outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
}
}
-
+
+ if (!pairedOligos) { if (reorient) { m->mothurOut("[WARNING]: You cannot use reorient without paired barcodes or primers, skipping."); m->mothurOutEndLine(); reorient = false; } }
+
if (m->control_pressed) { return 0; }
//fills lines and qlines
if(numBarcodes != 0){
success = trimOligos->stripBarcode(currSeq, currQual, barcodeIndex);
- if(success > bdiffs) { trashCode += 'b'; }
+ if(success > bdiffs) {
+ trashCode += 'b';
+ }
else{ currentSeqsDiffs += success; }
}
if(numFPrimers != 0){
success = trimOligos->stripForward(currSeq, currQual, primerIndex, keepforward);
if(success > pdiffs) {
- //if (pairedOligos) { trashCode += trimOligos->getTrashCode(); }
- //else { trashCode += 'f'; }
- trashCode += 'f';
+ trashCode += 'f';
}
else{ currentSeqsDiffs += success; }
}
if(numBarcodes != 0){
thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex);
- if(thisSuccess > bdiffs) { thisTrashCode += 'b'; }
+ if(thisSuccess > bdiffs) { thisTrashCode += "b"; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
if(numFPrimers != 0){
thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, keepforward);
- if(thisSuccess > pdiffs) {
- //if (pairedOligos) { thisTrashCode += rtrimOligos->getTrashCode(); }
- //else { thisTrashCode += 'f'; }
- thisTrashCode += 'f';
- }
+ if(thisSuccess > pdiffs) { thisTrashCode += "f"; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
savedQual.flipQScores();
currQual.setScores(savedQual.getScores());
}
- }
+ }else { trashCode += "(" + thisTrashCode + ")"; }
}
if(keepFirst != 0){
}
if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; }
-
+
//add in potential combos
if(barcodeNameVector.size() == 0){
barcodes[""] = 0;