referenceSeqs.resize(numRefSeqs);
referenceNames.resize(numRefSeqs);
for(int i=0;i<numRefSeqs;i++){
- referenceSeqs[i] = refs[i].getAligned();
+ if (aligned) { referenceSeqs[i] = refs[i].getAligned(); }
+ else { referenceSeqs[i] = refs[i].getUnaligned(); }
referenceNames[i] = refs[i].getName();
}