Repetitive code should be moved into a function for easier maintainability

[carolyncaron]

PR #39 introduced repetitive code in files: includes/vcf_filter.trpdownload.genotype_matrix.inc and includes/vcf_filter.trpdownload.hapmap.inc

For easier maintainability, it would be ideal to add a single function to the api instead. Alternatively, there already exists the api function vcf_filter_read_VCF_into_array() which may be suitable in this case.

See my comment from the review process here: #39 (review)

[laceysanderson]

Additionally, we need to switch over to using the api function because it uses the PL. This is currently causing discrepancies between output formats using the API function (ABH) and those which don't (HAPMAP, Genotype Matrix).