genomebridge/adam — pull request #19 by fnothaft (2014-07-30 16:30:25+00:00)
Title: Added unit test for tracked layout with unaligned reads.

I've added a failing unit test that tries to order an unaligned read on top of the ordered tracked layout. It fails with an NPE. I'm not sure what the behavior is supposed to be when dealing with unaligned reads; it seems that if we expect to not receive unaligned reads, we should check the alignment status and throw an IllegalArgumentException.