Problem with alt_2p5g_phy and polarity inversion.

alt_2p5g_phy (1G/2.5G/5G/10G Multirate Ethernet PHY for Stratix 10) does support polarity inversion, and there are a couple of paths to enable it when the GUI doesn't expose the control directly.

What the IP supports

The underlying transceiver Native PHY used by this IP supports both static and dynamic polarity inversion, depending on which PCS mode is in use

Standard PCS supports both static and dynamic polarity inversion. However, the Enhanced PCS only supports the static polarity inversion feature. Stratix 10 · General

Standard PCS path (static + dynamic)

If your 2.5G configuration uses the Standard PCS:

Enable TX polarity inversion via the tx_std_polinv port, which controls polarity inversion of TX parallel data to the PMA. When you turn on this parameter, you also need to turn on the Enable tx_polinv port. Stratix 10 · General

Enable RX polarity inversion via the rx_std_polinv port, which inverts the polarity of RX parallel data. When you turn on this parameter, you also need to enable the Enable rx_polinv port. Stratix 10 · General

For dynamic control, to enable receiver polarity inversion in Basic/Custom (Standard PCS), Basic/Custom w/ Rate Match (Standard PCS), and Standard PCS low latency mode, select the Enable RX polarity inversion option and the Enable rx_polinv port option in the Native PHY IP core — this mode adds the rx_polinv port. Stratix 10 · General

Enhanced PCS path (static only)

If your configuration uses the Enhanced PCS (common for higher-rate gearbox modes):

The transceiver Native PHY in Enhanced PCS mode does not have tx_polinv and rx_polinv ports. You can use the Gearbox Enable RX data polarity inversion and Enable TX data polarity inversion settings to implement static polarity inversion. Arria 10 · Transceiver/PHY

You can implement dynamic polarity inversion by reconfiguring the PHY with different Gearbox Enable RX data polarity inversion and Enable TX data polarity inversion settings. Arria 10 · Transceiver/PHY

Specifically: to enable TX data polarity inversion when using the Enhanced PCS, select the Enable TX data polarity inversion option in the Gearbox section of the Native PHY IP core. Stratix 10 · General · TX

To enable RX data polarity inversion when using the Enhanced PCS, select the Enable RX data polarity inversion option in the Gearbox section of the Native PHY IP core. Stratix 10 · General