gistfile1.pl

            my $gs = ${$self->symbols}{GAP};
            # map gaps prior and post start/end
            my ($newst, $newend) = ($start, $end);
            while ($rawseq =~ m{([$gs]+)}g) {
                my $len = CORE::length($1);
                my $current = pos($rawseq) - $len;
                # optimization : bail if current gap is past the end
                last if $current >= $newend;
                $newst += $len if $current <= $newst;
                $newend += $len if $current <= $newend;
            }
            $seqstr = substr($rawseq, $newst, $newend -$newst + 1);
            $seqstr =~ s/[$gs]//g unless $gaps;