Each module has its own configuration section named after the module name. The
configuration section will be "[::module_filename_prefix]"
where module_filename_prefix is the filename of the module with the
.p4m extension removed. For example, the init_exp.p4m module has a
configuration section of [::init_exp].
Each module is loaded into its own namespace, also named after the module in
the same manner. Thus in the above example the Initialise Experiment Files
module uses the namespace ::init_exp. This means that all local
variables within that module will be within that name space and will not clash
with identical named variables in other modules. When pregap4 reads the
configuration file any configuration section starting in double colon is taken
to be a name space and the following configuration is executed in that
namespace. So the following example enables the Initialise Experiment Files
module, but disables the Estimate Base Accuracies module.
[::init_exp] set enabled 1 [::eba] set enabled 0
In the following sections the variables, inputs and outputs of each module are
listed. Every module has an enabled local variable. This may be either
0 for disabled or 1 for enabled. Disabled modules are still
listed in the configuration panel, although they will not be executed.
The tables in each section below list the module filename, the local variables
and a very brief description of their valid values, the files used or produced
by this module, the possible sequence specific errors that can be produced
(which will be written to the failure file as the reason for failure), and the
format of any SEQ lines in the module report. Other information may
also be reported, but the SEQ lines are easily recognisable to
facilitate easy parsing of results.