feat: transform subcommand

[aryarm]

resolves #33
note: please merge this before #43 !

Overview

This PR adds a subcommand to output haplotypes in VCF format, so that we can obtain counts of each haplotype in each chromosome of each sample. This functionality is primarily handled by a new Haplotype.transform() method.
There is also a Haplotypes.transform() method to transform multiple haplotypes at once. At the moment, Haplotypes.transform() just calls Haplotype.transform() repeatedly, but I think there might be ways to make this faster.

There are also new methods to write the haplotypes to a VCF and some small improvements to make reading from VCFs less memory-intensive.

Usage and docs

I've documented the transform subcommand here in the commands section.

Usage of the transform() methods for the Haplotype and Haplotypes classes are documented in the API docs here and here, respectively.

Testing

I added the following tests to the TestHaplotypes class in tests/test_data.py:

1. test_hap_transform()
   Try the Haplotype.transform() method on a basic haplotype and its genotypes.
2. test_haps_transform()
   Try the Haplotypes.transform() method on a set of basic haplotypes and genotypes.
3. test_hap_gt_write()
   Try to write haplotypes to a VCF. Read the VCF back and check that it looks like what we would expect.