[Suggestion] Make fragment building as a separate subcommand

[elhossary]

Fragment building is currently part of the align command, and it is time-consuming like the aligning process.
Also, It feels like the process is hanging after the aligning finishes because no messages delivered to the user that tell that the fragment building has started.
So,
It would be convenient to make it a separate subcommand like "coverage" to make it easier if the process interrupted after aligning and before fragment building and make it more informative regarding the progress of fragment building.