Cysts and pregnancy

Last week I went to the ER and they said I tested positive for pregnancy on both urine and blood tests but they said I'm still very early but I have a cyst that could compromise the pregnancy all together .. Has Anyone else had this problem ... I would very much like to keep this baby and my boyfriend seems to be excited about it as well but I'm very nerves .. I've been cramping but not bleeding ... Last period was July 9th so I'm technically almost a week late