Change the fetching of repeat masked sequence. At the moment the subseq method of the Bio::EnsEMBL::RepeatMaskedSlice gets the RepeatFeatures for the whole slice. This script was using a slice for the whole chromosome and using the subseq method for getting the fragments which resulted in getting all the RepeatFeatures for every single fragment.
Change the fetching of repeat masked sequence. At the moment the subseq method of the Bio::EnsEMBL::RepeatMaskedSlice gets the RepeatFeatures for the whole slice. This script was using a slice for the whole chromosome and using the subseq method for getting the fragments which resulted in getting all the RepeatFeatures for every single fragment.

Change $SliceAdaptor to $slice_adaptor and $seq to $this_slice.

ckongEbi/ensembl-compara,etapanari/ensembl-compara,Ensembl/ensembl-compara,etapanari/ensembl-compara,etapanari/ensembl-compara,kumarsaurabh20/ensembl-compara,danstaines/ensembl-compara,danstaines/ensembl-compara,Ensembl/ensembl-compara,kumarsaurabh20/ensembl-compara,Ensembl/ensembl-compara,ckongEbi/ensembl-compara,Ensembl/ensembl-compara,danstaines/ensembl-compara,dbolser-ebi/ensembl-compara,etapanari/ensembl-compara,ckongEbi/ensembl-compara,Ensembl/ensembl-compara,dbolser-ebi/ensembl-compara,kumarsaurabh20/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,dbolser-ebi/ensembl-compara,kumarsaurabh20/ensembl-compara,danstaines/ensembl-compara,danstaines/ensembl-compara