Benjamin Schuster-Boeckler

+1

I recompiled 0.5.2 with gcc-8.3.0 against htslib-1.11.0. I still get the same error: ``` MethylDackel extract -@ 2 -q 5 -l hg38_main.bed.gz --cytosine_report --OT 8,124,2,0 --OB 2,120,0,104 -o merged_701503 ref.fa...

I just tried with 0.6.0 and I still get `Invalid bounds string` with any pattern that contains a 0

hmm... so how does this work for trimmed reads? I interpret this syntax like this: If not all reads are 150bp, then F1 reads will still have their first 10bp...

yes, but I don't know how many bases were quality trimmed for each read, because the trimming is adaptive. Also, there could have been different adapter/barcode contents. That means that...

I think my brain is slightly fried, it's late and I have been staring at code for too long 😅 I'm probably missing something totally obvious. I mean this: ```...

Sorry, I was so knackered yesterday evening I couldn't respond any more. So, one case is that we have barcodes at the beginnings and ends of fragments, and the demultiplexing...

Ok, one last request for help: my mbias plots look like this one here:  Red is Read 1, blue is read 2. The data come from one of...

nope, they are definitely true commas. I reverted to 4.0 and it works, back to 5.1 or current HEAD, and it doesn't

The `0`s are not correctly handled somehow. With 4.0, this worked `--OT 10,0,0,140`, but in 5.1, it throws said error. However, this works: `--OT 10,150,1,140`. In this context: I don't...