option for shuffle to maintain spacing

[jayhesselberth]

from the paper:

The p-value and the direction of difference from the null hypothesis (that the positions of Q and R are independent) are obtained by permutation. Each permutation randomizes the query intervals uniformly across the chromosome, maintaining the spacing between intervals.

emphasis added. seems like a reasonable option for bed_shuffle().

[jayhesselberth]

the easiest way to do this would be:

1. calculate interval spacing
2. pick a random start for the first interval
3. use the spacings to set the coordinates for the other intervals.

would need to deal with spacing per chromosome, and also make sure that all intervals on a chrom are in-bounds, given the random start.

[jayhesselberth]

for simplicity, the above should probably ignore incl and excl params. and issue a message to that effect.

[jayhesselberth]

Could also pick a random offset with the spacing dists, using that as the first and then circling back when the end is reached.

[jayhesselberth]

closing for now