}
Sequence temp = templateDB->findClosestSequence(candidateSeq);
- Sequence* templateSeq = &temp;
+ Sequence* templateSeq = new Sequence(temp.getName(), temp.getAligned());
float searchScore = templateDB->getSearchScore();
//rerun alignment
Sequence temp2 = templateDB->findClosestSequence(copy);
- Sequence* templateSeq2 = &temp2;
+ Sequence* templateSeq2 = new Sequence(temp2.getName(), temp2.getAligned());
searchScore = templateDB->getSearchScore();
//check if any better
if (copy->getNumBases() > candidateSeq->getNumBases()) {
candidateSeq->setAligned(copy->getAligned()); //use reverse compliments alignment since its better
- templateSeq = templateSeq2;
+ delete templateSeq;
+ templateSeq = templateSeq2;
delete nast;
nast = nast2;
needToDeleteCopy = true;
}else{
wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
delete nast2;
+ delete templateSeq2;
delete copy;
}
}
report.print();
delete nast;
+ delete templateSeq;
if (needToDeleteCopy) { delete copy; }
pDataArray->count++;
delete candidateSeq;
//report progress
- if((pDataArray->count) % 100 == 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 100 == 0){ pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n"); }
}
//report progress
- if((pDataArray->count) % 100 != 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 100 != 0){ pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n"); }
delete alignment;
delete templateDB;