1 #ifndef INOUTSTREAMS_DEF
2 #define INOUTSTREAMS_DEF
3 
4 #include "IncludeDefine.h"
5 #include SAMTOOLS_BGZF_H
6 
7 class InOutStreams {
8     public:
9     ostream *logStdOut, *outSAM;
10     ofstream logStdOutFile, outSAMfile;
11     BGZF *outBAMfileUnsorted, *outBAMfileCoord, *outQuantBAMfile;
12 
13     ofstream outChimSAM, outChimJunction, logMain, logProgress, logFinal, outUnmappedReadsStream[MAX_N_MATES];
14     ifstream readIn[MAX_N_MATES];
15 
16     //compilation-optional streams
17     ofstream outLocalChains;
18 
19     InOutStreams();
20     ~InOutStreams();
21 };
22 
23 #endif
24