Refactor GenomicRegionSet IO handling about reg-gen

[fabio-t]

As @jovesus pointed out, when a GRS is filled from a bed file it's always sorted. Also, duplicate lines are always kept. These two things were there before but I'm not sure if they should be like this.

In general, a GenomicRegionSet is not really a Set. It's wrapper around a List, with List semantics. Just a little quirk.

[fabio-t]

The basic idea is done. BigBed is still not supported since we have to decide how to handle it. Various ways available:

• Simple conversion. I already have utility methods in motif analysis to convert from bed to bigbed and viceversa. Every application should know how to change the "score" field to make it fit the 0-1000 range, depending on the meaning such score has. This is simple but yields no advantage.

• Make a GRSFileIO.BigBed. Instead of converting bed to big bed and viceversa, this would directly write to/read from BigBed files. It has the advantage that it forces us to stop using the Bed utilities (or write a python wrapper), and it should be more efficient than making BED temporary files.

• Keep a BigBed behind the GRS. This is a significant change and I'm not sure it's worth it. We would gain a lot by improving the memory efficiency of the GenomicRegion, instead of essentially writing a DB layer on top the BigBeds.