chromosome names now come from command line, and there are no intermediate files anymore
chromosome names now come from command line, and there are no intermediate
files anymore

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