Adding a minimum coverage parameter to SomaticSpike with a default of 5.
--This should hopefully screen out a lot of the garbage spike ins.
Adding a log notification each time a site is skipped due to low coverage.
Minor improvements to documentation of SomaticSpike.
Merge branch 'master' into exome

Conflicts:
	SomaticSpike/src/org/broadinstitute/cga/tools/gatk/walkers/cancer/simulation/SomaticSpike.java