Fixed minor bugs in variant generation.
Fixed minor bugs in variant generation.

ekalosak/server,ga4gh/server,dcolligan/server,adamnovak/server,david4096/ga4gh-server,UMMS-Biocore/ga4gh-server,pcingola/server,srblum/hackathon-server,srblum/server,diekhans/ga4gh-server,jeromekelleher/server,pansapiens/server,pansapiens/server,ohsu-computational-biology/server,dcolligan/server,macieksmuga/server,diekhans/ga4gh-server,david4096/ga4gh-server,saupchurch/server,shajoezhu/server,srblum/server,ga4gh/server,saupchurch/server,ohsu-computational-biology/server,hjellinek/server,david4096/ga4gh-server,hjellinek/server,saupchurch/server,adamnovak/server,shajoezhu/server,diekhans/ga4gh-server,ekalosak/server,pansapiens/server,ekalosak/server,srblum/hackathon-server,jeromekelleher/server,ga4gh/server,pcingola/server,ohsu-computational-biology/server,pcingola/server,adamnovak/server,UMMS-Biocore/ga4gh-server,hjellinek/server,dcolligan/server,srblum/server,srblum/hackathon-server,macieksmuga/server,UMMS-Biocore/ga4gh-server,macieksmuga/server