Modified pileup transforms to improve performance. Also, added options to specify whether reads at secondary alignments should be converted to pileups.
Merge pull request #129 from fnothaft/pileup-perf-and-options

Modified pileup transforms to improve performance + to add options
Update README.md

To improve the experience for users trying to build ADAM from source, I think it's worth explicitly adding the command to up the PermGen size and to turn off running tests, which should reduce the number of emails to the mailing list about failing builds and allow the new user to get moving with the jar file sooner rather than later.

Feel free to discard if you think either change does more harm than good.
Merge pull request #139 from hammer/patch-1

Update README.md
Update README.md

Change the remote URL to use HTTPS rather than SSH, as [GitHub recommends for users behind a firewall or proxy](https://help.github.com/articles/which-remote-url-should-i-use).
Merge pull request #140 from hammer/patch-2

Update README.md