void Genome::insertSequences()
{
if (P->genomeFastaFiles.at(0)!="-")
{
time_t rawtime;
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " ..... Inserting extra sequences into genome indexes" <<endl;
//move the junctions to free up space for seqs
// chrStart/Name/Length nChrReal include the extra sequences
// nGenome is the old, small genome size
uint sjdblen=P->nGenome-(P->chrStart.back()-P->genomeInsertL);//length of sjdb sequences
memmove(G+P->chrStart.back(),G+P->chrStart.back()-P->genomeInsertL,sjdblen);
memset(G+P->chrStart.back()-P->genomeInsertL, GENOME_spacingChar, P->genomeInsertL);//fill empty space with spacing characters
genomeScanFastaFiles(P, G+P->chrStart.back()-P->genomeInsertL, true); //read the seqs from file(s) into the free space
uint64 nGenomeOld=P->nGenome;
P->nGenome=P->chrStart.back()+sjdblen;
//insert new sequences into the SA
insertSeqSA(SA, SAinsert, SAi, G, G+P->chrStart.back()-P->genomeInsertL, nGenomeOld-sjdblen, P->genomeInsertL, sjdblen, P);
//insert new sequences into the SAi
//update P
//save the genome if necessary
};
};
void Genome::genomeLoad(){//allocate and load Genome
time_t rawtime;
time ( &rawtime );
*(P->inOut->logStdOut) << timeMonthDayTime(rawtime) << " ..... Loading genome\n" <<flush;
uint *shmNG=NULL, *shmNSA=NULL; //pointers to shm stored values , *shmSG, *shmSSA
uint64 shmSize=0;//, shmStartG=0; shmStartSA=0;
uint L=200,K=6;
Parameters *P1 = new Parameters;
ifstream parFile((P->genomeDir+("/genomeParameters.txt")).c_str());
if (parFile.good()) {
P->inOut->logMain << "Reading genome generation parameters:\n";
P1->inOut = P->inOut;
P1->scanAllLines(parFile,3,-1);
parFile.close();
} else {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: could not open genome file "<< P->genomeDir+("/genomeParameters.txt") << endl;
errOut << "SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions\n" <<flush;
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P);
};
//check genome version
if (P1->versionGenome.size()==0 || P1->versionGenome[0]==0) {//
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: read no value for the versionGenome parameter from genomeParameters.txt file\n";
errOut << "SOLUTION: please re-generate genome from scratch with the latest version of STAR\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P);
} else if (P->sjdbFileChrStartEnd.at(0)=="-" && P1->versionGenome.at(0) >= P->versionGenome.at(0)) {//
P->inOut->logMain << "Genome version is compatible with current STAR version\n";
} else if (P->sjdbFileChrStartEnd.at(0)!="-" && P1->versionGenome.at(0) >= P->versionGenome.at(1)) {//
P->inOut->logMain << "Genome version is compatible with current STAR version\n";
} else {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: Genome version is INCOMPATIBLE with current STAR version\n";
errOut << "SOLUTION: please re-generate genome from scratch with the latest version of STAR\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P);
};
//find chr starts from files
P->chrInfoLoad();
//check if sjdbInfo.txt exists => genome was generated with junctions
bool sjdbInfoExists=false;
struct stat sjdb1;
if ( stat( (P->genomeDir+"/sjdbInfo.txt").c_str(), &sjdb1) == 0 )
{//file exists
sjdbInfoExists=true;
};
if ( P->sjdbInsert.yes && sjdbInfoExists && P1->sjdbInsert.save=="")
{//if sjdbInsert, and genome had junctions, and genome is old - it should be re-generated with new STAR
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: old Genome is INCOMPATIBLE with on the fly junction insertion\n";
errOut << "SOLUTION: please re-generate genome from scratch with the latest version of STAR\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P);
};
//record required genome parameters in P
P->genomeSAindexNbases=P1->genomeSAindexNbases;
P->genomeChrBinNbits=P1->genomeChrBinNbits;
P->genomeSAsparseD=P1->genomeSAsparseD;
