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  • Aaron's avatar
    Fixed logic relating to "split" coverage. · 9fe56c08
    Aaron authored
    	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.