAXIMUM_READ_LENGTH,m_f))
continue;
if(bufferForLine[0]=='#'){
continue;// skip csfasta comment
}
// read two lines
if(bufferForLine[0]=='>'){
char*returnValue=fgets(bufferForLine,RAY_MAXIMUM_READ_LENGTH,m_f);
assert(returnValue != NULL);
for(int j=0;j<(int)strlen(bufferForLine);j++){
if(bufferForLine[j]==DOUBLE_ENCODING_A_COLOR){
bufferForLine[j]=SYMBOL_A;
}else if(bufferForLine[j]==DOUBLE_ENCODING_T_COLOR){
bufferForLine[j]=SYMBOL_T;
}else if(bufferForLine[j]==DOUBLE_ENCODING_C_COLOR){
bufferForLine[j]=SYMBOL_C;
}else if(bufferForLine[j]==DOUBLE_ENCODING_G_COLOR){
bufferForLine[j]=SYMBOL_G;
}
}
Read t;
// remove the leading T & first color
t.constructor(bufferForLine+2,seqMyAllocator,true);
reads->push_back(&t);
loadedSequences++;
m_loaded++;
}
}
if(m_loaded==m_size){
fclose(m_f);
}
}
// a very simple and compact fastq.gz reader
void FastqGzLoader::load(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator,int period) {
char buffer[4096];
int rotatingVariable=0;
int loadedSequences=0;
while(loadedSequences<maxToLoad && Z_NULL!=gzgets(m_f,buffer,4096)) {
if(rotatingVariable==1) {
Read t;
t.constructor(buffer,seqMyAllocator,true);
reads->push_back(&t);
}
rotatingVariable++;
// a period is reached for each read.
if(rotatingVariable==period) {
rotatingVariable=0;
loadedSequences++;
m_loaded++;
}
}
if(m_loaded==m_size) {
gzclose(m_f);
}
}
void SequencesLoader::registerSequence(){
if(m_myReads->size()% NUMBER_OF_SEQUENCES_PERIOD ==0){
LargeCount amount=m_myReads->size();
cout<<"Rank "<<m_rank<<" has "<<amount<<" sequence reads"<<endl;
if(m_parameters->showMemoryUsage()){
showMemoryUsage(m_rank);
}
}
#ifdef ASSERT
assert(m_distribution_sequence_id<m_loader.size());
#endif
Read*theRead=m_loader.at(m_distribution_sequence_id);
char read[RAY_MAXIMUM_READ_LENGTH];
theRead->getSeq(read,m_parameters->getColorSpaceMode(),false);
//cout<<"DEBUG2 Read="<<m_distribution_sequence_id<<" color="<<m_parameters->getColorSpaceMode()<<" Seq= "<<read<<endl;
Read myRead;
myRead.constructor(read,&(*m_persistentAllocator),true);
m_myReads->push_back(&myRead);
if(m_LOADER_isLeftFile){
ReadHandle leftSequenceGlobalId=m_distribution_currentSequenceId;
LargeIndex leftSequenceIdOnRank=m_myReads->size()-1;
#ifdef ASSERT
assert(m_loader.size()!=0);
#endif
ReadHandle rightSequenceGlobalId=leftSequenceGlobalId+m_loader.size();
#ifdef ASSERT
assert(leftSequenceGlobalId<rightSequenceGlobalId);
assert(leftSequenceGlobalId>=0);
assert(leftSequenceGlobalId<m_totalNumberOfSequences);
assert(rightSequenceGlobalId>=0);
assert(rightSequenceGlobalId<m_totalNumberOfSequences);
#endif
int rightSequenceRank=m_parameters->getRankFromGlobalId(rightSequenceGlobalId);
#ifdef ASSERT
if(rightSequenceRank>=m_size){
cout<<"m_distribution_currentSequenceId="<<m_distribution_currentSequenceId<<" m_distribution_sequence_id="<<m_distribution_sequence_id<<" LoaderSize="<<m_loader.size()<<" Rank="<<rightSequenceRank<<" Size="<<m_size<<endl;
assert(rightSequenceRank<m_size);
}
#endif
LargeIndex rightSequenceIdOnRank=m_parameters->getIdFromGlobalId(rightSequenceGlobalId);
int library=m_parameters->getLibrary(m_distribution_file_id);
(*m_myReads)[leftSequenceIdOnRank]->setLeftType();