if (P->parArray.at(P->sjdbOverhang_par)->inputLevel==0 && P1->sjdbOverhang>0)
{//if --sjdbOverhang was not defined by user and it was defined >0 at the genome generation step, then use sjdbOverhang from the genome generation step
P->sjdbOverhang=P1->sjdbOverhang;
P->inOut->logMain << "--sjdbOverhang = " << P->sjdbOverhang << " taken from the generated genome\n";
} else if (sjdbInfoExists && P->parArray.at(P->sjdbOverhang_par)->inputLevel>0 && P->sjdbOverhang!=P1->sjdbOverhang)
{//if sjdbOverhang was defined at the genome generation step,the mapping step value has to agree with it
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: present --sjdbOverhang="<<P->sjdbOverhang << " is not equal to the value at the genome generation step ="<< P1->sjdbOverhang << "\n";
errOut << "SOLUTION: \n" <<flush;
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P);
};
P->sjdbLength = P->sjdbOverhang==0 ? 0 : P->sjdbOverhang*2+1;
P->inOut->logMain << "Started loading the genome: " << asctime (localtime ( &rawtime ))<<"\n"<<flush;
ifstream GenomeIn, SAin, SAiIn;
P->nGenome = OpenStream("Genome",GenomeIn);
P->nSAbyte = OpenStream("SA",SAin);
OpenStream("/SAindex",SAiIn);
uint SAiInBytes=0;
SAiInBytes += fstreamReadBig(SAiIn,(char*) &P->genomeSAindexNbases, sizeof(P->genomeSAindexNbases));
P->genomeSAindexStart = new uint[P->genomeSAindexNbases+1];
SAiInBytes += fstreamReadBig(SAiIn,(char*) P->genomeSAindexStart, sizeof(P->genomeSAindexStart[0])*(P->genomeSAindexNbases+1));
P->nSAi=P->genomeSAindexStart[P->genomeSAindexNbases];
P->inOut->logMain << "Read from SAindex: genomeSAindexNbases=" << P->genomeSAindexNbases <<" nSAi="<< P->nSAi <<endl;
/////////////////////////////////// at this point all array sizes should be known: calculate packed array lengths
P->GstrandBit = (uint) floor(log(P->nGenome)/log(2))+1;
if (P->GstrandBit<32) P->GstrandBit=32; //TODO: use simple access function for SA
P->GstrandMask = ~(1LLU<<P->GstrandBit);
P->nSA=(P->nSAbyte*8)/(P->GstrandBit+1);
SA.defineBits(P->GstrandBit+1,P->nSA);
P->SAiMarkNbit=P->GstrandBit+1;
P->SAiMarkAbsentBit=P->GstrandBit+2;
P->SAiMarkNmaskC=1LLU << P->SAiMarkNbit;
P->SAiMarkNmask=~P->SAiMarkNmaskC;
P->SAiMarkAbsentMaskC=1LLU << P->SAiMarkAbsentBit;
P->SAiMarkAbsentMask=~P->SAiMarkAbsentMaskC;
SAi.defineBits(P->GstrandBit+3,P->nSAi);
P->inOut->logMain << "nGenome=" << P->nGenome << "; nSAbyte=" << P->nSAbyte <<endl<< flush;
P->inOut->logMain <<"GstrandBit="<<int(P->GstrandBit)<<" SA number of indices="<<P->nSA<<endl<<flush;
shmSize=SA.lengthByte + P->nGenome+L+L+SHM_startG+8;
shmSize+= SAi.lengthByte;
if (P->annotScoreScale>0) shmSize+=P->nGenome;
if ((P->genomeLoad=="LoadAndKeep" ||
P->genomeLoad=="LoadAndRemove" ||
P->genomeLoad=="LoadAndExit" ||
P->genomeLoad=="Remove") && sharedMemory == NULL)
{
bool unloadLast = P->genomeLoad=="LoadAndRemove";
try
{
sharedMemory = new SharedMemory(shmKey, unloadLast);
sharedMemory->SetErrorStream(P->inOut->logStdOut);
if (!sharedMemory->NeedsAllocation())
P->inOut->logMain <<"Found genome in shared memory\n"<<flush;
if (P->genomeLoad=="Remove") {//kill the genome and exit
if (sharedMemory->NeedsAllocation()) {//did not find genome in shared memory, nothing to kill
ostringstream errOut;
errOut << "EXITING: Did not find the genome in memory, did not remove any genomes from shared memory\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P);
} else {
sharedMemory->Clean();
P->inOut->logMain <<"DONE: removed the genome from shared memory\n"<<flush;
return;
};
}
if (sharedMemory->NeedsAllocation()){
P->inOut->logMain <<"Allocating shared memory for genome\n"<<flush;
sharedMemory->Allocate(shmSize);
}
}
catch (const SharedMemoryException & exc)
{
HandleSharedMemoryException(exc, shmSize);
}
shmStart = (char*) sharedMemory->GetMapped();
shmNG= (uint*) (shmStart+SHM_sizeG);
shmNSA= (uint*) (shmStart+SHM_sizeSA);
if (!sharedMemory->IsAllocator())
{
