A Boston IRS agent accused of sexually assaulting a handcuffed college student at gunpoint inside his government-owned car last summer was indicted on rape charges yesterday, prompting one Bay State congressman to vow to launch an inquiry into the agency’s handling of the incident.James Clarke, 44, an IRS agent based out of the agency’s Boston office, was charged with aggravated rape, rape, indecent assault and battery, strangulation and assault and battery with a dangerous weapon, according to Suffolk District Attorney Daniel F.