Detect truncated file

[AlistairNWard]

Now we have a json that summarizes chromosome lengths for different genomes, can we identify which genome the BAM is aligned to. We could a) show some summary of these details, and b) if we see that a number of chromosomes are missing, we can point it out. This might mean that the json with reference genome metadata needs updating to indicate which reference sequences are expected, so 1-22, X, and Y for human, and not the other contigs.