There are some circumstances where exon coordinate recalculation is not the...

There are some circumstances where exon coordinate recalculation is not the right thing to do and the user has them correctly set out (ori spanning transcription models). Rather than tie this directly into the coordinate recalculations we are allowing skipping this procedure. It is up to the user to do the right thing if using this module. It also does not alter any existing functionality

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -1141,6 +1141,8 @@ sub store_alt_alleles {
                The gene to store in the database
   Arg [2]    : ignore_release in xrefs [default 1] set to 0 to use release info 
                in external database references
+  Arg [3]    : prevent coordinate recalculation if you are persisting 
+               transcripts with this gene
   Example    : $gene_adaptor->store($gene);
   Description: Stores a gene in the database.
   Returntype : the database identifier (dbID) of the newly stored gene
@@ -1152,7 +1154,7 @@ sub store_alt_alleles {
 =cut
 
 sub store {
-  my ($self, $gene, $ignore_release) = @_;
+  my ($self, $gene, $ignore_release, $skip_recalculating_coordinates) = @_;
 
   if (!ref $gene || !$gene->isa('Bio::EnsEMBL::Gene')) {
 	throw("Must store a gene object, not a $gene");
@@ -1281,7 +1283,7 @@ sub store {
 	my $new = $transcripts->[$i];
 	my $old = $original_transcripts->[$i];
 
-	$transcript_adaptor->store($new, $gene_dbID, $analysis_id);
+	$transcript_adaptor->store($new, $gene_dbID, $analysis_id, $skip_recalculating_coordinates);
 
 	if (!defined($new_canonical_transcript_id)
 		&& $new->is_canonical())

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -749,6 +749,8 @@ sub fetch_all_by_biotype {
                backward compatibility only and used to fall back to the gene
                analysis_id if no analysis object is attached to the transcript
                (which you should do for new code).
+  Arg [4]    : prevent coordinate recalculation if you are persisting 
+               transcripts with this gene
   Example    : $transID = $tr_adaptor->store($transcript, $gene->dbID);
   Description: Stores a transcript in the database and returns the new
                internal identifier for the stored transcript.
@@ -760,7 +762,7 @@ sub fetch_all_by_biotype {
 =cut
 
 sub store {
-  my ( $self, $transcript, $gene_dbID, $analysis_id ) = @_;
+  my ( $self, $transcript, $gene_dbID, $analysis_id, $skip_recalculating_coordinates ) = @_;
 
   if (    !ref($transcript)
        || !$transcript->isa('Bio::EnsEMBL::Transcript') )
@@ -775,7 +777,12 @@ sub store {
   }
 
   # Force lazy-loading of exons and ensure coords are correct.
-  $transcript->recalculate_coordinates();
+  # If we have been told not to do this then skip doing this
+  # and we assume the user knows what they are doing. You have been
+  # warned
+  if(! $skip_recalculating_coordinates) {
+    $transcript->recalculate_coordinates();
+  }
 
   my $is_current = ( defined( $transcript->is_current() )
                      ? $transcript->is_current()