// genome is in shared memory or being loaded
// wait for the process that will populate it
// and record the sizes
uint iwait=0;
while (*shmNG != P->nGenome) {
iwait++;
P->inOut->logMain <<"Another job is still loading the genome, sleeping for 1 min\n" <<flush;
sleep(60);
if (iwait==100) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: waited too long for the other job to finish loading the genome" << strerror(errno) << "\n" <<flush;
errOut << "SOLUTION: remove the shared memory chunk by running STAR with --genomeLoad Remove, and restart STAR" <<flush;
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_LOADING_WAITED_TOO_LONG, *P);
};
};
if (P->nSAbyte!=*shmNSA)
{
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: the SA file size did not match what we found in shared memory" << "\n" << flush;
errOut << "SOLUTION: remove the shared memory chunk by running STAR with --genomeLoad Remove, and restart STAR" << flush;
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INCONSISTENT_DATA, *P);
}
P->inOut->logMain << "Using shared memory for genome. key=0x" <<hex<<shmKey<<dec<< "; shmid="<< sharedMemory->GetId() <<endl<<flush;
}
G1=shmStart+SHM_startG;
SA.pointArray(G1+P->nGenome+L+L);
char* shmNext=SA.charArray+P->nSAbyte;
SAi.pointArray(shmNext);
shmNext += SAi.lengthByte;
// if (twoPass.pass1readsN==0) {//not 2-pass
// shmStartG=SHM_startSHM;
// shmStartSA=0;
// } else {//2-pass
// ostringstream errOut;
// errOut << "EXITING because of FATAL ERROR: 2-pass procedure cannot be used with genome already loaded im memory' "\n" ;
// errOut << "SOLUTION: check shared memory settigns as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory\n" <<flush;
// exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_SHM, *P);
// };
if (P->annotScoreScale>0) {//optional allocation
sigG = shmNext;
shmNext += P->nGenome;
}
}
else if (P->genomeLoad=="NoSharedMemory") // simply allocate memory, do not use shared memory
{
P->genomeInsertL=0;
if (P->genomeFastaFiles.at(0)!="-")
{//will insert sequences in the genome, now estimate the extra size
uint oldlen=P->chrStart.back();//record the old length
P->genomeInsertL=genomeScanFastaFiles(P,G,false)-oldlen;
};
try {
if (P->sjdbInsert.pass1 || P->sjdbInsert.pass2)
{//reserve extra memory for insertion at the 1st and/or 2nd step
nGenomePass1=P->nGenome+P->genomeInsertL;
nSApass1=P->nSA+2*P->genomeInsertL;
if (P->sjdbInsert.pass1)
{
nGenomePass1+=P->limitSjdbInsertNsj*P->sjdbLength;
nSApass1+=2*P->limitSjdbInsertNsj*P->sjdbLength;
};
nGenomePass2=nGenomePass1;
nSApass2=nSApass1;
if (P->sjdbInsert.pass2)
{
nGenomePass2+=P->limitSjdbInsertNsj*P->sjdbLength;
nSApass2+=2*P->limitSjdbInsertNsj*P->sjdbLength;
};
G1=new char[nGenomePass2+L+L];
SApass2.defineBits(P->GstrandBit+1,nSApass2);
SApass2.allocateArray();
SApass1.defineBits(P->GstrandBit+1,nSApass1);
SApass1.pointArray(SApass2.charArray+SApass2.lengthByte-SApass1.lengthByte);
SA.pointArray(SApass1.charArray+SApass1.lengthByte-SA.lengthByte);
} else
{//no sjdb insertions
if (P->genomeInsertL==0)
{// no sequence insertion, simple allocation
G1=new char[P->nGenome+L+L];
SA.allocateArray();
} else
{
G1=new char[P->nGenome+L+L+P->genomeInsertL];
SApass1.defineBits(P->GstrandBit+1,P->nSA+2*P->genomeInsertL);//TODO: re-define GstrandBit if necessary
SApass1.allocateArray();
SA.pointArray(SApass1.charArray+SApass1.lengthByte-SA.lengthByte);
};
};
SAi.allocateArray();
P->inOut->logMain <<"Shared memory is not used for genomes. Allocated a private copy of the genome.\n"<<flush;
} catch (exception & exc) {
ostringstream errOut;
errOut <<"EXITING: fatal error trying to allocate genome arrays, exception thrown: "<<exc.what()<<endl;
errOut <<"Possible cause 1: not enough RAM. Check if you have enough RAM " << P->nGenome+L+L+SA.lengthByte+SAi.lengthByte+2000000000 << " bytes\n";
