The short answer is that there is no sex in this book.
However, some readers are convinced that Gene is sexually attracted to Phineas. For one, the descriptions of Phineas are very physical in nature. Gene pays such close attention to his body, his good looks, his movement. Check this out: "His skin radiated a reddish-copper glow of tan, his brown hair had been a little bleached by the sun, and I noticed that the tan made his eyes shine with a cool blue-green fire" (3.71). Or earlier in the text, "He weighed a hundred and fifty pounds, a galling ten pounds more than I did, which flowed from his legs to torso around shoulders to arms and full strong neck in an uninterrupted, unemphatic unity of strength" (1.28). If you agree with this theory, it gives you a new lens to help understand Gene's mixed feelings for Finny. What appears as jealousy may just be attraction, confusion, and so on.
On the other hand, this theory may not be right. Gene and Phineas might just have a very close friendship.