Display VCF variant indels at non-padded location

Indels are intended to have leading bases which match the reference. To best display where the variant actually varies, we attempt to remove the leading padding. This is done by examining all variants, and taking the shortest common leading prefix where they all match the reference. Only performed for variants of type MIXED or INDEL. Previously we just added 1 to the start position.

See http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

IGV-1903 #comment