- // we just inserted something
- // remove these inserts now - should be very first entry
- int count = seqInserts.get(rec.getStart() + refnext);
- override = new int[] { rec.getStart() + refnext,
- count - lastinserts };
- lastinserts = 0;
+ if (!seqInserts.containsKey(rec.getStart() + refnext))
+ {
+ // ERROR
+ int pos = rec.getStart() + refnext;
+ System.out.println("Insertion not added to seqInserts: " + pos);
+ }
+ else
+ {
+
+ // we just inserted something
+ // remove these inserts now - should be very first entry
+ int count = seqInserts.get(rec.getStart() + refnext);
+ override = new int[] { rec.getStart() + refnext,
+ count - lastinserts };
+ lastinserts = 0;
+ }