Brent Pedersen

I'm not opposed to this, but if the use is coverage calculation, why not just use the values in the `*.dist.txt' files? there you can get the actual coverage.

I agree this would be useful. I'll think about how to expose and implement.

This is not off my radar, I'm still considering what to add. I'd also like to output mean/s.d. by chromosome so that a user could get a z-score as needed.

this could probably be added to the summary output...

This is pretty easy to implement. Would like to get others to weigh in on how broadly useful this is. Is this something that's commonly needed for long-read data? cc...

yes, for CRAM it will report the sum of all samples. it should be checked in CRAM too. the index can't know about the different samples.

smoove won't work with multiple samples per bam (I don't think lumpy will either).

Hi, you can get the regular distribution from the cumulative with something like: ``` dist[i] = cumulative[i+1] - cumulative[i] ``` for each depth as `i`.

mosdepth just calculates depth in the alignments as they are given regardless of if they are in HLA or no.

mosdepth requires tab-delimited files. I'd accept a PR to inject the depth into the 5th column when a file has more than 5 columns.