add functions to perform various checks on bioframes: is_sorted, is_overlapping, etc...

[golobor]

No description provided.

[Phlya]

How do you define sortedness for chromosomes?

[endrebak]

In pyranges I use the natural sort order.

from natsort import natsorted
natsort(["chr1", "chr11", "chr2"])
# ['chr1', 'chr2', 'chr11']

but I have only worked with human genomes. This might be the wrong order for other species? And it is not perfect. For human genomes, I would consider "chrM" to come after "chrX" and "chrY".

[gfudenberg]

checks are now in bioframe.core.checks, sorting is now in bioframe.ops.sort_bedframe