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#ifndef CODE_BAMoutput
#define CODE_BAMoutput
#include "IncludeDefine.h"
#include SAMTOOLS_BGZF_H
#include "Parameters.h"
class BAMoutput {//
public:
//sorted output
BAMoutput (int iChunk, string tmpDir, Parameters &Pin);
void coordOneAlign (char *bamIn, uint bamSize, uint iRead);
void coordBins ();
void coordFlush ();
//unsorted output
BAMoutput (BGZF *bgzfBAMin, Parameters &Pin);
void unsortedOneAlign (char *bamIn, uint bamSize, uint bamSize2);
void unsortedFlush ();
void coordUnmappedPrepareBySJout();
uint32 nBins; //number of bins to split genome into
uint* binTotalN; //total number of aligns in each bin
uint* binTotalBytes;//total size of aligns in each bin
private:
uint64 bamArraySize; //this size will be allocated
char* bamArray; //large array to store the bam alignments, pre-sorted
uint64 binSize, binSize1;//storage size of each bin
uint64 binGlen;//bin genomic length
char **binStart; //pointers to starts of the bins
uint64 *binBytes, binBytes1;//number of bytes currently written to each bin
ofstream **binStream;//output streams for each bin
BGZF *bgzfBAM;
Parameters &P;
string bamDir;
};
#endif
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