finalize the set_somatic tool
better support for the gene column
parsers for new cancer tools
remove uncessary imports; refactor
better parsing of PED files.
missing file
Add --show-samples to the output of gemini region

This fixes issue #259
Merge pull request #262 from lbeltrame/add-samples-region

Add --show-samples to the output of gemini region
add new indices
better logging:
better logging:
merge in a transaction and delay indexing until final db.
Merge branch 'master' of github.com:arq5x/gemini
Avoid issues with numpy 1.7/1.8 discrepency in automated conda installation. Fixes #264
Ensure mapping quality is a single value. Supports platypus VCF output
Added SPLICE_REGION to snpEff effects
Merge pull request #266 from dgaston/master

Added SPLICE_REGION to snpEff effects
Provide framework to make data files optional with switch to add new ones to avoid large downloads not used by default. Turn off gerp_bp download by default since it's 2/3 of the current download directory and not enabled without a flag
Fix issue with missing __init__.py files that use namespace packages, which setuptools/pip toss away: update to latest ipython-cluster-helper with fix and manually patch for python-graph-core. Thanks to Kie for the report on the mailing list
don't index until end