bug fixes to windowed VC and start/stop/ori_in_vc
bug fixes to windowed VC and start/stop/ori_in_vc

Ensembl/ensembl,danstaines/ensembl,mjg17/ensembl,muffato/ensembl,at7/ensembl,mjg17/ensembl,muffato/ensembl,muffato/ensembl,james-monkeyshines/ensembl,Ensembl/ensembl,james-monkeyshines/ensembl,willmclaren/ensembl,danstaines/ensembl,danstaines/ensembl,mjg17/ensembl,muffato/ensembl,willmclaren/ensembl,james-monkeyshines/ensembl,mjg17/ensembl,james-monkeyshines/ensembl,at7/ensembl,at7/ensembl,at7/ensembl,Ensembl/ensembl,Ensembl/ensembl