[Biojava-dev] PhredTools.getPhredSymbol(dna,int) with ambiguity symbol

[Jim Johnson]

Mark,

I'm working with a researcher to develop a package to 
evaluate contig assemblies (initially phrap, then CAP).

I am initially writing a parser for phrap ace format files.

I wrote my original parser so that it created a GappedPhredSequence
for the consensus and each read sequence.

I'm now rewriting this attempting to use 
PhredTools.createPhred(SymbolList dna, SymbolList quality)

However, I'm getting exceptions from 
PhredTools.getPhredSymbol(Symbol dna, Symbol integer)
when I encountered an ambiguity symbol, e.g. 'n'.  

Do you have any advice as to using PhredTools with regards 
to ambiguity symbols?

Thanks,

JJ

-- 
James E. Johnson <jj@mail.ahc.umn.edu> 
Center for Computational Genomics and Bioinformatics
Mayo Mail Code 43, AHC, University of Minnesota
420 Delaware St SE
Minneapolis, MN 55455 
612-626-6937