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How can we do with the System incompatible

I used to do with the iso7816 run on nRF51822 SDK9 and S110_v8.0. However,as the BLE stack is running, the iso7816 interface clock signal is abnormal. as the picture below,notice:the iso7816 clock signal was create by the PPI with GPIOTE and timer. the clock signal was divided into several fragments, in result,the iso7816 can not work anymore. I used to ask the NORDIC AE to analysis of it, and he telled me that as the bluetooth is running, the softdevice would take up some times, so we can set a flag to indicate the SoftDevice's state, as the system is free and no interrupt is occur, so we can do with the iso781's command, Therefore,how can we know when the system is free ?

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