walk by reads
fixed sorting error (Comparison method violates its general contract)
limit whitespace diffs
added back walk by reads (removed accidentally when trying to limit
diffs)
fixed pileup sort order (put highest quality 1st)
Merge commit '87054028aef2485519355fef25de9038e6787114'

Conflicts:
	src/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTect.java