The requirement of the 'counts' column header in the copy-numbers csv presents an inconsistency with the rrat package, which returns a file with schema (see https://github.com/crosenth/rrat/blob/master/rrat.py#L253)
|--------+---------|
| tax_id | medians |
|--------+---------|
Curious what motivated the renaming, and what the best course of action might be for addressing the inconsistency.