bam_PE?

[nponts]

Hi,
How do I set up read_mode to bam_PE please?
Cheers!

[jrboyd]

You set read_mode when creating the QcConfigSignal object.

Something like:
QcConfigSignal(..., read_mode = "bam_PE")

If you give me more details about how you're trying to use ssvQC I can be more helpful/specific probably.

[nponts]

Hi again, and thank you for this light-speed answer! It actually answers the question :)

But now I have another one...
I ran a quick-and-dirty test on a couple of bams to get a hand on the tool. I could not got through with the mention of non unique ids in prepare_fetch_GRanges_names(qgr, include_id = TRUE) :
qgr$id must be unique. qgr$id is either directly supplied or taken from qgr$name or names(qgr).

By-passed it with the matched_only option set to false but I'm not sure it's a good thing...

[jrboyd]

OK. There are several ways to make a valid ssvQC object so it's really unclear to me what you're trying to do or when this error is coming up. Could you elaborate?