Andrew Whitwham
Andrew Whitwham
Let's start with your concrete example. The two occasions where `bam_plp_auto` is used in samtools the error detection is done by looking at the last argument. If it is <...
Unless someone comes up with a concrete proposal. I don't think we are going to change the general logging anytime soon. For the functions mentioned, we do need more documentation.
@migrau. If you want us to look at the problem could you open a new issue, This one is from 2019.
It is still on the list of things to do. Unfortunately it is not that high up on the list at the moment.
Sorry for not replying sooner. So htslib currently does not support Azure storage, I'm not even sure anyone has asked for it before. We would like to support it but...
We can look at this when we next make `coverage` changes, though that probably will not be soon.
> Running `samtools-1.10` with a region, like this: > > ``` > samtools view http://s3.amazonaws.com/iobio/NA12878/NA12878.autsome.bam 22 > ``` > > results in: > > ``` > samtools view: error closing...
It would take some reworking of the stats but that might not be a bad thing. As for JSON, how about posting an example of the kind of output you...
Thanks for that @Poshi. When I get back to markdup I take a look at adding a JSON option and individual library stats.
That's interesting. There should only be fixed memory usage for markdup. Could you tell me how you are running the command and what options you are using?