Normalize coverage
Unit tests for normalization methods
Args.txt files updated to work with new normalize argument
normalize by samples first and contigs second
added nose temp output directory to gitignore
Normalize per sample as well, plus made normalization into methods
Merged upstream changes
if normalize parameter specified we normalize coverage before we log transform (log transform is always done)
Made normalizing coverage default. Updated tests and reference result files to reflect that.
Merge branch 'master' into normalize_coverage