ISBPs are now allowed to have some mismatches in the alignment. parameters have been added into the config.yaml file and are used accordingly in the rules and filterBam.py script

new rule gmapIndexTarget to prepare the whole genome index of the target genome. This index is needed to rescue genes without any mapping result in targeted mapping and gmap on target

BUG: remove -w from the fgrep command in the split per chrom rule. This cause a bug resulting into empty output

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

BUG: output directory not detected by snakemake. needed to add directory() statement for the gmapstats output.