gVCF combiner: Do proper minrep before and after merging (#5112)
gVCF combiner: Do proper minrep before and after merging (#5112)

* Do proper minrep before and after merge

This ensures that variants that are identical across combiner inputs
are properly deduplicated during merge, and then we get the appropriate
representation of all alleles after merging.

* Fix incorrect insertion case in fix_up

* Remove set creation in finding reference

hail-is/hail,danking/hail,hail-is/hail,danking/hail,danking/hail,cseed/hail,hail-is/hail,cseed/hail,cseed/hail,hail-is/hail,danking/hail,cseed/hail,hail-is/hail,cseed/hail,hail-is/hail,cseed/hail,cseed/hail,danking/hail,hail-is/hail,danking/hail,hail-is/hail,danking/hail,cseed/hail,danking/hail