[Biojava-dev] Problem converting ab1 to fastq files in Biojava 1.8

[Sebastian garcia lopez]

Good day to all,

Excuse me for my english, I wil try to explain in a better way my problem:
I need to parser ab1 file into fastq file, the problem is that I do not
know the form to obtain the quality scores from ab1. to obtain the
sequence, I use ABIFChromatogram, and in fact, I can obtain the sequence,
yet I do not know how I can obtain the quality scores to build my fastq
file.  The problem is that the "trace-offsets" do not correspond with
quality scores.  If it is helpful, I put a fragment of the code that I am
using


ABIFChromatogram y = new ABIFChromatogram();//ya casi lo logro, falta ver
como leer esos alignment
y=ABIFChromatogram.create(new File(Path));
Alignment to=y.getBaseCalls();
SymbolList dnaSeq=to.symbolListForLabel("dna");
SymbolList trace=to.symbolListForLabel("trace-offsets");

System.out.println(dnaSeq.seqString());
System.out.println(trace.seqString());

Please, if somebody know the mode to obtain the scores from ab1 files in
Biojava, please let me know.

Thank you.

-- 
Sebastián García López
Electronic Engineer
Universidad Nacional de Colombia at Manizales

Ms.Eng. Industrial Automation Student
Control and Digital Signal Processing Research Group (GC&PDS)
Universidad Nacional de Colombia at Manizales
MCP-Microsoft Certified Professional

Email:        deltadedirac at gmail.com
                 sgarcialop at unal.edu.co
Skype:       sebastiang55
Mobile:      +57 3147569794