Fixed logic relating to "split" coverage.

	1. Fixed bug in BamAncillary::getBamBlocks where the switch statement was misbehaving.  Changed to if/else
	2. Added countSplitHits to bedFile class to proper count coverage from "blocked" alignments. Previously, coverage
           was counted separately for __each__ block yet what we actually want is the base coverage to be counted for each block,
           but we only want the blocks to be treated as __one__ alignment or feature.
	3. Updated coverageBed to use getBamBlocks.