add input pointing to the mapping/chrom/temp directory containing all the mapping files (blat, gmap)

now the nomenclature of the new geen ids can be setup in the config.yaml file. Also 2 new rules to compile the blat results and the anchoring summary

bug in  mapHomologousRegions shell command: need to use {wildcards.chrom} instead of {chrom} in the shell to properly expand the chrom variable