(*m_myReads)[leftSequenceIdOnRank]->getPairedRead()->constructor(rightSequenceRank,rightSequenceIdOnRank,library);
}else if(m_LOADER_isRightFile){
#ifdef ASSERT
assert(m_loader.size()!=0);
#endif
ReadHandle rightSequenceGlobalId=(m_distribution_currentSequenceId);
LargeIndex rightSequenceIdOnRank=m_myReads->size()-1;
ReadHandle leftSequenceGlobalId=rightSequenceGlobalId-m_loader.size();
#ifdef ASSERT
assert(leftSequenceGlobalId>=0);
if(leftSequenceGlobalId>=m_totalNumberOfSequences){
cout<<"Error: invalid ReadHandle object, leftSequenceGlobalId: "<<leftSequenceGlobalId;
cout<<" m_totalNumberOfSequences: "<<m_totalNumberOfSequences;
cout<<" rightSequenceGlobalId: "<<rightSequenceGlobalId<<endl;
cout<<" m_distribution_currentSequenceId "<<m_distribution_currentSequenceId;
cout<<" m_loader.size: "<<m_loader.size();
cout<<" rightSequenceIdOnRank: "<<rightSequenceIdOnRank<<" m_myReads->size: "<<m_myReads->size();
cout<<endl;
}
assert(leftSequenceGlobalId<m_totalNumberOfSequences);
assert(rightSequenceGlobalId>=0);
assert(rightSequenceGlobalId<m_totalNumberOfSequences);
#endif
Rank leftSequenceRank=m_parameters->getRankFromGlobalId(leftSequenceGlobalId);
#ifdef ASSERT
if(leftSequenceRank>=m_size){
cout<<"Global="<<leftSequenceGlobalId<<" rank="<<leftSequenceRank<<endl;
}
assert(leftSequenceRank<m_size);
#endif
LargeIndex leftSequenceIdOnRank=m_parameters->getIdFromGlobalId(leftSequenceGlobalId);
int library=m_parameters->getLibrary(m_distribution_file_id);
(*m_myReads)[rightSequenceIdOnRank]->setRightType();
(*m_myReads)[rightSequenceIdOnRank]->getPairedRead()->constructor(leftSequenceRank,leftSequenceIdOnRank,library);
// left sequence in interleaved file
}else if(m_isInterleavedFile && ((m_distribution_sequence_id)%2)==0){
ReadHandle rightSequenceGlobalId=(m_distribution_currentSequenceId)+1;
#ifdef ASSERT
assert(rightSequenceGlobalId>=0);
assert(rightSequenceGlobalId<m_totalNumberOfSequences);
#endif
Rank rightSequenceRank=m_parameters->getRankFromGlobalId(rightSequenceGlobalId);
LargeIndex rightSequenceIdOnRank=m_parameters->getIdFromGlobalId(rightSequenceGlobalId);
LargeIndex leftSequenceIdOnRank=m_myReads->size()-1;
int library=m_parameters->getLibrary(m_distribution_file_id);
(*m_myReads)[leftSequenceIdOnRank]->setLeftType();
(*m_myReads)[leftSequenceIdOnRank]->getPairedRead()->constructor(rightSequenceRank,rightSequenceIdOnRank,library);
// only the right sequence.
}else if(m_isInterleavedFile &&((m_distribution_sequence_id)%2)==1){
ReadHandle rightSequenceGlobalId=(m_distribution_currentSequenceId);
LargeIndex rightSequenceIdOnRank=m_myReads->size()-1;
ReadHandle leftSequenceGlobalId=rightSequenceGlobalId-1;
#ifdef ASSERT
assert(leftSequenceGlobalId>=0);
assert(leftSequenceGlobalId<m_totalNumberOfSequences);
assert(rightSequenceGlobalId>=0);
assert(rightSequenceGlobalId<m_totalNumberOfSequences);
#endif
Rank leftSequenceRank=m_parameters->getRankFromGlobalId(leftSequenceGlobalId);
LargeIndex leftSequenceIdOnRank=m_parameters->getIdFromGlobalId(leftSequenceGlobalId);
int library=m_parameters->getLibrary(m_distribution_file_id);
(*m_myReads)[rightSequenceIdOnRank]->setRightType();
(*m_myReads)[rightSequenceIdOnRank]->getPairedRead()->constructor(leftSequenceRank,leftSequenceIdOnRank,library);
}
}
