I am trying to use a pipeline for aligning data from a technique developed by another lab: https://github.com/SavageLab/dipseq/blob/master/README.md It was written a couple years ago and I think that it's not compatible with the most up to date samtools distribution.
I am trying to debug it and fix it so I can use it for my data analysis. The current error I am having is:
[E::bgzf_flush] hwrite error (wrong size) samtools view: writing to standard output failed: Broken pipe [E::bgzf_close] file write error samtools view: error closing standard output: -1
Does anyone know why it might be incopatible with samtools and how to approach solving this problem?