Randomly shuffle intervals

$ cat A.bed
chr1  0  100  a1  1  +
chr1  0  1000 a2  2  -

$ cat my.genome
chr1  10000
chr2  8000
chr3  5000
chr4  2000

$ bedtools shuffle -i A.bed -g my.genome -chrom -noOverlapping

chr1  9560  9660  a1  1  +
chr1  7258  8258  a2  2  -

more :
http://bedtools.readthedocs.org/en/latest/content/tools/shuffle.html