Debugging FAST-MAP: Frequently-asked questions

As a regular FAST-MAP user, what are the tricks that I can use that
can make debugging FAST-MAP easier in the event that it failed?

[6/11/97]

• Always use "allele_call_GEL" or "allele_call_STU", "image_call_GEL" or "image_call_STU" when you can (see also generating bug reports) ;

• Use "allele_call" or "image_call" only when you want to batch-process more than one gel/study unattended (say, overnight);

• Make sure all the "redo" settings are set to "no" so that FAST-MAP will skip the ones it has already processed and go to the genotyping where it failed;

• If you know the problematic marker, re-define the panel in the "panels" file to contain only that marker. For example, make a new entry of the panel with only the problematic marker -- FAST-MAP will use the last definition.

  Remember to re-define the original panel back (such as deleting th temporary panel defintion above) when you are done debugging.

• When you find out that you have to press space bar to keep going,

            (1) abort by typing "control-C" a couple of times,
            (2) type   
                      >> more off
            and 
            (3) re-execute your previous allele call command.
           

  [ In UNIX speak, "more" means having to scroll page by page by pressing the space bar at the "More?" prompt.]