What can I do if I am applying for a PhD in CS in a US university and?
Other than what the others have answered, you should send your unofficial transcripts to an alternative college or university, as your unofficial transcripts may not be accepted or may delay your admission process to a particular school and so another might be chosen. If you're dead set on that one particular College then you need to be meticulous about your approach in going after the things you need to do.