arq5x/bedtools — pull request #76 by brentp (2013-06-27 20:19:41+00:00)
Title: ENH: shuffle intervals to non-overlapping locations.

This definitely needs some review and some tests but "seems to work". It allows shuffling a set of intervals to non-overlapping locations. This may be a useful constraint, e.g. in cases where we are simulating deletions, loss-of-heterozygosity or copy-number events.

It progressively adds each interval to the _exclude map, so it may become slow (or impossible to place later intervals) when the -i BED file has many / large intervals.