- seqs[i] = new Sequence(id, seq, begin, end);
-
- seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
+ sqs[i] = new Sequence(id, seq, begin, end);
+ if (seq.length()!=(end-begin+1))
+ {
+ sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
+ }