Pardons can take place before, during and after adjudication. People can be pardoned before being charged.
The alleged crimes include the period of time as Secretary of State where hundreds of millions of dollars processed through her and/or her foundation, and the Clinton foundation donors were given huge government contracts, etc.
All crimes related to the Clinton Foundation, including insider trading, illegal acceptance, any potential tax or non-profit laws...
and any crimes regarding the private server, including perjury. FBI Director Comey made a lengthy list of all the infractions where those who have committed far less have been imprisoned, before recommending no prosecution to the justice department that has been alleged to have been corrupt.
A presidential pardon would be all inclusive and even preempt a trial or investigation.