make the mapped reads summary report more robust

make the mapped reads summary report more robust
It's really useful for the summary report to report everything that
mapped to the genome as a single entry, and everything that mapped
to the contamination or spike-ins as seperate entries.

This version tags files that aren't symlined as 'last_dir_element/filename'
and files that are symlinked into the genome directory as 'filename'.
Since I have the spike-ins symlinked in, and the last element of the path
name is the genome name it makes it easy to use the 'last_dir_element'
as the name to group all the per chromosome reads to.