Vaughn, Cox's roommate at the time, told police he was sleeping, while Thomas said he had kissed the accuser but then left her alone when he determined she was intoxicated. Cox was at the apartment with his girlfriend, according to an arrest affidavit.
The accuser came forward Oct. 28, 2010, after she learned she was pregnant. She said she didn't file a complaint sooner because she wasn't sure she had been raped and didn't want to make unfounded charges.
Police arrested Cox after investigators said Cox's DNA matched a sample taken from the accuser. The affidavit said the woman was shocked when test results indicated Cox was the father.
The woman told investigators that doctors put the date of conception around the time she went to Cox's apartment with friends in the early hours of Sept. 6, 2010, according to the arrest warrant affidavit.
The woman said she has no recollection of most of that night and wasn't sure anyone had sex with her until she learned she was pregnant. She said she had not had consensual sex for several weeks before or after the date of conception reported by doctors.
The woman said she and Cox's girlfriend at the time had gone to a club Sept. 5, and they met Cox and Thomas. When the club closed at 1:30 a.m., they all went to Cox's apartment.
The woman said she believed she had been drugged because she felt unusually woozy after four drinks.
Cox has repeatedly denied having sex with the accuser. He has pleaded not guilty to one count of sexual assault while the victim was physically helpless, and one count of sexual assault while the victim was incapable of determining the nature of the conduct.
If convicted, he faces two years to life in prison. He has remained free on $50,000 bail.
A witness list remains sealed and prosecutors as well as Cox's attorney, Harvey A. Steinberg, have declined to comment on whether Vaughn and Thomas would testify. The accuser's attorney, Craig Silverman, has also declined to comment.
Cox, a former Oklahoma State standout was selected in the fifth round in 2010. He started nine games as a rookie. He was cut in September by the team, which cited his performance in training camp, not the pending charges as the reason.
Potential jurors were asked to fill out questionnaires on Monday and were scheduled to be questioned by lawyers for both sides on Tuesday.