Needs to support pipes

[necrolyte2]

Currently it expects a file as the output parameter to run
Would be much more efficient if a person wanted to use PIPE's

[astewart-twist]

It'd be great if this could feed right into https://github.com/pysam-developers/pysam

[necrolyte2]

pysam doesn't support reading input directly from python objects(you have to supply a file path or - to read from stdin)

Regardless, I think this project is a bit deprecated since using the sh module is probably going to be much easier for you