Use API/PL for Genotype Matrix & Hapmap format

[laceysanderson]

Metadata

• Issue Repetitive code should be moved into a function for easier maintainability #48

• I feel this PR is ready to be merged.
• This PR is dependent upon [PR #/ nothing]

Documentation:

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.

Description

This PR updates the Genotype Matrix and HAPMAP formats to use the vcf_filter_read_VCF_into_array() API function. This has the benefit of removing repetitive code. Furthermore, the API function corrects the GT using the PL. This PR also adds simple tests for the genotype matrix and hapmap formats.

Testing?

• I tested on a generic Tripal Site
• I tested on a KnowPulse Clone
• This PR includes automated testing

This PR includes automated testing :-D Please check that the files short.genotype_matrix.txt and short.hapmap.txt match what you expect. NOTE: when comparing with raw vcf, the calls may not match the GT... rather use the PL to determine what you should expect.

Manual Testing: (NOT NECESSARY due to automated testing ;-P)
A) Create a genotype matrix and hapmap version of a given file before switching to the branch and after switching to the branch. You should notice small differences in the genotype calls based on the PL correction and a fix to the first line of SNPs (added newline).

B) Check the calls from the VCF and compare to the output genotype matrix and hapmap files. Ensure that the calls are what you expect.

[carolyncaron]

This PR works as expected and is ready to be merged. 👍 I tweaked the test files since there were highly improbable genotypes being represent (half called, half missing) and no missing calls, so I altered the half-missing to fully missing (./.) There were double quotes throughout the VCF which didn't appear to impact the tests but I removed them anyway.