Multiple regions files

[af8]

Hi Brent,

Simple question.

I saw that you have a branch multiple-by opened. I would be really interested in not having to parse the same WGS bam multiple times to obtain coverage information for distinct regions files (ex: mappable bed, exons bed, custom-genes.bed). Is it something you still have in your radar or not ?

(Soon, I guess that implementing workflows with --d4 will be an answer to that issue too)

Thank you, Anthony

[brentp]

Hi Anthony, yes, this is a perfect example of something you can do trivially with d4. It is so fast that you can extract this information in seconds for each d4 file. For that reason, I won't support multiple --by files. I am happy to answer any questions as you get started with d4.

[af8]

I would be more than happy to get started with d4 but actually I am not sure what to do with a d4 file in my hands ;-)

• Do you consider d4 (in mosdepth) ready for production ?
• Is there documentation to learn how to manipulate the d4 file (to get for instance the --quantize and --thresholds outputs from it) ?

[brentp]

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