Brent Pedersen

Does this answer your question? There should still be the html output...

Hi Steve, yes, this is certainly possible. I tried to get a static build that would do this, but it was a bit fragile. Instead, you can build mosdepth yourself...

If you have a public gs url, I can test. I think I have this working.

I am having trouble getting this into the static build. But, you can build htslib with --enable-gs and then build mosdepth yourself and get it to work (it works on...

As it goes, right after posting that. I figured that if I do the static build without d4, then it works for `gs://` urls. Here is that binary attached. [mosdepth.gz](https://github.com/brentp/mosdepth/files/8599146/mosdepth.gz)...

some users rely on bedgraph format. (3 columns + 4th indicating depth). So we cannot inject a fake 4th column when they give a 3-column file.

no. do not add a command-line option. every additional option increases the number of emails I get about 2X. thanks for the work on this, by the way, I think...

I think that solution will cause other problems. can you share a bam I can use to recreate?

@torfinnnome I think this is related to another, recently reported issue. Do you see huge memory use if you do not specify any threads?

sorry for leaving this. I don't even have a good excuse. your solution does affect the output in some cases, but I think it's a reasonable compromise that if you...