Brent Pedersen

You make a good point. We are working on improving the documentation and functionality in d4.

Hi, I'd need an example bam that demonstrates this issue to be able to debug.

you can email them to me or add them here to the issue with .gz extension.

hi, this must be a bug in htslib because if you do: ``` $ samtools depth -r 1:1-249212864 concate.cram | tail ``` then you see that the last entry is...

Hi, mosdepth will use an amount of memory that is about: `4 bytes * length-of-longest-chromosome`. So, on human, where the largest chromosome is about 250 megabases, it will use about...

Hi, this is likely not a mosdepth issue. The memory used by mosdepth is fixed. So it's something with your scheduler (PBS) or parallelizer (gnu parallel) and the way you're...

you mean using using the python script to make the plots? you can probably just edit the script. I'll have a look at some point, but might be faster if...

I'd accept a PR where if one specified, e.g.: `--thresholds -10,-25,-50`, it would invert to count bases below.

In order to use mosdepth, your data must be coordinate sorted. I don't know about peak calling, that would depend on the tool that's used for that application.

Yes, with long reads, it's harder to get enough data in each bin. I would expect it to be still informative--but not too surprised if it's off. You could try...