Fix denominator in output stats to all mapped reads only, not all in BAM #11
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@TCLamnidis and I realised recently that DeDup incorrectly reports dedupping stats when unmapped reads are included in the BAM file. In EAGER1, unmapped reads were removed by default, but eager2 has a different behaviour.
By leaving in unmapped reads, and using 'totals reads' in the BAM file, this makes an artificially large denominator that makes cluster factors/duplication rates much smaller than they actually are.
As de-dupping is performed on coordinates on the reference genome, dedupping only effects mapped reads therefore all stats should be based on that value.