VCFFile.pm header fix; sim_bubble_vcf merge inputs; Better IntervalTree

1. VCFFile.pm: Fix dropping of some VCF header lines (header code could do with rewrite)
2. sim_bubble_vcf.pl: remove mutations if done to all (including deletions, which
                      end up changing coordinates
3. lib/IntervalList.pm lib/IntervalTree.pm
   * Tidied up documentation
   * Return interval with item when doing fetch
vcf scripts exit with -1 on failure