Merge pull request #1727 from nakib103/fix_qc_dump

DumpVEP: fix QC step for using non-reference sequence
Ensembl · Jul 25, 2024 · 9ac6dbd · 9ac6dbd
2 parents 89164a3 + 2dd392a
commit 9ac6dbd
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/QCDump.pm b/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/QCDump.pm
@@ -234,7 +234,7 @@ sub check_dirs {
 
   # get slices
   my $sa = $dba->get_SliceAdaptor;
-  my @slices = @{$sa->fetch_all('toplevel')};
+  my @slices = @{$sa->fetch_all('toplevel', undef, 1)};
   push @slices, map {$_->alternate_slice} map {@{$_->get_all_AssemblyExceptionFeatures}} @slices;
   push @slices, @{$sa->fetch_all('lrg', undef, 1, undef, 1)} if $self->param('lrg');