Brent Pedersen

Hi Isaac, if you look through the issues, there are a lot of questions like this. I think that mosdepth does a good job of giving a sane answer. Reasons...

That *is* odd. Nothing comes to mind. I guess you could do a plot with indexcov and see the coverage across the genome.

Hi, So each contig is a gene? Do the genes have ':' in the names? Can you show a few of the 49 rows and then a few of the...

do the missing IDs have 0 coverage?

Hi, here's what I see. Your global.dist file contains 135302 unique regions. thresholds bed file contains 128605 unique regions. Now, if I look at a few of the differences: ```...

the names in the first column of the bed output must always come from the chromosome/contig column of the bam. mosdepth will put the gene name in the 5th column...

Hi, for now, I suggest to use nim < 2.0.0. I'll update to latest nim in the neext few months.

--by just tells mosdepth that you want extra information for those regions or that region. But it must still read the entire chromosome. It's built to be fast on whole-file...

Hi, I have a PR open on bioconda to update mosdepth, once that is merged, the quay container will also update.

Thanks for the clear report. I see what you mean. Due to the way I wrote that part, it's not an easy fix. I'll have a closer look next week...