When pregap4 is started the user first needs to select the files to process. This is done using the "Files to Process" command (from the File menu). Alternatively the files can be specified on the command line at the time of starting up Pregap4. The "Configure Modules" tab allows for the currently available modules to be enabled or disabled, and the module parameters edited accordingly.
Once all modules have been configured (so that none have edit listed
next to their name) pregap4 is ready to begin processing. This is
started by pressing
"Run" or by selecting "Run" from the File menu.
When pregap4 has a setup that would be useful in the future "Save All Parameters (in all modules)" from the Modules menu can be used, and pregap4 will store all the module parameters to a configuration file ready for subsequent runs.
To run pregap4 in a non interactive mode use "pregap4
-nowin". This will not bring up a graphical interface and will attempt to
"Run" automatically. Hence it is necessary to also specify the files to
process on the command line and also to have previously configured pregap4.
When processing has finished pregap4 will produce a report containing information from each module and the final list of passed and failed sequences.
If for any reason pregap4 fails a particular step in the processing, users are strongly recommended to correct whatever has caused the module to fail, clean up any files it has created, and then repeat the whole process. That is, until users have a good understanding of what happens at each stage of processing, it is better to repeat all the steps with the original list of files, than to try to guess which step to continue from.