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#include "SoloBarcode.h"
#include <array>
bool SoloBarcode::extractBarcode(string &seqIn, string &qualIn, const uint32 adapterStart, string &bSeq, string &bQual)
{//input: sequence seqIn, adapter start adapterStart
//output: start position of the barcode
array<int32,2> pos={0,0};
for (uint32 ii=0; ii<2; ii++) {
switch (anchorType[ii]) {//this calculates the position of the anchor base
case 0: //read start
pos[ii]=0;
break;
case 1: //read end
pos[ii]=seqIn.size()-1;
break;
case 2: //adapter start
pos[ii]=(int32)adapterStart;
break;
case 3: //adapter end
pos[ii]=(int32)adapterStart+adapterLength-1;
break;
};
pos[ii]+=anchorDist[ii];
};
bSeq="";
bQual="";
if (pos[0]<0 || pos[1]>(int32)seqIn.size() || pos[0]>pos[1]) //something went wrong
return false;
bSeq =seqIn.substr(pos[0],pos[1]-pos[0]+1);
bQual=qualIn.substr(pos[0],pos[1]-pos[0]+1);
return true;
};
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