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#include "Parameters.h"
#include "ErrorWarning.h"
#include <fstream>
#include <sys/stat.h>
void Parameters::openReadsFiles()
{
if (readFilesCommandString=="") {//read from file
for (uint ii=0;ii<readFilesIn.size();ii++) {//open readIn files
readFilesCommandPID[ii]=0;//no command process IDs
if ( inOut->readIn[ii].is_open() ) inOut->readIn[ii].close();
string rfName=readFilesPrefixFinal + readFilesIn.at(ii);
inOut->readIn[ii].open(rfName.c_str()); //try to open the Sequences file right away, exit if failed
if (inOut->readIn[ii].fail()) {
ostringstream errOut;
errOut <<"EXITING because of fatal input ERROR: could not open readFilesIn=" << rfName <<"\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
};
} else {//create fifo files, execute pre-processing command
vector<string> readsCommandFileName;
for (uint imate=0;imate<readFilesNames.size();imate++) {//open readIn files
ostringstream sysCom;
sysCom << outFileTmp <<"tmp.fifo.read"<<imate+1;
readFilesInTmp.push_back(sysCom.str());
remove(readFilesInTmp.at(imate).c_str());
if (mkfifo(readFilesInTmp.at(imate).c_str(), S_IRUSR | S_IWUSR ) != 0) {
exitWithError("Exiting because of *FATAL ERROR*: could not create FIFO file " + readFilesInTmp.at(imate) + "\n"
+ "SOLUTION: check the if run directory supports FIFO files.\n"
+ "If run partition does not support FIFO (e.g. Windows partitions FAT, NTFS), "
+ "re-run on a Linux partition, or point --outTmpDir to a Linux partition.\n"
, std::cerr, inOut->logMain, EXIT_CODE_FIFO, *this);
};
inOut->logMain << "\n Input read files for mate "<< imate+1 <<" :\n";
readsCommandFileName.push_back(outFileTmp+"/readsCommand_read" + to_string(imate+1));
fstream readsCommandFile( readsCommandFileName.at(imate).c_str(), ios::out);
readsCommandFile.close();
readsCommandFile.open( readsCommandFileName.at(imate).c_str(), ios::in | ios::out);
//first line in the commands file
if (sysShell!="-") {//executed via specified shell
readsCommandFile << "#!" <<sysShell <<"\n";
};
readsCommandFile << "exec > \""<<readFilesInTmp.at(imate)<<"\"\n" ; // redirect stdout to temp fifo files
for (uint32 ifile=0; ifile<readFilesN; ifile++) {
system(("ls -lL " + readFilesNames[imate][ifile] + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str());
ifstream readFilesIn_info((outFileTmp+"/readFilesIn.info").c_str());
inOut->logMain <<readFilesIn_info.rdbuf();
{//try to open the files - throw an error if a file cannot be opened
ifstream rftry(readFilesNames.at(imate).back().c_str());
if (!rftry.good()){
exitWithError("EXITING: because of fatal INPUT file error: could not open read file: " + \
readFilesNames.at(imate).back() + \
"\nSOLUTION: check that this file exists and has read permision.\n", \
std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
rftry.close();
};
readsCommandFile <<"echo FILE "<< ifile << "\n";
readsCommandFile << readFilesCommandString <<" "<< ("\""+readFilesNames[imate][ifile]+"\"") <<"\n";
};
readsCommandFile.flush();
readsCommandFile.seekg(0,ios::beg);
inOut->logMain <<"\n readsCommandsFile:\n"<<readsCommandFile.rdbuf()<<endl;
readsCommandFile.close();
chmod(readsCommandFileName.at(imate).c_str(),S_IXUSR | S_IRUSR | S_IWUSR);
readFilesCommandPID[imate]=0;
ostringstream errOut;
pid_t PID=vfork();
switch (PID) {
case -1:
errOut << "EXITING: because of fatal EXECUTION error: Failed vforking readFilesCommand\n";
errOut << errno << ": " << strerror(errno) << "\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
break;
case 0:
//this is the child
execlp(readsCommandFileName.at(imate).c_str(), readsCommandFileName.at(imate).c_str(), (char*) NULL);
exit(0);
default:
//this is the father, record PID of the children
readFilesCommandPID[imate]=PID;
};
inOut->readIn[imate].open(readFilesInTmp.at(imate).c_str());
};
};
readFilesIndex=0;
if (readFilesTypeN==10) {//SAM file - skip header lines
readSAMheader(readFilesCommandString, readFilesNames.at(0));
};
};
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