Graceful handling of unknown chromosome

[rhdolin]

Currently, when converter encounters an unknown chromosome, it is unable to determine a corresponding reference sequence, resulting in an exception, as in this case:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample
chrR	301	.	A	G	.	.	.	GT:PS	0/1:.

We will likely want to add another exclusion criteria, for cases where VCF CHROM is not recognized. These would then also go into the invalidRecord log.