errOut <<"Possible cause 2: not enough virtual memory allowed with ulimit. SOLUTION: run ulimit -v " << P->nGenome+L+L+SA.lengthByte+SAi.lengthByte+2000000000<<endl <<flush;
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_MEMORY_ALLOCATION, *P);
};
}
// if (twopass1readsN==0) {//not 2-pass
// shmStartG=SHM_startSHM;
// shmStartSA=0;
// } else {//2-pass
// ostringstream errOut;
// errOut << "EXITING because of FATAL ERROR: 2-pass procedure cannot be used with genome already loaded im memory' "\n" ;
// errOut << "SOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory\n" <<flush;
// exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_SHM, *P);
// };
G=G1+L;
bool isAllocatorProcess = sharedMemory != NULL && sharedMemory->IsAllocator();
if (P->genomeLoad=="NoSharedMemory" || isAllocatorProcess) {//load genome and SAs from files
//load genome
P->inOut->logMain <<"Genome file size: "<<P->nGenome <<" bytes; state: good=" <<GenomeIn.good()\
<<" eof="<<GenomeIn.eof()<<" fail="<<GenomeIn.fail()<<" bad="<<GenomeIn.bad()<<"\n"<<flush;
P->inOut->logMain <<"Loading Genome ... " << flush;
uint genomeReadBytesN=fstreamReadBig(GenomeIn,G,P->nGenome);
P->inOut->logMain <<"done! state: good=" <<GenomeIn.good()\
<<" eof="<<GenomeIn.eof()<<" fail="<<GenomeIn.fail()<<" bad="<<GenomeIn.bad()<<"; loaded "<<genomeReadBytesN<<" bytes\n" << flush;
GenomeIn.close();
for (uint ii=0;ii<L;ii++) {// attach a tail with the largest symbol
G1[ii]=K-1;
G[P->nGenome+ii]=K-1;
};
//load SAs
P->inOut->logMain <<"SA file size: "<<SA.lengthByte <<" bytes; state: good=" <<SAin.good()\
<<" eof="<<SAin.eof()<<" fail="<<SAin.fail()<<" bad="<<SAin.bad()<<"\n"<<flush;
P->inOut->logMain <<"Loading SA ... " << flush;
genomeReadBytesN=fstreamReadBig(SAin,SA.charArray, SA.lengthByte);
P->inOut->logMain <<"done! state: good=" <<SAin.good()\
<<" eof="<<SAin.eof()<<" fail="<<SAin.fail()<<" bad="<<SAin.bad()<<"; loaded "<<genomeReadBytesN<<" bytes\n" << flush;
SAin.close();
P->inOut->logMain <<"Loading SAindex ... " << flush;
SAiInBytes +=fstreamReadBig(SAiIn,SAi.charArray, SAi.lengthByte);
P->inOut->logMain <<"done: "<<SAiInBytes<<" bytes\n" << flush;
};
SAiIn.close();
if ((P->genomeLoad=="LoadAndKeep" ||
P->genomeLoad=="LoadAndRemove" ||
P->genomeLoad=="LoadAndExit") && isAllocatorProcess )
{
//record sizes. This marks the end of genome loading
*shmNG=P->nGenome;
*shmNSA=P->nSAbyte;
};
time ( &rawtime );
P->inOut->logMain << "Finished loading the genome: " << asctime (localtime ( &rawtime )) <<"\n"<<flush;
#ifdef COMPILE_FOR_MAC
{
uint sum1=0;
for (uint ii=0;ii<P->nGenome; ii++) sum1 += (uint) (unsigned char) G[ii];
P->inOut->logMain << "Sum of all Genome bytes: " <<sum1 <<"\n"<<flush;
sum1=0;
for (uint ii=0;ii<SA.lengthByte; ii++) sum1 += (uint) (unsigned char) SA.charArray[ii];
P->inOut->logMain << "Sum of all SA bytes: " <<sum1 <<"\n"<<flush;
sum1=0;
for (uint ii=0;ii<SAi.lengthByte; ii++) sum1 += (uint) (unsigned char) SAi.charArray[ii];
P->inOut->logMain << "Sum of all SAi bytes: " <<sum1 <<"\n"<<flush;
};
#endif
if (P->genomeLoad=="LoadAndExit") {
uint shmSum=0;
for (uint ii=0;ii<shmSize;ii++) shmSum+=shmStart[ii];
P->inOut->logMain << "genomeLoad=LoadAndExit: completed, the genome is loaded and kept in RAM, EXITING now.\n"<<flush;
return;
};
insertSequences();
P->chrBinFill();
//splice junctions database
if (P->nGenome==P->chrStart[P->nChrReal]) {//no sjdb
P->sjdbN=0;
P->sjGstart=P->chrStart[P->nChrReal]+1; //not sure why I need that
} else {//there are sjdb chromosomes
ifstream sjdbInfo((P->genomeDir+"/sjdbInfo.txt").c_str());
if (sjdbInfo.fail()) {
ostringstream errOut;
errOut << "EXITING because of FATAL error, could not open file " << (P->genomeDir+"/sjdbInfo.txt") <<"\n";
errOut << "SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions\n" <<flush;
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
sjdbInfo >> P->sjdbN >> P->sjdbOverhang;
