Commit 9755392d authored by Steve Trevanion's avatar Steve Trevanion
Browse files

get non reference slices when using split_chromosomes_by_size in the density scripts

parent 877b760f
...@@ -1131,6 +1131,7 @@ sub split_chromosomes_by_size { ...@@ -1131,6 +1131,7 @@ sub split_chromosomes_by_size {
my $cutoff = shift || 5000000; my $cutoff = shift || 5000000;
my $dup = shift || 0; my $dup = shift || 0;
my $cs_version = shift; my $cs_version = shift;
my $include_non_reference = 1; #get non reference slices
my $slice_adaptor = $self->dba->get_SliceAdaptor; my $slice_adaptor = $self->dba->get_SliceAdaptor;
my $top_slices; my $top_slices;
if ($self->param('chromosomes')) { if ($self->param('chromosomes')) {
...@@ -1138,7 +1139,7 @@ sub split_chromosomes_by_size { ...@@ -1138,7 +1139,7 @@ sub split_chromosomes_by_size {
push @{ $top_slices }, $slice_adaptor->fetch_by_region('chromosome', $chr); push @{ $top_slices }, $slice_adaptor->fetch_by_region('chromosome', $chr);
} }
} else { } else {
$top_slices = $slice_adaptor->fetch_all('chromosome',$cs_version,0,$dup); $top_slices = $slice_adaptor->fetch_all('chromosome',$cs_version,$include_non_reference,$dup);
} }
my ($big_chr, $small_chr, $min_big_chr, $min_small_chr); my ($big_chr, $small_chr, $min_big_chr, $min_small_chr);
......
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