[maq-help] Viewing all chromosomes in tgap-maq

[<jef...@uc...>]

I am using tgap-maq to view the results of my maq alignments, as there seem 
to be memory issues using maqview on my system.  I can get tgap-maq to work 
to view the first chromosome in my alignment, but I seem to be unable to view 
any of the other chromosomes in my genome (i.e. when the base pair count 
resets back to 0).  I know that the alignment worked across the whole genome, 
because all the maq output files have information about all chromosomes.  Can 
anyone tell me how to go about viewing chromosomes other than the first one 
in the alignment using tgap-maq?  Thank you!

(Alternately, if anyone has ideas of how to fix the malloc problems I'm running 
into using maqindex and maqview in Mac OS X 10.4, please let me know!)

Jeff Carey
University of Chicago
jef...@uc...