Move "PhaseVariants" tool under GMT.

The test does not currently test anything as it points to
non-existent files.
Fix behavior of bases_for_sample

It was not handling the case where the sample_data was just '.', nor the
case where the genotype information was just '.'.

I just made alt_bases_for_sample lean on bases_for_sample, there is
probably a more efficient way to do this though.
Remove 'use Genome' from File/Vcf/Entry.pm
Whitespace.
Remove un-needed constructor.
Remove un-needed comments.
Print command using debug message.
Remove unused local variable
Switch to snake_case so we get hyphenated params instead of mixed-case.
Add note about switching to shellcmd.

If we switch now the test starts failing.
Remove unused includes.
Rename 'get_alleles' to 'get_allele_indexes'

This name was confusing.  I will later create a 'get_alleles' that
returns a list of alleles.
Fix test inputs

\("T") is not the same as ["T"]
This was not caught because the member variable is never used, but it
will be soon.
Add 'get_alleles'
Use 'get_alleles' instead of 'get_allele_indexes'
Merge pull request #182 from davidlmorton/bases_for_sample

Fix 'bases_for_sample' and move logic to Genotype object
Merge pull request #177 from tmooney/move_phase_variants

Move "PhaseVariants" tool under GMT.