Improve the bed split method

[mfoll]

My R script is not splitting regions in the bed file but is rather grouping them to launch in parallel. This is good for exomes as the bed file contains many line (~ one per exon), but the user should also have the option to allow cutting lines of the bed to make calculation faster when they contain only a few large lines. This is related to #39 where for full genomes there is no bed so we will have to cut the chromosomes in chunks.

[mfoll]

Of course splitting a region is not always good if you split right in the middle of an indel, so it should remain the user choice (like with an option allow_bed_cut or something like this).

[mfoll]

Actually I'm not sure my last comment is true because:

• we don't consider MNP
• samtools keep the full reads overlapping a position and then indels will never be cut

[mfoll]

In this paper they seem to have the right way of doing it with "bins of equal depth":
http://biorxiv.org/content/biorxiv/early/2014/12/05/012179.full.pdf