Added gemini amend to edit an existing database.
Fixed error with JSON formatting.

Also moved the format selection to this module, as it makes
more sense here.
Added a database_transaction context.

This will open a database, return a cursor to it, commit and
close the connection when the with statement has ended.
Moved PED file parsing to the ped module.
Added gemini amend.
Moved format selection to the GeminiQuery module.
Bug fixes for JSON output, the unit test for amend
and test-genotypes.

test-genotypes now returns more than two decimal places.
Bug fix for missing attributes.
Utility function to quote a string.
Fix new unit tests.
Merge branch 'master' of github.com:arq5x/gemini