TL;DR: There is a tool: https://github.com/SitePen/remap-istanbul described as A tool for remapping Istanbul coverage via Source Maps
The article on Sitepan describes it in more detail:
Intern as well as other JavaScript testing frameworks utilise Istanbul
for their code coverage analysis. As we started to adopt more and more
TypeScript for our own projects, we continued to struggle with getting
a clear picture of our code coverage as all the reports only included
the coverage of our emitted code. We had to try to use the compilers
in our minds to try to figure out where we were missing test coverage.
We also like to set metrics around our coverage to let us track if we
are headed the right direction.A couple of us started exploring how we might be able to accomplish
mapping the coverage report back to its origins and after a bit of
work, we created remap-istanbul, a package that allows Istanbul
coverage information to be mapped back to its source when there are
Source Maps available. While we have been focused on TypeScript, it
can be used wherever the coverage is being produced on emitted code,
including the tools mentioned above!
How to use the tool with gulp: https://github.com/SitePen/remap-istanbul#gulp-plugin