The datasheet of the SAMG55 MCU and the ASF for it seem to have some inconsistencies between themselves, making using the timer counter module for signal generation and/or triggering interrupts a nightmare. I have written down some of my findings here, for those people Googling around, hoping to know why they cannot get it to work.
Because I don’t wish trying to figure this out for anyone upon themselves I have written them down here for some clarification.
In the datasheet it refers to Timer Counter A and Timer Counter B. Within the asf module these are known as TC0 and TC1.
The timer counter on the SAMG55 consists of 6 channels. Three of these are bound to TC0 and three of these are bound to TC1. Confusingly, these channels are labeled 0…5, meaning that TC0 is both the first timer/counter and also channel 0 of TC0 itself. Please see table below for clarification.
| Timer/Counter | Channel | Name |
| TC0 | 0 | TC0 |
| TC0 | 1 | TC1 |
| TC0 | 2 | TC2 |
| TC1 | 0 | TC3 |
| TC1 | 1 | TC4 |
| TC1 | 2 | TC5 |
Furthermore, it seems like the peripheral clock is not enabled per peripheral (TC0 and TC1) but by channel (TC0..TC5) So if you want to use TC1 Channel 0 (So TC3) you need to enable the clock for ID_TC3.
Example
In order to enable interrupts on the first channel of timer counter 1. (So TC3) The following code will suffice.
sysclk_enable_peripheral_clock(ID_TC3); //Enable channel 3's clock.
uint32_t tc_configuration = TC_CMR_TCCLKS_TIMER_CLOCK1|TC_CMR_CPCTRG; //Set clk to MCK/2 and reset the counter on capcture compare register C.
tc_init(TC1,0,tc_configuration); //Init
tc_enable_interrupt(TC1,0,TC_IER_CPCS); //Enable the compare C interrupt
tc_write_rc(TC1,0,1024); //Write a value to register C
tc_start(TC1,0);
//Set the interrupt priority for TC3
NVIC_DisableIRQ(TC3_IRQn);
NVIC_ClearPendingIRQ(TC3_IRQn);
NVIC_SetPriority(TC3_IRQn, 2);
NVIC_EnableIRQ(TC3_IRQn);
The above example should configure channel 3, which is the first channel of timer/counter 1 to trigger an interrupt. This interrupt triggers TC3_Handler. This took me far too long to figure out, so I hope it does not for you.