Transcriptome::Transcriptome (Parameters* Pin) {
P=Pin;
trInfoDir = P->sjdbGTFfile=="-" ? P->genomeDir : P->sjdbInsert.outDir; //if GTF file is given at the mapping stage, it's always used for transcript info
if ( P->quant.trSAM.yes ) {//load exon-transcript structures
//load tr and ex info
ifstream trinfo;
ifstrOpen(trInfoDir+"/transcriptInfo.tab", "ERROR_011001", "SOLUTION: utilize --sjdbGTFfile /path/to/annotantions.gtf option at the genome generation step or mapping step",P, trinfo);
trinfo >> nTr;
trS=new uint [nTr];
trE=new uint [nTr];
trEmax=new uint [nTr];
trExI=new uint32 [nTr];
trExN=new uint16 [nTr];
trStr=new uint8 [nTr];
trID.resize(nTr);
for (uint32 itr=0; itr<nTr; itr++) {
uint16 str1;
trinfo >> trID[itr] >> trS[itr] >> trE[itr] >> trEmax[itr] >> str1 >> trExN[itr] >> trExI[itr];
trStr[itr]=str1;
};
P->inOut->logMain << "Loaded transcript database, nTr="<<nTr<<endl;
trinfo.close();
ifstream exinfo;
ifstrOpen(trInfoDir+"/exonInfo.tab", "ERROR_011002", "SOLUTION: utilize --sjdbGTFfile /path/to/annotantions.gtf option at the genome generation step or mapping step", P, exinfo);
exinfo >> nEx;
exSE = new uint32 [2*nEx];
exLenCum = new uint32 [nEx];
for (uint32 iex=0; iex<nEx; iex++) {
exinfo >> exSE[2*iex] >> exSE[2*iex+1] >> exLenCum[iex]; //reading all elements one after another
};
P->inOut->logMain << "Loaded exon database, nEx="<<nEx<<endl;
exinfo.close();
//
Ptr=Pin;
} else if ( P->quant.geCount.yes ) {//load exon-gene structures
void ifstrOpenGenomeFile (std::string fileName, std::string errorID, Parameters *P, ifstream & ifStream) {
//open one of the genome files
ifstrOpen(P->genomeDirOut+"/"+fileName, errorID, "if this file is missing from the genome directory, you will need to *re-generate the genome*", P, ifStream);
};
void sjdbInsertJunctions(Parameters * P, Parameters * P1, Genome & genome, SjdbClass & sjdbLoci)
{
time_t rawtime;
if (P->sjdbN>0 && sjdbLoci.chr.size()==0)
{//load from the saved genome, only if the loading did not happen already (if sjdb insertion happens at the 1st pass, sjdbLoci will be populated
ifstream & sjdbStreamIn = ifstrOpen(P->genomeDir+"/sjdbList.out.tab", ERROR_OUT, "SOLUTION: re-generate the genome in genomeDir=" + P->genomeDir, P);
sjdbLoadFromStream(sjdbStreamIn, sjdbLoci);
sjdbLoci.priority.resize(sjdbLoci.chr.size(),30);
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the generated genome " << P->genomeDir+"/sjdbList.out.tab" <<": "<<sjdbLoci.chr.size()<<" total junctions\n\n";
};
if (P->twoPass.pass2)
{//load 1st pass new junctions
//sjdbLoci already contains the junctions from before 1st pass
ifstream sjdbStreamIn ( P->twoPass.pass1sjFile.c_str() );
if (sjdbStreamIn.fail()) {
ostringstream errOut;
errOut << "FATAL INPUT error, could not open input file with junctions from the 1st pass="******"\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
sjdbLoadFromStream(sjdbStreamIn, sjdbLoci);
sjdbLoci.priority.resize(sjdbLoci.chr.size(),0);
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the 1st pass file: " << P->twoPass.pass1sjFile <<": "<<sjdbLoci.chr.size()<<" total junctions\n\n";
} else
{//loading junctions from GTF or tab or from the saved genome is only allowed at the 1st pass
//at the 2nd pass these are already in the sjdbLoci
if (P->sjdbFileChrStartEnd.at(0)!="-")
{//load from junction files
