[Bioperl-l] Score computation in psl.pm

[Wes Barris]

Hi,

I found this line in psl.pm:

my $score   = sprintf "%.2f", ( 100 * ( $matches + $mismatches + $rep_matches ) / $q_length );

However, from the BLAT program documentation:

-minScore=N sets minimum score.  This is twice the matches minus the mismatches minus some 
sort of gap penalty.  Default is 30


It seems to me that the score computed in psl.pm should be based on something more like
this:

100 * (2* $matches - $mismatches + $rep_matches) / $q_length
-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au