Extend samples table with new columns when amending.

This allows you to add phenotype fields to your samples after
you have already created the database.
Make top-level imports be lazy.

Startup time was super slow, this speeds it up around 20x by
avoiding importing all of the modules unless they are being used.
Fix TPED output.

TPED output had the following issues:
1) the identifier was not unique for a small subset of the variants,
so variant_id is appended to the identifier to make it unique
2) TPED needs both alleles set even if the chromosome is haploid, so
we treat haploid or single-allele called males as homozygous on
the sex chromosomes. heterozygous males are set as missing, unless
the variant is in the PAR region then it is set to being heterozygous.
females have all variants called on the Y chromosome set to missing.
missing include
Merge branch 'master' of github.com:arq5x/gemini
Remove stale databases before running the tests.
Fix for not finding the installed extra annotations.
Fix the unit test for --format tped.

Brought the unit test up to date with the code; the format of the
ID column changed, which was causing the unit test to fail.