- alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
- Nast nast(alignment, queryParts[i], parentParts[i]);
- delete alignment;
+ if ((queryParts[i]->getUnaligned() == "") || (parentParts[i]->getUnaligned() == "")) {;}
+ else {
+ Alignment* alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, longest+1); //default gapopen, match, mismatch, longestbase
+
+ Nast nast(alignment, queryParts[i], parentParts[i]);
+ delete alignment;
+ }