indexcov: limit to standard chromosomes about goleft

[brentp]

ok. what is needed for hg38/hg38 Un and random? I could make it default to removing those.

Or I can add --exclude that takes a list of chromosomes.

You're thinking just to remove this from the visual output? Or from the .bed.gz as well?

[chapmanb]

Brent;
Here's the gist of the ones from hg38 and hg19 that would be good to drop:

https://gist.github.com/chapmanb/e8b91a7f4426bdfcc0f8a15b7539a7b0

So chrUn, random, hap, alts and HLAs. Removing from everything works great, I don't think we'll be assessing coverage much on these and just creates a bunch of extra.

Alternatively, having a flag for what to include/exclude would be great and I can do myself. --include would be easier than --exclude to avoid huge command lines on hg38 (or a file of exclude inputs).

Thanks much for considering this.

[brentp]

Thanks Brad. I'll make it an exclude pattern with this default:

^chrEBV$|^NC|_random$|Un_|^HLA\-|_alt$|hap\d$

that removes all of the chromosomes you sent except chrM. You will be able to set from the command-line if needed, but I think those are sensible defaults. Does that seem reasonable to you?

[chapmanb]

That would be perfect -- thanks so much.

[brentp]

Hi Brad, I implemented this and pushed a new release. Thanks for the feedback.

[chapmanb]

Perfect, thanks so much Brent. I updated the bioconda package for this so it's all rolled out. Much appreciated.