call with filters cn, ci, sem

[gevro]

Hi,
I'm trying to run call with --filter cn --filter ci --filter sem. But getting this error:
ValueError: 'sem' filter requires column 'sem'

However, I ran segmetrics with --ci and --sem.

[etal]

Hmm. In the .cns emitted by segmetrics, is there another column generated with a name similar to "sem"? If the column names diverged, that would be a simple bug to fix.

[gevro]

The .cns file output by segmetrics has a column 'sem'. So I'm not sure why the call program is not working with sem. Suggests the bug might be in the 'call' program.

[SenLiBio]

The .cns file output by segmetrics has a column 'sem'. So I'm not sure why the call program is not working with sem. Suggests the bug might be in the 'call' program.

Hi,

I ran into the same issue earlier. In my case, it worked when I applied only one filter criterion at a time — for example, using just --filter sem allowed it to recognize the 'sem' column properly.

It seems that the call command might not support multiple --filter parameters simultaneously. You could try running it with one filter at a time to see if that resolves the issue.

Hope that helps!

Best,
Sen