massie/adam — pull request #10 by fnothaft (2013-10-24 05:01:38+00:00)
Title: Split reads2ref into read to pileup and compression operation

Created new command to handle compression. This way, reads2ref conversion does not need to be lossy if the user would rather trade size for data. Users can still perform both read to pileup conversion and compression in one stage by invoking the reads2ref command with the -compress switch. I've also added a separate conversion just for compressing pileups (PileupCompressor), and added this to AdamMain.

Along the way, I also realized that there was a functional error in the reads2ref conversion that was taking the wrong quality score for bases. This change fixes that as well.