[collaboration] Add support for Stranded RNA-seq

[Romain Lannes]

Hi, 

At the moment, Pysam does not support stranded RNA-seq analysis. What I mean is that with stranded RNA-seq, one can determine the strand orientation of the original RNA fragment using the SAM FLAG in combination with knowledge of the library preparation protocol. This is different from simply looking at whether individual reads map forward or reverse. For example, with paired-end sequencing, you'll typically have two reads from the same RNA fragment that map in opposite orientations, but what matters is determining the strand orientation of the original fragment they came from.

I'd like to contribute this feature via a pull request, but I have to admit I don't know Cython. If anyone would be interested in collaborating to add this functionality to Pysam, I'd really appreciate the help!

Sincerly, 

Romain