Cleaned up minor_alleles, enabled haplotype completion.

Restructured the code in Genotype analyzer (see issue #2) and draw_genotype.r (now
called get_allele_frequencies.r and only returns allele_frequencies).
Genotypes are now drawn allele by allele using a perl sub instead.

This also enables allele completion for haploid genotypes (see issue #15). Ploidy
is determnined using the info field of a VCF file and the DP (depth) field,
along with a threshold that can be set by the user (option -d, default 15).
If no alternative genotypes are given for a certain SNP by the VCF file,
the SNP genotype will be considered haploid if the read depth is below
this threshold.

The error (in cleanup) Internal error: could not get STATE from IPC::Run"
that was diplayed previously seems to have been solved in the restructuring
process for unknown reasons.
Added .gitignore and removed an old file.
Merge branch 'master' of https://github.com/Skalbaggsmos/aDNA-phenotype