[Biojava-l] I don't know why I can't let my program read SCF files.

[Shin Negishi]

Dear Sir,

  My name is Shin Negishi. I am a graduate student of Tokyo Institute of
Technology.
I belong to Dr.Gondo's laboratory. Dr. Gondo is the leader of Population and
Quantitative
genomics team in RIKEN GSC and is also a visiting professor of the graduate
school.
My research field is SNP discovery. I would like to make a software for SNP
discovery.
So I must make programs which can read files in various format. Now, I try
to let my
program read SCF files. But, I can't do it. Please help me! I put the part
of my program
and error massages below:


import java.io.*;
import org.biojava.bio.*;
import org.biojava.bio.chromatogram.*;
import org.biojava.bio.program.scf.SCF;
import org.biojava.bio.seq.*;

public class Test {
  public static void main(String[] args)
  throws Exception {
    File traceFile = new File(args[0]);

    //read the trace
    SCF traces = SCF.create(traceFile);

    int[] t = traces.getTrace(NucleotideTools.t());
    int[] g = traces.getTrace(NucleotideTools.g());
    int[] c = traces.getTrace(NucleotideTools.c());
    int[] a = traces.getTrace(NucleotideTools.a());
  }
}


Error Massages:

org.biojava.bio.symbol.IllegalSymbolException: No Symbol for Y
	at
org.biojava.bio.program.scf.SCF$DefaultUncertaintyDecoder.decode(SCF.java:24
1)
	at org.biojava.bio.program.scf.SCF$V2Parser.parseBases(SCF.java:626)
	at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:312)
	at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:177)
	at org.biojava.bio.program.scf.SCF.load(SCF.java:123)
	at org.biojava.bio.program.scf.SCF.load(SCF.java:118)
	at org.biojava.bio.program.scf.SCF.create(SCF.java:105)
	at Test.main(Test.java:21)
org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException: Base
call decoding failure
	at org.biojava.bio.program.scf.SCF$V2Parser.parseBases(SCF.java:630)
	at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:312)
	at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:177)
	at org.biojava.bio.program.scf.SCF.load(SCF.java:123)
	at org.biojava.bio.program.scf.SCF.load(SCF.java:118)
	at org.biojava.bio.program.scf.SCF.create(SCF.java:105)
	at Test.main(Test.java:21)
Exception in thread "main"

Regards,
Shin Negishi
shin at gsc.riken.go.jp
Department of Computational Intelligence and Systems Science
Interdisciplinary Graduate School of Science and Engineering
Tokyo Institute of Technology