The decline in abundance of Lyman-$alpha$ (Ly$alpha$) emitting galaxies at $z gtrsim 6$ is a powerful and commonly used probe to constrain the progress of cosmic reionization. We use the CoDaII simulation, which is a radiation hydrodynamic simulation featuring a box of $sim 94$ comoving Mpc side length, to compute the Ly$alpha$ transmission properties of the intergalactic medium (IGM) at $zsim 5.8$ to $7$. Our results mainly confirm previous studies, i.e., we find a declining Ly$alpha$ transmission with redshift and a large sightline-to-sightline variation. However, motivated by the recent discovery of blue Ly$alpha$ peaks at high redshift, we also analyze the IGM transmission on the blue side, which shows a rapid decline at $zgtrsim 6$ of the blue transmission. This low transmission can be attributed not only to the presence of neutral regions but also to the residual neutral hydrogen within ionized regions, for which a density even as low as $n_{rm HI}sim 10^{-9},mathrm{cm}^{-3}$ (sometimes combined with kinematic effects) leads to a significantly reduced visibility. Still, we find that $sim 5%$ of sightlines towards $M_{mathrm{1600AB}}sim -21$ galaxies at $zsim 7$ are transparent enough to allow a transmission of a blue Ly$alpha$ peak. We discuss our results in the context of the interpretation of observations.
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