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#ifndef CODE_SoloBarcode
#define CODE_SoloBarcode
#include "IncludeDefine.h"
class SoloBarcode {//complex barcodes
public:
uint32 mate;//0 or 1
//array: 0=start, 1=end
int32 anchorType[2];//0=read start; 1=read end; 2=adapter start; 3=adapter end
int32 anchorDist[2];//distance to anchor
uint32 adapterLength;//length of the adapter
vector<vector<uint64>> wl;//whitelists, one for each length
uint64 wlFactor;//factor and modulo for converting each whitelist index into global index
vector<uint32> wlAdd;//additive for each length
uint32 minLen;//minimum length for this barcode
uint32 totalSize;//total size of all whitelists
uint64 ilen, icb;//indexes
bool extractBarcode(string &seqIn, string &qualIn, const uint32 aStart, string &bSeq, string &bQual);
void sortWhiteList();
void extractPositionsFromString(string &strIn);
};
#endif
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