DeDup log file incorrectly reports deduplication rate

[jfy133]

DeDup currently calculates the deduplication rate based on number of reads after deduplicated over total reads in the BAM file. This is an incorrect calculation as if the BAM file includes unmapped reads, this vastly reduces the rate because of very large denominators.

The denominator should be mapped reads prior deduplication, as deduplication rate can only be calculated for reads upon which deduplication can be applied.