fixed duplicate counting bug, now can be run chromosome by chromosome
fixed duplicate counting bug, now can be run chromosome by chromosome

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