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