#6 recommended hack to deal with mis-annotated references where ribosomal slippage significantly misplaced

[Jeffrey Hoover]

insert

        # hack to handle references where misplaced slippage site causes frameshift
        if ( $$expected{order} == 1 ) {
            if ( defined $exon5 && $$exon{subject_begin} > $$expected{subject_end} - 100 ) {
                my $expframe = $$exon5{frame} + $ori * $slippage_shift;
                if ( $ori > 0 ) {
                    if ( $expframe < 1 ) { $expframe += 3 }
                    elsif ( $expframe > 3 ) { $expframe -= 3 }
                }
                else {
                    if ( $expframe > -1 ) { $expframe -= 3 }
                    elsif ( $expframe < -3 ) { $expframe += 3 }
                }
                if ( $dbg ) {
                    print "bad ref hack expected frame: $expframe\n";
                }
                if ( $$exon{frame} == $expframe ) { $expected = ${$$structure{exons}}[1] }
            }
        }

after

    if ( defined $expected ) {

[Jeffrey Hoover]

also need to insert this code:

# format and return exons
my @tmp = shift @exons;
while ( @exons ) {
    my $exon = shift @exons;
    my $prev = $tmp[@tmp-1];
    if ( $$prev{frame} == $$exon{frame} ) {
        $$prev{subject_end} = $$exon{subject_end};
        $$prev{dna_end} = $$exon{dna_end}
    }
    else {
        push @tmp, $exon;
    }
}
@exons = @tmp;