sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
//sq.setSequenceFeatures(sp.getSequenceFeatures());
int inspos=-1;
- for (int ap=0;p<annotations.size();)
+ for (int ap=0;ap<annotations.size();)
{
if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
if (inspos==-1)