This is the code accompanying this blog post about writing a code coverage tool. The code is more or less as described in the post, except for some small things like a nicer command line interface.

Unlike the code in the post, this uses maven, so you should be able to compile with

mvn compile

and run the instrumentation with

mvn exec:java -Dcoverage.report.path=baseline.lcov \
  -Dexec.mainClass="io.badawi.coverage.Main" -Dexec.args="-d instrumented <java-files>"

You need lcov and genhtml to work with the generated coverage reports. These are pretty widespread and should be easy to get via whatever package manager you use (I've tried sudo apt-get install lcov on Ubuntu and brew install lcov on OS X).