Genotypes scoring is not representative of linkage

[mtekman]

The region given in the image below is outlined by linkage as significant for an AR model, with the affected individual being homozygous at this locus.

The scoring does not affect this, mostly I believe because it takes into account the values of the alleles and not the colouring, which would be far more useful.

I propose three modes of operation:

• Scoring based on numbering
• Scoring based on allele colouring
• Scoring based on a combination of both (as now)

It is then up to the user to decide which method best helps their analysis

Test_data:

test_data.zip.tar.gz