要设置ATSAMC21的PWM占空比为99%，可以使用Atmel START配置工具和ASF（Atmel Software Framework）来实现。以下是一个示例代码，通过使用ASF库函数来设置PWM占空比为99%。

#include 

#define PWM_MODULE      TC3
#define PWM_CHANNEL     0
#define PWM_FREQUENCY  10000
#define PWM_DUTY_CYCLE 99

int main(void)
{
    /* 初始化系统 */
    system_init();
    
    /* 配置PWM引脚 */
    struct system_pinmux_config pinmux_config = {
        .mux_position = MUX_PA18E_TC3_WO0,
        .direction    = SYSTEM_PINMUX_PIN_DIR_OUTPUT,
        .input_pull   = SYSTEM_PINMUX_PIN_PULL_NONE,
        .powersave    = false
    };
    system_pinmux_pin_set_config(PIN_PA18E_TC3_WO0, &pinmux_config);
    
    /* 配置PWM模块 */
    struct tc_config config_tc;
    tc_get_config_defaults(&config_tc);
    config_tc.counter_size = TC_COUNTER_SIZE_16BIT;
    config_tc.counter_16_bit.compare_capture_channel[0] = PWM_DUTY_CYCLE * (65535 / 100);
    config_tc.counter_16_bit.wave_generation = TC_WAVE_GENERATION_MATCH_FREQ;
    config_tc.counter_16_bit.waveform_invert_output = TC_WAVEFORM_INVERT_OUTPUT_CHANNEL_0;
    config_tc.counter_16_bit.pwm_channel[0].enabled = true;
    config_tc.counter_16_bit.pwm_channel[0].pin_out = PIN_PA18E_TC3_WO0;
    config_tc.counter_16_bit.pwm_channel[0].pin_mux = PINMUX_PA18E_TC3_WO0;
    tc_init(&PWM_MODULE, PWM_CHANNEL, &config_tc);
    
    /* 启动PWM */
    tc_enable(&PWM_MODULE);
    
    while (1) {
        /* 无限循环 */
    }
}

请注意，使用此示例代码需要先配置Atmel START工具和ASF库。您可以根据您的具体需求进行修改和适配。