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#include "Genome.h"
#include "SuffixArrayFuns.h"
#include "PackedArray.h"
#include "ErrorWarning.h"
#include "streamFuns.h"
#include "SharedMemory.h"
#include "genomeScanFastaFiles.h"
#include "systemFunctions.h"
#include <time.h>
#include <cmath>
#include <unistd.h>
#include <sys/stat.h>
Genome::Genome (Parameters &P, ParametersGenome &pGe): shmStart(NULL), P(P), pGe(pGe), sharedMemory(NULL)
{
struct stat stbuf;
stat(pGe.gDir.c_str(), &stbuf);
shmKey=stbuf.st_ino;
genomeOut.g=this;//will change if genomeOut is different from genomeMain
genomeOut.convYes=false;
sjdbOverhang = pGe.sjdbOverhang; //will be re-defined later if another value was used for the generated genome
sjdbLength = pGe.sjdbOverhang==0 ? 0 : pGe.sjdbOverhang*2+1;
};
// Genome::~Genome()
// {
// if (sharedMemory != NULL)
// delete sharedMemory;
// sharedMemory = NULL;
// }
void Genome::freeMemory(){//free big chunks of memory used by genome and suffix array
if (pGe.gLoad=="NoSharedMemory") {//can deallocate only for non-shared memory
delete[] G1;
G1=NULL;
SA.deallocateArray();
SApass2.deallocateArray();
SAi.deallocateArray();
P.inOut->logMain << "RAM after freeing genome index memory:\n"
<< linuxProcMemory() << flush;
};
};
uint Genome::OpenStream(string name, ifstream & stream, uint size)
{
stream.open((pGe.gDir+ "/" +name).c_str(), ios::binary);
if (!stream.good()) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: could not open genome file: "<< pGe.gDir << "/" << name <<"\n";
errOut << "SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permissions\n" <<flush;
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_GENOME_FILES, P);
};
if (size>0) {
P.inOut->logMain << name << ": size given as a parameter = " << size <<"\n";
} else {
P.inOut->logMain << "Checking " << name << " size";
stream.seekg (0, ios::end);
int64 size1 = stream.tellg();
if (size1<=0) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: failed reading from genome file: "<< pGe.gDir << "/" << name <<"\n";
errOut << "SOLUTION: re-generate the genome index\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, 1, P);
};
size=(uint) size1;
stream.clear();
stream.seekg (0, ios::beg);
P.inOut->logMain << "file size: "<< size <<" bytes; state: good=" <<stream.good()\
<<" eof="<<stream.eof()<<" fail="<<stream.fail()<<" bad="<<stream.bad()<<"\n"<<flush;
};
return size;
};
void Genome::HandleSharedMemoryException(const SharedMemoryException & exc, uint64 shmSize)
{
ostringstream errOut;
errOut << "Shared memory error: " << exc.GetErrorCode() << ", errno: " << strerror(exc.GetErrorDetail()) << "(" << errno << ")" << endl;
int exitCode = EXIT_CODE_SHM;
switch (exc.GetErrorCode())
{
case EOPENFAILED:
errOut << "EXITING because of FATAL ERROR: problems with shared memory: error from shmget() or shm_open()." << endl << flush;
errOut << "SOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory" << endl << flush;
break;
case EEXISTS:
errOut << "EXITING: fatal error from shmget() trying to allocate shared memory piece." << endl;
errOut << "Possible cause 1: not enough RAM. Check if you have enough RAM of at least " << shmSize+2000000000 << " bytes" << endl;
errOut << "Possible cause 2: not enough virtual memory allowed with ulimit. SOLUTION: run ulimit -v " << shmSize+2000000000 << endl;
errOut << "Possible cause 3: allowed shared memory size is not large enough. SOLUTIONS: (i) consult STAR manual on how to increase shared memory allocation; " \
"(ii) ask your system administrator to increase shared memory allocation; (iii) run STAR with --genomeLoad NoSharedMemory" << endl<<flush;
break;
case EFTRUNCATE:
errOut << "EXITING: fatal error from ftruncate() error shared memory." << endl;
errOut << "Possible cause 1: not enough RAM. Check if you have enough RAM of at least " << shmSize+2000000000 << " bytes" << endl << flush;
exitCode = EXIT_CODE_MEMORY_ALLOCATION;
break;
case EMAPFAILED:
errOut << "EXITING because of FATAL ERROR: problems with shared memory: error from shmat() while trying to get address of the shared memory piece." << endl << flush;
errOut << "SOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory" << endl << flush;
break;
case ECLOSE:
errOut << "EXITING because of FATAL ERROR: could not close the shared memory object." << endl << flush;
break;
case EUNLINK:
#ifdef POSIX_SHARED_MEM
errOut << "EXITING because of FATAL ERROR: could not delete the shared object." << endl << flush;
#else
errOut << "EXITING because of FATAL ERROR: problems with shared memory: error from shmctl() while trying to remove shared memory piece." << endl << flush;
errOut << "SOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory" << endl << flush;
#endif
break;
default:
errOut << "EXITING because of FATAL ERROR: There was an issue with the shared memory allocation. Try running STAR with --genomeLoad NoSharedMemory to avoid using shared memory.";
break;
}
try
{
if (sharedMemory != NULL)
sharedMemory->Clean();
}
catch(...)
