Observations of high-redshift Ly-alpha sources are a major tool for studying the high-redshift Universe. We discuss the effect of the reionizing intergalactic medium on the observability of Ly-alpha sources based on large simulations of early structure formation with radiative transfer. This takes into account self-consistently the reionization history, density, velocity and ionization structures and nonlinear source clustering. We find that all fields are highly anisotropic and as a consequence there are very large variations in opacity among the different lines-of-sight. The velocity effects, from both infall and source peculiar velocity are most important for the luminous sources, affecting the line profile and depressing the bright end of the luminosity function. The line profiles are generally asymmetric and the line centers of the luminous sources are always absorbed due to the high density of the local IGM. For both luminous and average sources the damping wing effects are of similar magnitude and remain significant until fairly late. The ionizing flux in the ionized patch surrounding a high density peak is generally strongly dominated, particularly at late times, by the cluster of faint sources, rather than the central massive galaxy. The IGM absorption does not change appreciably the correlation function of sources at high redshift. Our derived luminosity function assuming constant mass-to-light ratio provides an excellent match to the shape of the observed luminosity function at z=6.6 with faint-end slope of alpha=-1.5. The resulting mass-to-light ratio implies that the majority of sources responsible for reionization are too faint to be observed by the current surveys. (abridged)
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