diff --git a/modules/Bio/EnsEMBL/IdMapping/Cache.pm b/modules/Bio/EnsEMBL/IdMapping/Cache.pm index 317fdfe39f38df0dd59b018b06b1ced403d8b016..e6cb1cc2533360ec068f5219edeb33b75837a821 100644 --- a/modules/Bio/EnsEMBL/IdMapping/Cache.pm +++ b/modules/Bio/EnsEMBL/IdMapping/Cache.pm @@ -188,6 +188,17 @@ sub build_cache_by_slice { sub build_cache_all { my $self = shift; +<<<<<<< Cache.pm + my $dbtype = shift; + + my $dba = $self->get_DBAdaptor($dbtype); + my $ga = $dba->get_GeneAdaptor; + + my $genes = $ga->fetch_all; + + # find common coord_system + my $common_cs_found = $self->find_common_coord_systems; +======= my $dbtype = shift; my $dba = $self->get_DBAdaptor($dbtype); @@ -203,12 +214,26 @@ sub build_cache_all { my $type = "$dbtype.ALL"; my $num_genes = $self->build_cache_from_genes($type, $genes, 'CHECK'); undef $genes; +>>>>>>> 1.16 +<<<<<<< Cache.pm + # Build cache. Setting $need_project to 'CHECK' will cause + # build_cache_from_genes() to check the coordinate system for each gene. + my $type = "$dbtype.ALL"; + my $num_genes = $self->build_cache_from_genes($type, $genes, 'CHECK'); + undef $genes; +======= # write cache to file, then flush cache to reclaim memory my $size = $self->write_all_to_file($type); +>>>>>>> 1.16 +<<<<<<< Cache.pm + # write cache to file, then flush cache to reclaim memory + my $size = $self->write_all_to_file($type); +======= # set cache method (required for loading cache later) $self->cache_method('ALL'); +>>>>>>> 1.16 return $num_genes, $size; }