LeftAlignAndTrimVariants doesn't work on MNPs

[jonn-smith]

The documentation for LeftAlignAndTrimVariants indicates that it only works for indels. It should be updated to work for MNPs as well.

This operation would simply remove any common leading bases from all alleles of a VariantContext and update the start position by however many bases were removed. It would be implemented in LeftAlignAndTrimVariants.java:289 replacing the noop for non-indels.

[GATKSupportTeam]

(related to Zendesk ticket #204638)

[droazen]

@gbrandt6 Here's another GATK ticket that might be suitable for learning GATK development.