Transparent glsl shader is still opaque in the lightmap.

I have a shader that is supposed to show reflections on glass. It uses Tags {"Queue"="Transparent" "IgnoreProjector"="True" "RenderType"="Transparent"} and Blend SrcAlpha OneMinusSrcAlpha. It also has "Transparent" in filename and shader name. Still when beast calculates lightmaps it is treated as if it has no transparency. I'm using custom CGPROGRAM.