[Biojava-dev] PhredFormat problems

[VERHOEF Frans]

Hi,

 

I've got some issues with the PhredFormat class. In the
readSequenceData(BufferedReader, SymbolTokenization, SeqIOListener )
method, a quality sequence is read and parsed into the individual
quality scores. Those individual scores are each given to
WordStreamParser (in the file WordTokenization) through the characters
method, which is pasting all the scores in a StringBuffer. However, the
spaces in between the quality scores are disappearing in the process.

When the close() method of WordStreamParser is called, it is trying to
do parse the quality score StringBuffer again, but since there are no
spaces in between the different values, it cannot parse it, with as a
result that once it tries to convert the string to an integer, it has a
problem because the number is huge.

 

So I assume the readSequenceData should not parse the quality sequence
string, but just hand the WordStreamParser the complete String. Am I
right? Can anyone still follow me?? ;-)

 

I also wonder whether anyone is using the phred classes.

 

Kind regards,

 

Frans Verhoef

Bioinformatics Specialist

Genome Institute of Singapore

Genome, #02-01, 60 Biopolis Street, Singapore 138672

Tel: +65 6478 8000

DID: +65 6478 8060

HP: +65 9848 4325

Email: verhoeff2 at gis.a-star.edu.sg

 

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