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
|
#ifndef CODE_ClipMate
#define CODE_ClipMate
#include "IncludeDefine.h"
#include "ClipCR4.h"
class ClipMate
{
public:
//clip parameters
int type; //standard sequence clip: 0=5p, 1=3p, -1=no clip; 10/11 = 10X CR4 5/3p clip
uint32 N;
uint32 NafterAd;
string adSeq;
vector<char> adSeqNum;
double adMMp;
//clipped info from clipChunk
char clippedInfo;
//clip results
uint32 clippedAdN; //adapter bases clipped
uint32 clippedAdMM; //adapter mismatches
uint32 clippedN; //total number of bases clipped
ClipCR4 *cr4; //CR4 clipping structure
void initialize(uint32 Nin, const string &adSeqIn, uint32 afterAdNin, double adMMpIn);
uint32 clip(uint &Lread, char *SeqNum);
void clipChunk(char *chArr, uint64 chSize);
};
#endif
|
