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

[Russ Kepler]

On Thursday, September 20, 2012 04:17:02 PM Andy Yates wrote:
> Hi,
> 
> It's been about 7-8 years since I last looked into the ABIFChromatogram
> object and I all remember failing to extract quality scores. Can you
> convert the AB1 file into an SCF trace and then use biojava? The staden io
> package comes with a binary called convert_trace which will get you into
> SCF. No guarantee the scores will be converted as well but it's worth a try
> I guess.

I had to add code to the BioJava 1.4 base to find and fetch the quality values 
from the .ab1 files.  (IIRC) It's only available if you use the KB caller when 
only calls BigDye traces.  Ultimately for my project I just ended up replacing 
the .ab1 data with TraceTuner output.  

I might have something in my cvs history if it's desired.