[Biojava-dev] Bug in PhredFormat??

[Schreiber, Mark]

Hi Frans -

I might be responsible for this. I haven't used the PhredFormat for a
while so this may have gone unoticed. I will fix it up as soon as I get
back to my main machine (after the weekend). Alternatively if you want
to post a fix to the list I'm sure someone can add it to CVS for you.

Thanks

Mark


-----Original Message-----
From: VERHOEF Frans [mailto:verhoeff2 at gis.a-star.edu.sg] 
Sent: Thursday, 27 November 2003 6:39 p.m.
To: biojava-dev at biojava.org
Subject: [Biojava-dev] Bug in PhredFormat??


Hi, 
I think I might have discovered a little bug. I used the latest version
from CVS.

This is what I tried to do:

StreamReader qualityIter = PhredTools.readPhredQuality( new
BufferedReader( new FileReader( qualityFile ) ) );

Where qualityFile is a File object pointing to an existing phred
quality-score fasta file. It compiles fine, but when I run it I get the
following Exception:

Exception
java.lang.ClassCastException
        at
org.biojava.bio.seq.io.StreamReader.<init>(StreamReader.java:130)
        at
org.biojava.bio.program.phred.PhredTools.readPhredQuality(PhredTools.jav
a:234)
        at
org.gis.server.pipeline.apps.SequenceInfoParser.parseResults(SequenceInf
oParser.java:67)
        at
org.gis.server.pipeline.apps.SequenceInfoParser.start(SequenceInfoParser
.java:52)
        at
org.gis.server.pipeline.apps.SequenceInfoParser.main(SequenceInfoParser.
java:133)

When checking the line 130 in StreamReader I find the following line:

 
((org.biojava.utils.ParseErrorSource)(this.format).addParseErrorListener
(this);

Where format is a PhredFormat class.
When checking out PhredFormat, I did find out that PhredFormat is not
implementing the ParseErrorSource. 
So I assume implementing the ParseErrorSource for PhredFormat would
solve the problem. If you want I can do it myself, though I do not have
a cvs account.

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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