P->inOut->logMain << "Processing splice junctions database sjdbN=" <<P->sjdbN<<", sjdbOverhang=" <<P->sjdbOverhang <<" \n";
P->sjChrStart=P->nChrReal;
P->sjGstart=P->chrStart[P->sjChrStart];
//fill the sj-db to genome translation array
P->sjDstart=new uint [P->sjdbN];
P->sjAstart=new uint [P->sjdbN];
P->sjdbStart=new uint [P->sjdbN];
P->sjdbEnd=new uint [P->sjdbN];
P->sjdbMotif=new uint8 [P->sjdbN];
P->sjdbShiftLeft=new uint8 [P->sjdbN];
P->sjdbShiftRight=new uint8 [P->sjdbN];
P->sjdbStrand=new uint8 [P->sjdbN];
for (uint ii=0;ii<P->sjdbN;ii++) {//get the info about junctions from sjdbInfo.txt
{
uint16 d1,d2,d3,d4;
sjdbInfo >> P->sjdbStart[ii] >> P->sjdbEnd[ii] >> d1 >> d2 >> d3 >> d4;
P->sjdbMotif[ii] = (uint8) d1;
P->sjdbShiftLeft[ii] = (uint8) d2;
P->sjdbShiftRight[ii] = (uint8) d3;
P->sjdbStrand[ii] = (uint8) d4;
};
P->sjDstart[ii] = P->sjdbStart[ii] - P->sjdbOverhang;
P->sjAstart[ii] = P->sjdbEnd[ii] + 1;
if (P->sjdbMotif[ii]==0) {//shinon-canonical junctions back to their true coordinates
P->sjDstart[ii] += P->sjdbShiftLeft[ii];
P->sjAstart[ii] += P->sjdbShiftLeft[ii];
};
};
};
//check and redefine some parameters
//max intron size
if (P->alignIntronMax==0 && P->alignMatesGapMax==0) {
P->inOut->logMain << "alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=" \
<< (1LLU<<P->winBinNbits)*P->winAnchorDistNbins <<endl;
} else {
//redefine winBinNbits
P->winBinNbits=max( (uint) floor(log2(P->nGenome/40000)+0.5), (uint) floor(log2(max(max(4LLU,P->alignIntronMax),P->alignMatesGapMax)/4)+0.5) );
P->inOut->logMain << "To accomodate alignIntronMax="<<P->alignIntronMax<<" redefined winBinNbits="<< P->winBinNbits <<endl;
};
if (P->winBinNbits > P->genomeChrBinNbits) {
P->inOut->logMain << "winBinNbits=" <<P->winBinNbits <<" > " << "genomeChrBinNbits=" << P->genomeChrBinNbits << " redefining:\n";
P->winBinNbits=P->genomeChrBinNbits;
P->inOut->logMain << "winBinNbits=" <<P->winBinNbits <<endl;
};
if (P->alignIntronMax==0 && P->alignMatesGapMax==0) {
} else {
//redefine winFlankNbins,winAnchorDistNbins
P->winFlankNbins=max(P->alignIntronMax,P->alignMatesGapMax)/(1LLU<<P->winBinNbits)+1;
P->winAnchorDistNbins=2*P->winFlankNbins;
P->inOut->logMain << "To accomodate alignIntronMax="<<P->alignIntronMax<<" and alignMatesGapMax="<<P->alignMatesGapMax<<\
", redefined winFlankNbins="<<P->winFlankNbins<<" and winAnchorDistNbins="<<P->winAnchorDistNbins<<endl;
};
P->winBinChrNbits=P->genomeChrBinNbits-P->winBinNbits;
P->winBinN = P->nGenome/(1LLU << P->winBinNbits)+1;//this may be chenaged later
};
void genomeGenerate(Parameters *P) {
//check parameters
if (P->sjdbOverhang<=0 && (P->sjdbFileChrStartEnd.at(0)!="-" || P->sjdbGTFfile!="-"))
{
ostringstream errOut;
errOut << "EXITING because of FATAL INPUT PARAMETER ERROR: for generating genome with annotations (--sjdbFileChrStartEnd or --sjdbGTFfile options)\n";
errOut << "you need to specify >0 --sjdbOverhang\n";
errOut << "SOLUTION: re-run genome generation specifying non-zero --sjdbOverhang, which ideally should be equal to OneMateLength-1, or could be chosen generically as ~100\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
}
if (P->sjdbFileChrStartEnd.at(0)=="-" && P->sjdbGTFfile=="-")
{
if (P->parArray.at(P->sjdbOverhang_par)->inputLevel>0 && P->sjdbOverhang>0)
{
ostringstream errOut;
errOut << "EXITING because of FATAL INPUT PARAMETER ERROR: when generating genome without annotations (--sjdbFileChrStartEnd or --sjdbGTFfile options)\n";
errOut << "do not specify >0 --sjdbOverhang\n";
errOut << "SOLUTION: re-run genome generation without --sjdbOverhang option\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
P->sjdbOverhang=0;
};
//time
time_t rawTime;
string timeString;
time(&rawTime);
P->inOut->logMain << timeMonthDayTime(rawTime) <<" ... Starting to generate Genome files\n" <<flush;
*P->inOut->logStdOut << timeMonthDayTime(rawTime) <<" ... Starting to generate Genome files\n" <<flush;
