Merge commit '9205157686d22eb1cb1f1fac7778fb5990b8e21a' into rchowe/master

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

The removal of TreeReducible<Integer> and the addition of @By(DataSource.READS) had to be merged.
Merge branch 'rchowe/master'