Added ConvertedBedResult to act as a software result for feature list
bed files, once they are converted to another reference sequence.
Start using ConvertedBedResult instead of directly calling convert_bed
Remove old TODO
Removed caching -- using software results now.
target_bed checks to make sure it exists when accessed
Added resolve_roi_for_reference, which checks references before converting the bed file. Also do a basic check for "chr" chromosomes if they do not belong.