Andrew Stewart

Hi @matalo33 - This would also be of interest to those using `blogdown` in R, which often makes heavy use of mathjax. I can provide example markdown from one of...

Hi @tamsen , any chance you could add the correct tarball to the repo for CreateGenomeSizeFile? [CreateGenomeSizeFile_5.2.9.122.tar.gz](https://github.com/astewart-twist/Pisces/blob/master/binaries/5.2.9.122/CreateGenomeSizeFile_5.2.9.122.tar.gz) is an empty file, and [CreateGenomeSizeFile_5.2.7.47.tar.gz](https://github.com/astewart-twist/Pisces/blob/master/binaries/5.2.7.47/CreateGenomeSizeFile_5.2.7.47.tar.gz) contains VennVCF, not CreateGenomeSizeFile.

+1

+1

Thank you @tamsen !!!!

Sure. As far as I can tell, it looks like pysamstats considers the same insertion/deletion/mismatch observed on both forward and reverse reads at the same position as 2 separate observations....

Not the consensus sequence, Alistair, just the consensus alignment stats. If you want to point to the relevant lines of code where something like that might best fit, I can...

@alimanfoo Any idea of when pysamstats will support more recent pysam versions?

I was just asking out of curiosity @alimanfoo. I'm more curious to see how any pileup computation changes between samtools 2 and 3 would affect pysamtools calculations. I'd be happy...