Correctly report coordinates and alleles for indels

This is a somewhat simplistic view of vcf indels, relying only on the length of the indels, and assuming that they are normalized.
I've also requested that @ernfrid take a look at the test cases and suggest others that should pass.
I am also wondering if I am duplicating code, but I didn't really see anything except VcfToBed, but these are our "annotation" style coordinates, not bed.