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#ifndef INOUTSTREAMS_DEF
#define INOUTSTREAMS_DEF
#include "IncludeDefine.h"
#include SAMTOOLS_BGZF_H
class InOutStreams {
public:
ostream *logStdOut, *outSAM;
ofstream logStdOutFile, outSAMfile;
BGZF *outBAMfileUnsorted, *outBAMfileCoord, *outQuantBAMfile;
ofstream outChimSAM, outChimJunction, logMain, logProgress, logFinal, outUnmappedReadsStream[MAX_N_MATES];
ifstream readIn[MAX_N_MATES];
//compilation-optional streams
ofstream outLocalChains;
InOutStreams();
~InOutStreams();
};
#endif
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