Devon Ryan

What do the MAPQ scores look like there? For overlapping PE reads it will alter the base call phred score up or down depending on whether the overlapping portions agree...

There's a longer thread with numerous example here: https://github.com/bioconda/bioconda-recipes/issues/41526 In short, the general error we're seeing (only on OSX-64) is: ``` Traceback (most recent call last): File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10,...

@wolfv Excellent, is a new release imminent?

Sigh, apparently the shebangs need to be patched. This is really poorly written, if someone actually wants to use this it's an easy enough fix.

One "fun" issue is that if there is no index for the genome (a .fai file) then running this or any similar tool in parallel will result in each process...

How are you installing MethylDackel and samtools?

Since you're familiar with conda already could you instead make a new conda environment with both samtools and MethylDackel? I've recently rebuilt both in Bioconda and can guarantee compatibility. Alternatively,...

@bioconda-bot please update

I did a bad job when writing the documentation for this. What I wrote in #102 is correct, I'll make a mental note to clarify this in the documentation.