+ // skipint at start of contig
+ // shift the start of this contig
+ if (scontigs[vc + 1] > skipint[1])
+ {
+ scontigs[vc] = skipint[1];
+ vc+=2;
+ }
+ else
+ {
+ if (scontigs[vc+1]==skipint[1])
+ {
+ // remove the contig
+ t = new int[scontigs.length - 2];
+ if (vc > 0)
+ {
+ System.arraycopy(scontigs, 0, t, 0, vc - 1);
+ }
+ if (vc + 2 < t.length)
+ {
+ System.arraycopy(scontigs, vc + 2, t, vc, t.length
+ - vc + 2);
+ }
+ scontigs=t;
+ } else {
+ // truncate contig to before the skipint region
+ scontigs[vc+1] = skipint[0]-1;
+ vc+=2;
+ }
+ }