I am writing code to parse a .phd file and create a PhredSequence. It is
failing with an IllegalSymbolException when I have an 'n' in the sequence.
Do CrossProductAlphabets only take AtomicSymbols?
David
Exception in thread "main" org.biojava.bio.symbol.IllegalSymbolException:
Token
`([cytosine adenine guanine thymine] 2)' does not appear as a named symbol
in al
phabet `PHRED'
at
org.biojava.bio.seq.io.NameTokenization.parseToken(NameTokenization.j
ava:105)
at
org.biojava.bio.program.phred.PhredTools.getPhredSymbol(PhredTools.ja
va:162)
rethrown as org.biojava.utils.NestedError
at
org.biojava.bio.program.phred.PhredTools.getPhredSymbol(PhredTools.ja
va:164)
at
org.biojava.bio.program.phred.PhredTools.createPhred(PhredTools.java:
142)
at
edu.washington.genome.seqio.phd.PhredBuilder.makeSequence(PhredBuilde
r.java:238)
at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:10
1)
at readPhd.main(readPhd.java:45)
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