Minor code cleanup.

 * clarified comments and adjusted syntax in a number of places.
 * renamed Common.loadReads -> loadReadsFromArguments
 * renamed Common.loadFile -> loadReads
 * renamed PileupElement.sequenceRead method to sequencedBases
 * removed unused Pileup.pileupsAtLoci method.
fix comment typos
Merge pull request #73 from hammerlab/minor-code-cleanup-may-20

Minor code cleanup.