Devon Ryan

Will do. I'm creating the indices at the moment.

A small update, I have a modified version of bwameth with a `--pbat` option that seems to be producing good results (I'm testing with DRR019425). I've only tested paired-end reads...

Please try the `pbat` branch with the `--pbat` option [from my fork here](https://github.com/dpryan79/bwa-meth/tree/pbat). That now seems to be working correctly for SE and PE data.

@avilella Did you have a chance to test that bwameth branch? If so, did it produce reasonable results?

Lovely, I wonder when they changed their behavior, as what Methyldackel does matches Bismark's original behavior.

Sorry for the delayed reply, I hadn't planned anything in this regard. PRs welcome :)

That's weird, thanks for reporting this. I'll try to track down this bug.

@DaGaMs Can you try this with version 0.5.2? I haven't changed any of the parsing for this in a number of releases, so I wonder if this is due to...

Define "abnormally low". Have you spot-checked a few regions to see if they're correct. There's no _a priori_ reason this shouldn't work.

Hmm, OK, that does look odd. I'll look into this.