When you have gained control of a Project via a Project creation, a standard open, or an open in preempt mode, you have the freedom to save the modifications you make to that Project at any point you deem appropriate. This is done with the “save” command (see section 3.4.13 for the usage statement). If you close a Project (see section 3.5.13.2) that contains changes without first saving it, the unsaved changes will be discarded. Note that if you have made any modifications to the Project, you MUST run the “save” command to commit those changes to the Project prior to triggering a computation with the “computation start” command. If you trigger a computation on a Project that contains unsaved modifications, an error will be generated.

When you have finished making changes to the Project, you can close it using the “close” command (see section 3.4.2 for the usage statement). The close statement discards any unsaved changes to the Project and frees the Project lock so someone else can access it without needing to preempt control. If there are unsaved changes to the Project, the CLI will show a warning to let you know that some changes are being discarded. If you are in interactive mode, a “yes”, “no”, “cancel” prompt will be shown to allow you to avoid discarding the changes if you didn’t really mean to close without saving. The CLI is still running after you use the close command, so you can open another Project and do more work.

When you are ready to shut down the doAmplicon instance you are running, you can use the “exit” command (see section 3.4.6 for the usage statement). As with the close command (section 3.5.13.2, above), the exit command will warn you if you try to exit an Project that contains unsaved changes and, in interactive mode, will prompt you to decide if you want to save before exiting. Since the exit command actually shuts down the doAmplicon instance, it will terminate any chain of commands wherever it is introduced (e.g., if you supply three scripts to be executed in succession by a doAmplicon instance and the first script has an exit in it, the other two scripts will not be executed).