Expose More Of The Cython Interface

[GoogleCodeExporter]

First off thank you for the very useful library.

I think it would be very helpful to expose more of the Cython interface. This 
would allow programs which need fast C level access to certain classes to be 
developed. I think this could be easily accomplished by moving all C variable 
and method declarations out of the pyx file and into the corresponding pxd 
files.

As a use case, I am currently developing a tool for analysis of normal/tumour 
data with the goal of finding somatic mutations. To do this I need to summarise 
the the number of bases matching the reference genome and the number not 
matching. This can be easily implemented in the Python API, but it is far to 
slow for practical use. What I have done as an interim solution is expose the 
IteratorColumn class from Cython by creating a modified csamtools.pxd file. 
This works perfectly, but is obviously a poor solutions as it is very brittle 
to changes in the pysam library.

Thanks,
Andrew

Original issue reported on code.google.com by AndrewJL...@gmail.com on 16 Jan 2012 at 8:49

[GoogleCodeExporter]

Thanks, I think I have now exposed the full interface.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 16 Aug 2012 at 8:30

• Changed state: Fixed