diff --git a/modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm b/modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm index f8203de453e53e4ce0983176827adebd73bdf104..67b757ae69c05a2434d69c4f607a61af3839c50b 100644 --- a/modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm +++ b/modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm @@ -224,7 +224,7 @@ sub _dump_dna { foreach my $s (@non_chromosomes) { $self->_dump_slice($s, $other_serializer, $other_rm_serializer); } - my ($hard_mask_fh, $hard_mask_file) = $self->_convert_softmask_to_hardmask($rm_non_specific_fh); + my ($hard_mask_fh, $hard_mask_file) = $self->_convert_softmask_to_hardmask($rm_non_specific_file); $self->tidy_file_handle( $non_specific_fh, $non_specific_file ); $self->tidy_file_handle( $rm_non_specific_fh, $rm_non_specific_file ); $self->tidy_file_handle( $hard_mask_fh, $hard_mask_file); @@ -244,7 +244,7 @@ sub _dump_dna { $self->_dump_slice($s, $chromo_serializer, $rm_chromo_serializer); - my ($chromo_hard_mask_fh, $chromo_hard_mask_file) = $self->_convert_softmask_to_hardmask($rm_chromo_fh); + my ($chromo_hard_mask_fh, $chromo_hard_mask_file) = $self->_convert_softmask_to_hardmask($rm_chromo_file_name); $self->tidy_file_handle($chromo_fh, $chromo_file_name); $self->tidy_file_handle($rm_chromo_fh, $rm_chromo_file_name);