Allow duplicate nodes in tsk_variant_init

[benjeffery]

One of the requirements of the new alignments code is that duplicate samples are allowed. As this code will use the existing genotype decoding machinery, we'll need to relax that requirement in the existing code.

[jeromekelleher]

Ah, I see where the confusion came from, sorry. No, it's not worth doing duplicate nodes in alignments if it means we have to meddle with the variant generator.