ekg/vcflib — pull request #12 by alimanfoo (2013-02-19 17:21:45+00:00)
Title: Cython extension

Hi Erik,

This pull request contains some initial tentative work on creating a Cython extension wrapping vcflib, for use in Python or other Cython extensions.

There are several changes in this pull request, if you'd rather have this broken down a bit then let me know, happy to do it.

Here's a summary of the main changes:

* wrap all includes of the smithwaterman disorder module with extern "C" to allow building the Cython C++ extension (N.B., this also requires a change in the smithwaterman submodule, so I've temporarily switched that submodule to point to my own fork)
* fix minor bug (?) in getSampleValue...() methods
* add filterIds method to VariantCallFile
* create vcflib.pyx and vcflib.pxd defining the vcflib Cython extension
* create setup.py to build the Cython extension