changes just for vega
Created by: ens-st3
(ii) sort_chromosomes can work with non-reference chromosomes (iii) updated allowed_duplicated_regions for pig chr Xs and human GRCh38 (iv) methods to generate sequence alignments
Created by: ens-st3
(ii) sort_chromosomes can work with non-reference chromosomes (iii) updated allowed_duplicated_regions for pig chr Xs and human GRCh38 (iv) methods to generate sequence alignments