Bob Literman

Definitely those are the commands. I don't run anything species-specific. Everything was run in batch with the commands as given. I ran the following command using the same data: sisrs...

Identical with 1CPU as well.

Running the entire SISRS sites program with 5CPU starting from the raw data yielded identical counts of variable, biallelic, and PI sites as well, on my end.

@rachelss Can you assign this to me?

Great. I think in light of that if there are no exceptions, I will hold off testing until the Python 3 conversion. That way I can continue with my stuff...

Check out other aligners, specifically with functionality at degenerate bases.

Long story short, what BBMap is doing now, a bash or Python script could do. I planned on integrating more down the line, but I'm open. As for installation, there...

I see. I work out of an HPC system, so I can't apt-get anything. All dependencies must be compiled from source onto the cluster.

I can definitely write a quick Python or Bash script for the scaffold renaming if it's less hassle. BBMap is just very versatile with NGS data, like samtools, bowtie, and...

I have been tinkering with some memory reduction adjustments (mainly to getPrunedDict and outputAlignment) and the Python port will really help streamline things. Don't worry about incorporating these into port...