{}
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, exitCode, P);
};
//////////////////////////////////////////////////////////////////////////////////////////
void Genome::chrInfoLoad() {//find chrStart,Length,nChr from Genome G
//load chr names
ifstream chrStreamIn ( (pGe.gDir+"/chrName.txt").c_str() );
if (chrStreamIn.fail()) {
ostringstream errOut;
errOut << "EXITING because of FATAL error, could not open file " << (pGe.gDir+"/chrName.txt") <<"\n";
errOut << "SOLUTION: re-generate genome files with STAR --runMode genomeGenerate\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
char chrInChar[1000];
while (chrStreamIn.good()) {
string chrIn;
chrStreamIn.getline(chrInChar,1000);
chrIn=chrInChar;
if (chrIn=="") break;
chrName.push_back(chrIn);
};
chrStreamIn.close();
nChrReal=chrName.size();
P.inOut->logMain << "Number of real (reference) chromosomes= " << nChrReal <<"\n"<<flush;
chrStart.resize(nChrReal+1);
chrLength.resize(nChrReal);
//load chr lengths
chrStreamIn.open( (pGe.gDir+"/chrLength.txt").c_str() );
if (chrStreamIn.fail()) {
ostringstream errOut;
errOut << "EXITING because of FATAL error, could not open file " << (pGe.gDir+"/chrLength.txt") <<"\n";
errOut << "SOLUTION: re-generate genome files with STAR --runMode genomeGenerate\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
for (uint ii=0;ii<nChrReal;ii++) {
chrStreamIn >> chrLength[ii];
};
chrStreamIn.close();
//load chr starts
chrStreamIn.open( (pGe.gDir+"/chrStart.txt").c_str() );
if (chrStreamIn.fail()) {
ostringstream errOut;
errOut << "EXITING because of FATAL error, could not open file " << (pGe.gDir+"/chrStart.txt") <<"\n";
errOut << "SOLUTION: re-generate genome files with STAR --runMode genomeGenerate\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
for (uint ii=0;ii<=nChrReal;ii++) {
chrStreamIn >> chrStart[ii];
};
chrStreamIn.close();
//log
for (uint ii=0; ii<nChrReal;ii++) {
P.inOut->logMain << ii+1 <<"\t"<< chrName[ii] <<"\t"<<chrLength[ii]<<"\t"<<chrStart[ii]<<"\n"<<flush;
chrNameIndex[chrName[ii]]=ii;
};
//chr sets
for (auto &cm: pGe.chrSet.mitoStrings) {
uint64 ind1 = std::find(chrName.begin(), chrName.end(), cm) - chrName.begin();
pGe.chrSet.mito.insert(ind1);
};
};
//////////////////////////////////////////////////////////
void Genome::chrBinFill() {
chrBinN = chrStart[nChrReal]/genomeChrBinNbases+1;
chrBin = new uint [chrBinN];
for (uint ii=0, ichr=1; ii<chrBinN; ++ii) {
if (ii*genomeChrBinNbases>=chrStart[ichr]) ichr++;
chrBin[ii]=ichr-1;
};
};
//////////////////////////////////////////////////////////
void Genome::genomeSequenceAllocate(uint64 nGenomeIn, uint64 &nG1allocOut, char*& Gout, char*& G1out)
{
nG1allocOut=(nGenomeIn + 100)*2; //extra 100 bytes at the beginning, just in case
if (P.limitGenomeGenerateRAM < (nG1allocOut+nG1allocOut/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 "<< nG1allocOut+nG1allocOut/3 <<" and make that much RAM available \n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
G1out=new char[nG1allocOut];
Gout=G1out+100;
memset(G1out,GENOME_spacingChar,nG1allocOut);//initialize to K-1 all bytes
};
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