[ENSCORESW-335]. Allowed the input param force_species to populate species....

[ENSCORESW-335]. Allowed the input param force_species to populate species. Does using a hash. Higher up the levels we use a hash map plus decoding aliases so no need to worry about clashes between common and scientific names

modules/Bio/EnsEMBL/Pipeline/FASTA/ReuseSpeciesFactory.pm

@@ -76,6 +76,7 @@ sub param_defaults {
 
 sub fetch_input {
   my ($self) = @_;
+  $self->_add_force_species_to_species();
   $self->SUPER::fetch_input();
   $self->throw("Need to define a release parameter") unless $self->param('release');
   
@@ -90,6 +91,16 @@ sub fetch_input {
   return;
 }
 
+#Allows a user to use '-force_species human' rather than '-force_species human -species human'
+sub _add_force_species_to_species {
+  my ($self) = @_;
+  my $force_species = $self->param('force_species');
+  my $species = $self->param('species');
+  my %final_species = map { $_ => 1 } (@{$force_species}, @{$species});
+  $self->param('species', [keys %final_species]);
+  return;
+}
+
 sub dna_flow {
   my ($self, $dba) = @_;
   my $parent_flow = $self->SUPER::dna_flow($dba);