- thisSuccess = rtrimOligos->stripForward(currSeq, currQual, thisPrimerIndex, keepforward);
- if(thisSuccess > pdiffs) { thisTrashCode += 'f'; }
+ thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, keepforward);
+ if(thisSuccess > pdiffs) {
+ //if (pairedOligos) { thisTrashCode += rtrimOligos->getTrashCode(); }
+ //else { thisTrashCode += 'f'; }
+ thisTrashCode += 'f';
+ }