//define some parameters from input parameters
P->genomeChrBinNbases=1LLU << P->genomeChrBinNbits;
//write genome parameters file
genomeParametersWrite(P->genomeDir+("/genomeParameters.txt"), P, "ERROR_00102");
char *G=NULL, *G1=NULL;
uint nGenomeReal=genomeScanFastaFiles(P,G,false);//first scan the fasta file to find all the sizes
P->chrBinFill();
uint L=10000;//maximum length of genome suffix
uint nG1alloc=(nGenomeReal + L)*2;
G1=new char[nG1alloc];
G=G1+L;
memset(G1,GENOME_spacingChar,nG1alloc);//initialize to K-1 all bytes
genomeScanFastaFiles(P,G,true); //load the genome sequence
uint N = nGenomeReal;
P->nGenome=N;
uint N2 = N*2;
ofstream chrN,chrS,chrL,chrNL;
ofstrOpen(P->genomeDir+"/chrName.txt","ERROR_00103", P, chrN);
ofstrOpen(P->genomeDir+"/chrStart.txt","ERROR_00103", P, chrS);
ofstrOpen(P->genomeDir+"/chrLength.txt","ERROR_00103", P, chrL);
ofstrOpen(P->genomeDir+"/chrNameLength.txt","ERROR_00103", P, chrNL);
for (uint ii=0;ii<P->nChrReal;ii++) {//output names, starts, lengths
chrN<<P->chrName[ii]<<"\n";
chrS<<P->chrStart[ii]<<"\n";
chrL<<P->chrLength.at(ii)<<"\n";
chrNL<<P->chrName[ii]<<"\t"<<P->chrLength.at(ii)<<"\n";
};
chrS<<P->chrStart[P->nChrReal]<<"\n";//size of the genome
chrN.close();chrL.close();chrS.close(); chrNL.close();
if (P->limitGenomeGenerateRAM < (nG1alloc+nG1alloc/3)) {//allocate nG1alloc/3 for SA generation
ostringstream errOut;
errOut <<"EXITING because of FATAL PARAMETER ERROR: limitGenomeGenerateRAM="<< (P->limitGenomeGenerateRAM) <<"is too small for your genome\n";
errOut <<"SOLUTION: please specify limitGenomeGenerateRAM not less than"<< nG1alloc+nG1alloc/3 <<" and make that much RAM available \n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
//preparing to generate SA
for (uint ii=0;ii<N;ii++) {//- strand
G[N2-1-ii]=G[ii]<4 ? 3-G[ii] : G[ii];
};
P->nSA=0;
for (uint ii=0;ii<N2;ii+=P->genomeSAsparseD) {
if (G[ii]<4) {
P->nSA++;
};
};
P->GstrandBit = (uint) floor(log(N)/log(2))+1;
if (P->GstrandBit<32) P->GstrandBit=32; //TODO: use simple access function for SA
P->GstrandMask = ~(1LLU<<P->GstrandBit);
PackedArray SA1;//SA without sjdb
SA1.defineBits(P->GstrandBit+1,P->nSA);
PackedArray SA2;//SA with sjdb, reserve more space
if (P->sjdbInsert.yes)
{//reserve space for junction insertion
SA2.defineBits(P->GstrandBit+1,P->nSA+2*P->limitSjdbInsertNsj*P->sjdbLength);//TODO: this allocation is wasteful, get a better estimate of the number of junctions
} else
{//same as SA1
SA2.defineBits(P->GstrandBit+1,P->nSA);
};
P->nSAbyte=SA2.lengthByte;
P->inOut->logMain << "Number of SA indices: "<< P->nSA << "\n"<<flush;
//sort SA
time ( &rawTime );
P->inOut->logMain << timeMonthDayTime(rawTime) <<" ... starting to sort Suffix Array. This may take a long time...\n" <<flush;
*P->inOut->logStdOut << timeMonthDayTime(rawTime) <<" ... starting to sort Suffix Array. This may take a long time...\n" <<flush;
// if (false)
{//sort SA chunks
for (uint ii=0;ii<N;ii++) {//re-fill the array backwards for sorting
swap(G[N2-1-ii],G[ii]);
};
globalG=G;
globalL=L/sizeof(uint);
//count the number of indices with 4nt prefix
uint indPrefN=1LLU << 16;
uint* indPrefCount = new uint [indPrefN];
memset(indPrefCount,0,indPrefN*sizeof(indPrefCount[0]));
P->nSA=0;
for (uint ii=0;ii<N2;ii+=P->genomeSAsparseD) {
if (G[ii]<4) {
uint p1=(G[ii]<<12) + (G[ii-1]<<8) + (G[ii-2]<<4) + G[ii-3];
indPrefCount[p1]++;
P->nSA++;
};
};
uint saChunkSize=(P->limitGenomeGenerateRAM-nG1alloc)/8/P->runThreadN; //number of SA indexes per chunk
saChunkSize=saChunkSize*6/10; //allow extra space for qsort
//uint saChunkN=((P->nSA/saChunkSize+1)/P->runThreadN+1)*P->runThreadN;//ensure saChunkN is divisible by P->runThreadN
//saChunkSize=P->nSA/saChunkN+100000;//final chunk size
if (P->runThreadN>1) saChunkSize=min(saChunkSize,P->nSA/(P->runThreadN-1));
uint saChunkN=P->nSA/saChunkSize;//estimate
