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The BQ24251 can only communication with legacy USB BC1.2 adapters not USB type C. In fact, TI currently doesn't have a charger with integrated USB Type C communication. You might need to add an interface chip in between. If you are only expecting 5V input to the charger and only want to control the output current from the USB Type C adapter, there are chips that can do this.
If you have a USB Type C port with output voltages >5V, then you will need a port controller like TPS25750.
I am confused as to why this would be an issue if I am only using the usb type c for powering the charger and I connect the usb to the microcontroller for communicating. I am only doing 5V input to the charger. Would the usb type c still not work in this case?
USB Type C ports/adapters have CC1 and CC2 lines that require communication in order to provide 5V 1.5A or 3A output. The BQ24250 does not provide this communication. If you have a host processor/controller that can this communication, then you can use whatever charger you want. The BQ24250 is a very old device and so has no method to method with USB Type C ports/adapters.
Furthermore, if you want to also communicate with legacy USB BC1.2 adapters, that communicate over D=/D- lines, you might consider changing to a more recent device like BQ25611D.
USB Type C typical refers to not only the hardware connector but also the communication protocol. The communication protocol is backwards compatible with BC1.0, which was part of USB 2.0. But USB Type C has additional communication options through the CC1 and CC2 lines.