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?
Watch this space for more debugging tricks in the future.
- Always use "allele_call_GEL" or "allele_call_STU",
"image_call_GEL" or "image_call_STU" when you can (see
generating bug reports)
- Use "allele_call" or "image_call" only when you want to
batch-process more than one gel/study unattended
- 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
(1) abort by typing "control-C" a couple of times,
>> more off
(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.]
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