void genomeParametersWrite(string fileName, Parameters* P, string errorOut)
{//write the genome information into the genomePar stream
ofstream & genomePar = ofstrOpen(fileName, errorOut, P);
genomePar << "### "<<P->commandLineFull <<"\n";
genomePar << "versionGenome\t" << P->versionSTAR <<"\n";
genomePar << "genomeFastaFiles\t";
for (uint ii=0;ii<P->genomeFastaFiles.size();ii++) genomePar << P->genomeFastaFiles.at(ii) << " ";
genomePar << "\n";
genomePar << "genomeSAindexNbases\t" << P->genomeSAindexNbases << "\n";
genomePar << "genomeChrBinNbits\t" << P->genomeChrBinNbits << "\n";
genomePar << "genomeSAsparseD\t" << P->genomeSAsparseD <<"\n";
genomePar << "sjdbOverhang\t" << P->sjdbOverhang <<"\n";
genomePar << "sjdbFileChrStartEnd\t";
for (uint ii=0;ii<P->sjdbFileChrStartEnd.size();ii++) genomePar<< P->sjdbFileChrStartEnd.at(ii) << " ";
genomePar<<"\n";
genomePar << "sjdbGTFfile\t" << P->sjdbGTFfile <<"\n";
genomePar << "sjdbGTFchrPrefix\t" << P->sjdbGTFchrPrefix <<"\n";
genomePar << "sjdbGTFfeatureExon\t" << P->sjdbGTFfeatureExon <<"\n";
genomePar << "sjdbGTFtagExonParentTranscript\t" << P->sjdbGTFtagExonParentTranscript <<"\n";
genomePar << "sjdbGTFtagExonParentGene\t" << P->sjdbGTFtagExonParentGene <<"\n";
genomePar << "sjdbInsertSave\t" << P->sjdbInsert.save <<"\n";
genomePar.close();
};
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;
};
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;
};
