{
// ERROR
int pos = rec.getStart() + refnext;
- System.out.println("Insertion not added to seqInserts: " + pos);
+ System.out.println(
+ "Read " + rec.getReadName() + " has an insertion at "
+ + pos + " which is not in seqInserts");
}
else
{
-
// we just inserted something
// remove these inserts now - should be very first entry
int count = seqInserts.get(rec.getStart() + refnext);