[maker-devel] Effect of the unmask option

[Michael Nuhn]

Hello Carson!

When running maker with the unmask option, how does maker use the 
predictions generated from running the gene predictors on the unmasked 
sequence?

The tutorial says:

"You do have the option to run ab initio gene predictors on both the 
masked and unmasked sequence if repeat masking worries you though. You 
do this by setting unmask:1 in the maker_opt.ctl configuration file."

http://gmod.org/wiki/MAKER_Tutorial_2012

But in the sub get_non_overlaping_abinits in maker::auto_annotator 
(maker version 2.27) they are skipped:

#only accept masked predictions unless I'm not masking or the predictor 
is genemark
my $src = $g->{algorithm};
unless($src =~ /_masked$|^pred_gff/ || $CTL_OPT->{_no_mask} || 
$CTL_OPT->{predictor} eq 'genemark') {
	   next;
}

Cheers,
Michael.