Brent Pedersen

mosdepth just reports the coverage as it is, without considering the reference bases.

I agree this is useful. But this should be simple to calculate externally.

Mosdepth gives you the CDF (cumulative). It loosk like the other tools is giving you the PDF (point). So the mosdepth plot tells you that about 50% of the genome...

the -n option only determines if the per-base bed.gz output is written. it does not affect the other files. you can modify the legend by editing the plot-dist.py script.

Hi, if you don't need d4 support, you can ignore this problem. Otherwise, you'll have to install d4 to a standard location or one that the compiler can find. If...

could you expand on the first point? you mean you want to avoid `argument list too long` error or something? for the 2nd point, indexcov only does within sample normalization,...

> > ? you mean you want to avoid argument list too long error or something? > > yes. Something like what the broad is doing with the '.list' suffix:...

Yes, sorted by start numerically with each chromosome. https://github.com/brentp/mosdepth/blob/master/mosdepth.nim#L342 Then sorted by the order of chromosomes in the sam header (with SN) so you'd have to use that information to...

thanks for figuring this out. is there a tracking issue for this problem on the plotly.js repo?

Looks like that should be do-able. It will be a couple of weeks before I can get to it. It will have to convert anything that's not already 16KB bins...