$support->log("!! = Very bad, %% = Somewhat bad, ?? = No mapping, might be bad\n");
my$ok=$support->iterate_chromosomes(
prev_stage=>'40-fix_overlaps',
this_stage=>'41-exon-conservation',
worker=>\&compare_exons,
$support->log("EXON KEY : !! = Very bad (pc mismatch), %% = Somewhat bad (mismatch), ?? = No mapping, might be bad\n");
$support->log("TRANSCRIPT KEY : @@ = Very bad (pc translation mismatch), = Very bad (pc transcript mismatch), ** = Somewhat bad (mismatch), XX = No mapping, might be bad\n");
$support->iterate_chromosomes(
prev_stage=>'40-fix_overlaps',
this_stage=>'41-conservation',
worker=>\&compare,
);
$support->log_stamped("Finished.\n");
sub compare{
my($asp)=@_;
if($support->param('check_exons')){
compare_exons($asp);
}
if($support->param('check_transcripts')){
compare_transcripts($asp);
}
return;
}
sub compare_exons{
my($asp)=@_;
my$R_chr=$asp->ref_chr;
my$A_chr=$asp->alt_chr;
my($asp)=@_;
my$R_chr=$asp->ref_chr;
my$A_chr=$asp->alt_chr;
my$R_slice=$asp->ref_slice;
my$A_slice=$asp->alt_slice;
my$new_slice_adaptor=$R_slice->adaptor();
my$old_exons=$A_slice->get_all_Exons;
while(my$old_exon=shift@$old_exons){
# Establish equivalent locations on old and new DBs