[Bioperl-l] Question re: Phred Base Quality Data & Bio::SeqIO::scf

[Cooper, Marc Emmerson]

Hi everyone, 

I'm looking for some information on base quality data via the Bio::SeqIO::scf package. 
Specifically, I recognize that there are methods to extract the base qualities for both
called and uncalled bases within the SCF file using _dump_base_qualities() or
_dump_base_qualities_incoming().  

I have generated an SCF file using phred and have written a small portion of perl code
to extract the quality data from the SCF file.  However upon examination of the output
I noticed that only the quality data for called bases is available and zero values are
assigned to the quality data for the three other potential bases at each base position.
   

Could anyone tell me whether it is possible to export quality data for the uncalled
bases using phred?  Or do SCF files generated by phred only contain quality data for
called bases?

Cheers,

Marc Cooper
Master's Candidate
Bioinformatics Research Group
Faculty of Computer Science
University of New Brunswick
Fredericton, NB  Canada  
E3B 5A3
email: marc.cooper at unb.ca