1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
|
#ifndef CODE_ReadAlignChunk
#define CODE_ReadAlignChunk
#include "IncludeDefine.h"
#include "Parameters.h"
#include "ReadAlign.h"
#include "OutSJ.h"
#include "Transcriptome.h"
#include "BAMoutput.h"
#include "Quantifications.h"
class ReadAlignChunk {//chunk of reads and alignments
public:
Parameters& P;
ReadAlign* RA;
Transcriptome *chunkTr;
char **chunkIn; //space for the chunk of input reads
array<uint64, MAX_N_MATES> chunkInSizeBytesTotal;
char *chunkOutBAM, *chunkOutBAM1;//space for the chunk of output SAM
OutSJ *chunkOutSJ, *chunkOutSJ1;
BAMoutput *chunkOutBAMcoord, *chunkOutBAMunsorted, *chunkOutBAMquant;
Quantifications *chunkQuants;
istringstream** readInStream;
ostringstream* chunkOutBAMstream;
ofstream chunkOutBAMfile;
string chunkOutBAMfileName;
bool noReadsLeft;
uint iChunkIn; //current chunk # as read from .fastq
uint iChunkOutSAM; //current chunk # writtedn to Aligned.out.sam
int iThread; //current thread
uint chunkOutBAMtotal; //total number of bytes in the write buffer
ReadAlignChunk(Parameters& Pin, Genome &genomeIn, Transcriptome *TrIn, int iChunk);
void processChunks();
void mapChunk();
void chunkFstreamOpen(string filePrefix, int iChunk, fstream &fstreamOut);
void chunkFstreamCat (fstream &chunkOut, ofstream &allOut, bool mutexFlag, pthread_mutex_t &mutexVal);
void chunkFilesCat(ostream *allOut, string filePrefix, uint &iC);
Genome &mapGen;
private:
};
#endif
|
