I'm pretty sure glass is transperent, it's hard to code as well, I hear raining outside and take a glance off my window for the beautiful weather, but all I see the the rain hitting ground particles. :l
Hope this gets fixed soon.
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This is partially fixed in 1.2.13.5 - there are some remaining situations where rain does not render through glass that can't be fixed, however.
This bug has been reported to our internal bug tracker for further testing and a fix. It is scheduled to be fixed in one of the future updates (no specific date can be provided).