+my $alleleS = 0;
+if (-e "$ARGV[0].alleles.results") { $alleleS = 1; }
+
+pod2usage(-msg => "--transcript-list cannot be set if allele-specific reference is not built!", -exitval => 2, -verbose => 2) if (!$alleleS && $transcript_list);
+pod2usage(-msg => "--gene-list and --transcript-list cannot be set at the same time!", -exitval => 2, -verbose => 2) if ($gene_list && $transcript_list);
+
+my $dir = "$FindBin::Bin/";