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#include "Parameters.h"
#include "ErrorWarning.h"
#include <fstream>
#include <sys/stat.h>
void Parameters::readSAMheader(const string readFilesCommandString, const vector<string> readFilesNames) {
if (readFilesCommandString=="") {//simply read from file
while (inOut->readIn[0].peek()=='@') {
string str1;
getline(inOut->readIn[0],str1);
if (str1.substr(1,2)!="HD" && str1.substr(1,2)!="SQ") {
samHeaderExtra += str1 + '\n';
};
};
return;
};
string tmpFifo=outFileTmp+"tmp.fifo.header";
remove(tmpFifo.c_str());
if (mkfifo(tmpFifo.c_str(), S_IRUSR | S_IWUSR ) != 0) {
exitWithError("Exiting because of *FATAL ERROR*: could not create FIFO file " + tmpFifo + "\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);
};
ifstream tmpFifoIn;
for (uint32 ii=0; ii<readFilesNames.size(); ii++) {
string com1=readFilesCommandString + " " + readFilesNames.at(ii) + " > " + tmpFifo + "&";
system(com1.c_str());
tmpFifoIn.open(tmpFifo);
while (tmpFifoIn.peek()=='@') {
string str1;
getline(tmpFifoIn,str1);
if (str1.substr(1,2)!="HD" && str1.substr(1,2)!="SQ" && (!twoPass.pass2) ) {
//SQ and HD header lines cannot be imported from uSAM; do not record the header again in the 2nd pass
samHeaderExtra += str1 + '\n';
};
};
tmpFifoIn.close();
};
};
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