sjdbLoadFromFiles(P,sjdbLoci);
sjdbLoci.priority.resize(sjdbLoci.chr.size(),10);
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the sjdbFileChrStartEnd file(s), " << sjdbLoci.chr.size()<<" total junctions\n\n";
};
if (P->sjdbGTFfile!="-")
{//load from GTF
loadGTF(sjdbLoci, P, P->sjdbInsert.outDir);
sjdbLoci.priority.resize(sjdbLoci.chr.size(),20);
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the GTF file: " << P->sjdbGTFfile<<": "<<sjdbLoci.chr.size()<<" total junctions\n\n";
};
};
char *Gsj=new char [2*P->sjdbLength*sjdbLoci.chr.size()+1];//array to store junction sequences, will be filled in sjdbPrepare
sjdbPrepare (sjdbLoci, P, P->chrStart[P->nChrReal], P->sjdbInsert.outDir, genome.G, Gsj);//P->nGenome - change when replacing junctions
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Finished preparing junctions" <<endl;
if (P->sjdbN>P->limitSjdbInsertNsj)
{
ostringstream errOut;
errOut << "Fatal LIMIT error: the number of junctions to be inserted on the fly ="<<P->sjdbN<<" is larger than the limitSjdbInsertNsj="<<P->limitSjdbInsertNsj<<"\n"; errOut << "Fatal LIMIT error: the number of junctions to be inserted on the fly ="<<P->sjdbN<<" is larger than the limitSjdbInsertNsj="<<P->limitSjdbInsertNsj<<"\n";
errOut << "SOLUTION: re-run with at least --limitSjdbInsertNsj "<<P->sjdbN<<"\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
//insert junctions into the genome and SA and SAi
sjdbBuildIndex (P, P1, Gsj, genome.G, genome.SA, (P->twoPass.pass2 ? genome.SApass2 : genome.SApass1), genome.SAi);
delete [] Gsj; //junction sequences have been added to G
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " ..... finished inserting junctions into genome" <<endl;
if (P->sjdbInsert.save=="All")
{//save and copy all genome files into sjdbInsert.outDir, except those created above
if (P->genomeDir != P->sjdbInsert.outDir)
{
copyFile(P->genomeDir+"/chrName.txt", P->sjdbInsert.outDir+"/chrName.txt");
copyFile(P->genomeDir+"/chrStart.txt", P->sjdbInsert.outDir+"/chrStart.txt");
copyFile(P->genomeDir+"/chrNameLength.txt", P->sjdbInsert.outDir+"/chrNameLength.txt");
copyFile(P->genomeDir+"/chrLength.txt", P->sjdbInsert.outDir+"/chrLength.txt");
};
genomeParametersWrite(P->sjdbInsert.outDir+("/genomeParameters.txt"), P, ERROR_OUT);
ofstream & genomeOut = ofstrOpen(P->sjdbInsert.outDir+"/Genome",ERROR_OUT, P);
fstreamWriteBig(genomeOut,genome.G,P->nGenome,P->sjdbInsert.outDir+"/Genome",ERROR_OUT,P);
genomeOut.close();
ofstream & saOut = ofstrOpen(P->sjdbInsert.outDir+"/SA",ERROR_OUT, P);
fstreamWriteBig(saOut,(char*) genome.SA.charArray, (streamsize) genome.SA.lengthByte, P->sjdbInsert.outDir+"/SA",ERROR_OUT,P);
saOut.close();
ofstream & saIndexOut = ofstrOpen(P->sjdbInsert.outDir+"/SAindex",ERROR_OUT, P);
fstreamWriteBig(saIndexOut, (char*) &P->genomeSAindexNbases, sizeof(P->genomeSAindexNbases),P->sjdbInsert.outDir+"/SAindex",ERROR_OUT,P);
fstreamWriteBig(saIndexOut, (char*) P->genomeSAindexStart, sizeof(P->genomeSAindexStart[0])*(P->genomeSAindexNbases+1),P->sjdbInsert.outDir+"/SAindex",ERROR_OUT,P);
fstreamWriteBig(saIndexOut, genome.SAi.charArray, genome.SAi.lengthByte,P->sjdbInsert.outDir+"/SAindex",ERROR_OUT,P);
saIndexOut.close();
};
//re-calculate genome-related parameters
P->winBinN = P->nGenome/(1LLU << P->winBinNbits)+1;
};
