idxdepth regex option not working

[weilu1998]

Hi,

I am using a contig-level reference genome and the contig names are not in the form of chr1-21. When I tried to use idxdepth to calculate depth all my contigs are skipped even after specifying the regex in autosome-regex or sex-chromosome-regex option. This is probably related to a previous issue. In that issue, all the alternative contigs are set to be skipped by default. How to change the default setting? Is there a option for that?

Thanks