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#include "InOutStreams.h"
#include "GlobalVariables.h"
InOutStreams::InOutStreams() {
logStdOut=NULL;
outSAM=NULL;
outBAMfileUnsorted=NULL;
outQuantBAMfile=NULL;
};
InOutStreams::~InOutStreams() {
if (logStdOut!=NULL) logStdOut->flush();
if (outSAM!=NULL) outSAM->flush();
logStdOutFile.flush();
outSAMfile.flush();
outChimSAM.flush();
outChimJunction.flush();
logProgress.flush();
logMain.flush();
logFinal.flush();
outLocalChains.flush();
//logStdOutFile.close(); //do not want to close these log files, as some destructors (e.g. ~SharedMemory) might still write there
//logMain.close();
outSAMfile.close();
outChimSAM.close();
outChimJunction.close();
logProgress.close();
logFinal.close();
outLocalChains.close();
for (int ii=0;ii<2;ii++) {
if (outUnmappedReadsStream[ii].is_open()) {
outUnmappedReadsStream[ii].flush();
outUnmappedReadsStream[ii].close();
}
};
};
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