[Biojava-l] concatenating chromatograms

[Russ Kepler]

On Wednesday 01 February 2006 11:41 pm, Heather Kent wrote:
> I would like to write a small application that would concatenate abi or scf
> chromatograms and write out a new chromatogram file..
>  has anyone done something similar to this or seen any code that would be
> helpful for me, i am new at programming
> and have been looking through the Biojava API

I'm familiar with the ABI trace code and what you want to do would not be 
difficult, but the result may not work the way that you want it to.  A 
basecaller will likely be fooled in the transition between the traces and 
miscall or call no peaks for some time unless you match the local frequencies 
of each trace around the transition, and tagging the start of one run to the 
end of the other is a pretty good way to not do that.

If you're not going to run things through a basecaller all you really need to 
do it is to catenate the trace and basecalls arrays and sequences.  These are 
all exposed in gets().  If the data is coming from a newish AB instrument you 
may want to add code to handle the Q values from the KB caller and catenate 
those arrays as well.

Writing the new file would be a new capability, but the existing reader should 
show you the way to do it.