Table of Contents


Compare Two Genomes

This is the sample script used in the tracing tutorials.

The currently-supported command-line options are as follows.

user

Name suffix to be used for log files. If omitted, the PID is used.

trace

Numeric trace level. A higher trace level causes more messages to appear. The default trace level is 2. Tracing will be directly to the standard output as well as to a traceUser.log file in the FIG temporary directory, where User is the value of the user option above.

sql

If specified, turns on tracing of SQL activity.

background

Save the standard and error output to files. The files will be created in the FIG temporary directory and will be named errUser.log and outUser.log, respectively, where User is the value of the user option above.

h

Display this command's parameters and options.

phone

Phone number to message when the script is complete.

# TODO: more options (use =item directive and add them to the StandardSetup # call below

CheckGenomePegs

CheckGenomePegs($sfx, $genomeID);

This method generates a call to FormatLocations in the Sprout object that can be used as an example of the Confess method.