USDA loan roof shingle replacement?

We are qualified for a USDA loan and the house we had an inspection on is in need of new roof shingles on most of the house and one or two small areas of ply-board replacement. The house is priced $30k under what it is worth (foreclosed home). The roofing is good enough to last another 2 years, but not certifiable. How likely is the usda appraiser to still allow the loan on an otherwise good conditioned home? Or, do we need to try and get the bank to pay for the roof/roll it into the loan?