Commit 9b6125e1 authored by Andy Yates's avatar Andy Yates
Browse files

Switching the logic around here. It makes sense if we are trying to read from...

Switching the logic around here. It makes sense if we are trying to read from a file which hasn't closed yet then maybe we're not going to get all the data into the file.
parent cf4d7a14
......@@ -224,9 +224,10 @@ 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_file);
$self->tidy_file_handle( $non_specific_fh, $non_specific_file );
$self->tidy_file_handle( $rm_non_specific_fh, $rm_non_specific_file );
my ($hard_mask_fh, $hard_mask_file) = $self->_convert_softmask_to_hardmask($rm_non_specific_file);
$self->tidy_file_handle( $hard_mask_fh, $hard_mask_file);
$self->info('Dumped non-chromosomes');
}
......@@ -244,10 +245,10 @@ 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_file_name);
$self->tidy_file_handle($chromo_fh, $chromo_file_name);
$self->tidy_file_handle($rm_chromo_fh, $rm_chromo_file_name);
my ($chromo_hard_mask_fh, $chromo_hard_mask_file) = $self->_convert_softmask_to_hardmask($rm_chromo_file_name);
$self->tidy_file_handle($chromo_hard_mask_fh, $chromo_hard_mask_file);
}
$self->info("Dumped chromosomes");
......
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