Fixes for qualimap 0.7.1, feedback from Homebrew/homebrew-science#336

Jeremy;
I was looking to incorporate qualimap into CloudBioLinux so would love to get this into homebrew-science. This handles all formatting suggestions from @sjackman. It fixes bin/qualimap patch by finding the original directory via the qualimap.jar symlink, then using that to reconstitute the classpath. If this works cleanly for you as well could you push upstream so we can hopefully get it into the main branch?

Let me know if you run into any problems, it's my first homebrew recipe.