Yep - this is a major pain. The IRS rests the onus on you to best interpret their cryptic guidance on what taxes you need to pay. My team and I are working very hard at http://zenLedger.io on these problems. We have poured over hundreds of hours reading tax codes, talking with CPAs and tax attorneys about this. And we are implementing our best understandings in a tax prep software. It is more difficult than you think. We are making hard default decisions like is the same token move from one exchange to another taxable and so on. If you have specific questions about how we are implementing these, ask your questions and we will give our opinions. We are software developers, not CPAs or Tax Prep professionals. So we are taking an engineering view of making sure every tiny little rule and exception is coded and accounted for in the software. In our more premium version, we will let you change the tax policy that is then applied to your returns. We will prepare the right tax forms but you will take responsibility for sending it. Sorry, it sounds like an advertisement but I wanted to communicate how much pain and work we are going through to address exactly what you are asking.
We are very close to a public release.