clean this up

[yannickwurm]

1. name columns right away and use names for subsetting

2. Use named arguments in functions . 2 examples here, but applies everywhere:

3. ugly :

4. use .vcf extention (unless the software is completely retarted)

[MPriebe]

1-3 have been addressed by @gabrielluishernandez and myself. 4 will have to wait until after the practicals are run because we don't have time