Added high-impact burden summary and c-alpha test.
Added scipy as a dependency.
Provide more flexible versioning in the setup.py and requirements.txt to allow usage of anaconda pre-built packages during installation
Improved gemini installer: use isolated Anaconda environment instead of virtualenv. Provide resiliancy to download problems from S3
Catch and remove broken symbolic links to gemini in the PATH when installing and updating
Update querying.rst

minor documentation bug fixes (extra comma, missing --header)
Merge pull request #185 from drmjc/patch-1

Update querying.rst
Ensure installation is in work directory after external call outs to prevent directory missing errors
[ENH] check vcf and vcf.gz timestamps before loading woth existing vcf.gz
Merge branch 'master' of github.com:arq5x/gemini
Merged.
New subtool: burden tests, added.

Run with no special arguments calculates
a table of the number of high impact variants
per gene per sample.

Run with --nonsynonymous it calculates the
same table, but looking at all non-synonymous
variants.

Run with --calpha, it runs the c-alpha test,
using case/control status as specified in
the sample table

Run with --calpha and optional --cases and
--controls lists of samples  runs the c-alpha test
with those samples set as cases and controls.

Unit tests added, along with necessary data files.
[BUG] comp_het fails with variants having mult. alt. alleles.  Now warns and skips until we support mult. alt. alleles.
Added scipy and pandas as dependencies.
Added burden test documentation.
Fixed formatting.
Added PID to logging messages.
Merge branch 'master' of github.com:roryk/gemini
Merge pull request #167 from roryk/master

burden testing
oops. appears anaconda includes pandas and scipy.