uint* indPrefStart = new uint [saChunkN*2]; //start and stop, *2 just in case
uint* indPrefChunkCount = new uint [saChunkN*2];
indPrefStart[0]=0;
saChunkN=0;//start counting chunks
uint chunkSize1=indPrefCount[0];
for (uint ii=1; ii<indPrefN; ii++) {
chunkSize1 += indPrefCount[ii];
if (chunkSize1 > saChunkSize) {
saChunkN++;
indPrefStart[saChunkN]=ii;
indPrefChunkCount[saChunkN-1]=chunkSize1-indPrefCount[ii];
chunkSize1=indPrefCount[ii];
};
};
saChunkN++;
indPrefStart[saChunkN]=indPrefN+1;
indPrefChunkCount[saChunkN-1]=chunkSize1;
P->inOut->logMain << "Number of chunks: " << saChunkN <<"; chunks size limit: " << saChunkSize*8 <<" bytes\n" <<flush;
time ( &rawTime );
P->inOut->logMain << timeMonthDayTime(rawTime) <<" ... sorting Suffix Array chunks and saving them to disk...\n" <<flush;
*P->inOut->logStdOut << timeMonthDayTime(rawTime) <<" ... sorting Suffix Array chunks and saving them to disk...\n" <<flush;
#pragma omp parallel for num_threads(P->runThreadN) ordered schedule(dynamic,1)
for (int iChunk=0; iChunk < (int) saChunkN; iChunk++) {//start the chunk cycle: sort each chunk with qsort and write to a file
uint* saChunk=new uint [indPrefChunkCount[iChunk]];//allocate local array for each chunk
for (uint ii=0,jj=0;ii<N2;ii+=P->genomeSAsparseD) {//fill the chunk with SA indices
if (G[ii]<4) {
uint p1=(G[ii]<<12) + (G[ii-1]<<8) + (G[ii-2]<<4) + G[ii-3];
if (p1>=indPrefStart[iChunk] && p1<indPrefStart[iChunk+1]) {
saChunk[jj]=ii;
jj++;
};
//TODO: if (jj==indPrefChunkCount[iChunk]) break;
};
};
//sort the chunk
qsort(saChunk,indPrefChunkCount[iChunk],sizeof(saChunk[0]),funCompareSuffixes);
for (uint ii=0;ii<indPrefChunkCount[iChunk];ii++) {
saChunk[ii]=N2-1-saChunk[ii];
};
//write files
ofstream saChunkFile;
string chunkFileName=P->genomeDir+"/SA_"+to_string( (uint) iChunk);
ofstrOpen(chunkFileName,"ERROR_00105", P, saChunkFile);
fstreamWriteBig(saChunkFile, (char*) saChunk, sizeof(saChunk[0])*indPrefChunkCount[iChunk],chunkFileName,"ERROR_00121",P);
saChunkFile.close();
delete [] saChunk;
saChunk=NULL;
};
time ( &rawTime );
P->inOut->logMain << timeMonthDayTime(rawTime) <<" ... loading chunks from disk, packing SA...\n" <<flush;
*P->inOut->logStdOut << timeMonthDayTime(rawTime) <<" ... loading chunks from disk, packing SA...\n" <<flush;
//read chunks and pack into full SA1
SA2.allocateArray();
SA1.pointArray(SA2.charArray + SA2.lengthByte-SA1.lengthByte); //SA1 is shifted to have space for junction insertion
uint N2bit= 1LLU << P->GstrandBit;
uint packedInd=0;
#define SA_CHUNK_BLOCK_SIZE 10000000
uint* saIn=new uint[SA_CHUNK_BLOCK_SIZE]; //TODO make adjustable
#ifdef genenomeGenerate_SA_textOutput
ofstream SAtxtStream ((P->genomeDir + "/SAtxt").c_str());
#endif
for (uint iChunk=0;iChunk<saChunkN;iChunk++) {//load files one by one and convert to packed
ostringstream saChunkFileNameStream("");
saChunkFileNameStream<< P->genomeDir << "/SA_" << iChunk;
ifstream saChunkFile(saChunkFileNameStream.str().c_str());
while (! saChunkFile.eof()) {//read blocks from each file
uint chunkBytesN=fstreamReadBig(saChunkFile,(char*) saIn,SA_CHUNK_BLOCK_SIZE*sizeof(saIn[0]));
for (uint ii=0;ii<chunkBytesN/sizeof(saIn[0]);ii++) {
SA1.writePacked( packedInd+ii, (saIn[ii]<N) ? saIn[ii] : ( (saIn[ii]-N) | N2bit ) );
#ifdef genenomeGenerate_SA_textOutput
SAtxtStream << saIn[ii] << "\n";
#endif
};
packedInd += chunkBytesN/sizeof(saIn[0]);
};
saChunkFile.close();
remove(saChunkFileNameStream.str().c_str());//remove the chunk file
};
#ifdef genenomeGenerate_SA_textOutput
SAtxtStream.close();
#endif
delete [] saIn;
if (packedInd != P->nSA ) {//
ostringstream errOut;
errOut << "EXITING because of FATAL problem while generating the suffix array\n";
errOut << "The number of indices read from chunks = "<<packedInd<<" is not equal to expected nSA="<<P->nSA<<"\n";
errOut << "SOLUTION: try to re-run suffix array generation, if it still does not work, report this problem to the author\n"<<flush;
