Q/Feat: Additionally clarity/control of HMMRATAC accessible region calling #711
Description
When using the HMMRATAC mode, I notice that often there are regions assigned the "open" state that are not annotated as accessible, even when nucleosome regions are called nearby. For example, if there's a gap between the surrounding nucleosome regions and the open region, or a nucleosome region is only present on one side of it.
How does HMMRATAC mode make these calls? Is there a set distance a nucleosome must be within? It would be helpful to see more clarity on how this works, and possibly the ability to set relevant parameters.