Regions missing from ratio file

[BhumikaPriyadarshini]

Hi,
I have query related to the regions missing in the ratio file. If I'm giving printNA = True, then some regions of all the genes provided in the bed file are having -1 as ratio as the information aren't available for the same. I checked the mapping quality, read quality, read depth etc, all are coming fine. In .cpn file, these same regions contain enough read counts also. Could you please help me with the same, how to get ratio for those missing regions? Additionally, I want to add those missing regions contain important domains like kinase domains, so it's crucial for me to extract the ratio for those regions.

Kindly help.
Thanks in advance.