Intersect Policy

When you give the Fragment Generator an interval of start and end to pull fragments from, which fragments will it return?

What if a fragment has 1bp of overlap within the just on the edge of the window? Does it also return that fragment as well?

These questions are answered by the intersect_policy argument, which shows up in many of the CLI and API commands.

intersect_policy can either be midpoint or any.

Midpoint

midpoint: The midpoint of the fragment determines whether the fragment will be returned or not. If the midpoint falls between start and end, then it will be returned. Else, it will not.

Any

any: As long as the fragment overlaps the interval between start and end in some capacity, then it will be returned. Else, it will not.