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Originally Posted by GlennGraham
In the interrupt handler, EncoderDataFlag.bit1 is set but I don't see anywhere that it is cleared. The comment says it indicates that data is ready to be read.
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I haven't used the code or encoder that you're talking about, but it sounds like the bit is used as a signal to the encoder or interrupt service routine that you are done looking at the last signal from the encoder and are ready to look at a new one. This would be cleared by the firmware the next time that the handler is called, similarly to the way that the interrupt flag works.