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
//DONE with suffix array generation
for (uint ii=0;ii<N;ii++) {//return to normal order for future use
swap(G[N2-1-ii],G[ii]);
};
delete [] indPrefCount;
delete [] indPrefStart;
delete [] indPrefChunkCount;
};
time ( &rawTime );
timeString=asctime(localtime ( &rawTime ));
timeString.erase(timeString.end()-1,timeString.end());
P->inOut->logMain << timeMonthDayTime(rawTime) <<" ... Finished generating suffix array\n" <<flush;
*P->inOut->logStdOut << timeMonthDayTime(rawTime) <<" ... Finished generating suffix array\n" <<flush;
////////////////////////////////////////
// SA index
//
// PackedArray SAold;
//
// if (true)
// {//testing: load SA from disk
// //read chunks and pack into full SA1
//
// ifstream oldSAin("./DirTrue/SA");
// oldSAin.seekg (0, ios::end);
// P->nSAbyte=(uint) oldSAin.tellg();
// oldSAin.clear();
// oldSAin.seekg (0, ios::beg);
//
// P->nSA=(P->nSAbyte*8)/(P->GstrandBit+1);
// SAold.defineBits(P->GstrandBit+1,P->nSA);
// SAold.allocateArray();
//
// oldSAin.read(SAold.charArray,SAold.lengthByte);
// oldSAin.close();
//
// SA1=SAold;
// SA2=SAold;
// };
PackedArray SAip;
genomeSAindex(G,SA1,P,SAip);
if (P->sjdbFileChrStartEnd.at(0)!="-" || P->sjdbGTFfile!="-")
{//insert junctions
SjdbClass sjdbLoci;
Genome mainGenome(P);
mainGenome.G=G;
mainGenome.SA=SA1;
mainGenome.SApass1=SA2;
mainGenome.SAi=SAip;
P->sjdbInsert.outDir=P->genomeDir;
P->sjdbN=0;//no junctions are loaded yet
P->twoPass.pass2=false;
Parameters *P1=new Parameters;
*P1=*P;
sjdbInsertJunctions(P, P1, mainGenome, sjdbLoci);
//write an extra 0 at the end of the array, filling the last bytes that otherwise are not accessible, but will be written to disk
//this is - to avoid valgrind complaints. Note that SA2 is allocated with plenty of space to spare.
SA2.writePacked(P->nSA,0);
};
//write genome to disk
time ( &rawTime );
P->inOut->logMain << timeMonthDayTime(rawTime) <<" ... writing Genome to disk ...\n" <<flush;
*P->inOut->logStdOut << timeMonthDayTime(rawTime) <<" ... writing Genome to disk ...\n" <<flush;
ofstream genomeOut;
ofstrOpen(P->genomeDir+"/Genome","ERROR_00104", P, genomeOut);
fstreamWriteBig(genomeOut,G,P->nGenome,P->genomeDir+"/Genome","ERROR_00120",P);
genomeOut.close();
//write SA
time ( &rawTime );
P->inOut->logMain << "SA size in bytes: "<< P->nSAbyte << "\n"<<flush;
P->inOut->logMain << timeMonthDayTime(rawTime) <<" ... writing Suffix Array to disk ...\n" <<flush;
*P->inOut->logStdOut << timeMonthDayTime(rawTime) <<" ... writing Suffix Array to disk ...\n" <<flush;
ofstream SAout;
ofstrOpen(P->genomeDir+"/SA","ERROR_00106", P, SAout);
fstreamWriteBig(SAout,(char*) SA2.charArray, (streamsize) P->nSAbyte,P->genomeDir+"/SA","ERROR_00122",P);
SAout.close();
//write SAi
time(&rawTime);
P->inOut->logMain << timeMonthDayTime(rawTime) <<" ... writing SAindex to disk\n" <<flush;
*P->inOut->logStdOut << timeMonthDayTime(rawTime) <<" ... writing SAindex to disk\n" <<flush;
//write SAi to disk
ofstream SAiOut;
ofstrOpen(P->genomeDir+"/SAindex","ERROR_00107", P, SAiOut);
fstreamWriteBig(SAiOut, (char*) &P->genomeSAindexNbases, sizeof(P->genomeSAindexNbases),P->genomeDir+"/SAindex","ERROR_00123",P);
fstreamWriteBig(SAiOut, (char*) P->genomeSAindexStart, sizeof(P->genomeSAindexStart[0])*(P->genomeSAindexNbases+1),P->genomeDir+"/SAindex","ERROR_00124",P);
fstreamWriteBig(SAiOut, SAip.charArray, SAip.lengthByte,P->genomeDir+"/SAindex","ERROR_00125",P);
SAiOut.close();
SA2.deallocateArray();
time(&rawTime);
timeString=asctime(localtime ( &rawTime ));
timeString.erase(timeString.end()-1,timeString.end());
time(&rawTime);
P->inOut->logMain << timeMonthDayTime(rawTime) << " ..... Finished successfully\n" <<flush;
*P->inOut->logStdOut << timeMonthDayTime(rawTime) << " ..... Finished successfully\n" <<flush;
};
