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