Kristoffer

I sent an email to your uni email address about this.

Implementing this during initial clustering is quite an undertaking. However, would it be sufficient for your purpose to do semi-global alignment in the reverse complement step and check the identity...

Hi @PKuperus, Thanks for reporting! The key line in the error message seems to be `error: [Errno 2] No such file or directory: 'make': 'make'`. You can install `make` by...

The `build-essential` builds other things as well which you might need for parasail, so if `apt-get -y install make` does not do it, maybe the heat weight `build-essential` will. I...

Ok good. Could you try removing the conda environment you previously set up for `NGSpeciesID` completely (with the erroneous parasail) and then do a fresh install? ``` conda deactivate NGSpeciesID...

The problem seems to be that you have some other program in your environment using a newer version of pysam. Creating a new environment in conda for NGSpeciesID and not...

Ok, I will look into this soon. Reading from the log, it seems that you have `NGSpeciesID` installed now (just not the medaka module). In that case, `NGSpeciesID` can be...

I agree that we should change to use -R for read group and make the current -R (rescue level) to whatever letter not implemented in BWA (so to not have...

Hi @danessel, Thanks for reporting. I could certainly add a feature to output either X/= cigars or M. In the meantime; I think [samtools fixmate](http://www.htslib.org/doc/samtools-fixmate.html) can do this conversion. (Based...

Perhaps there are some SNP/indel callers that require M cigars? But I agree that it reduces importance.