Commit c8c66c95 authored by Ian Longden's avatar Ian Longden
Browse files

phase not set yet so need to pass it

parent 656baf98
......@@ -88,8 +88,6 @@ sub new {
throw("Transcript argument is required.");
}
# Create a cdna <-> genomic mapper and load it with exon coords
my $mapper = _load_mapper($transcript);
my $exons = $transcript->get_all_Exons();
my $start_phase;
......@@ -99,6 +97,9 @@ sub new {
$start_phase = -1;
}
# Create a cdna <-> genomic mapper and load it with exon coords
my $mapper = _load_mapper($transcript,$start_phase);
my $self = bless({'exon_coord_mapper' => $mapper,
'start_phase' => $start_phase,
'cdna_coding_start' => $transcript->cdna_coding_start(),
......@@ -122,6 +123,7 @@ sub new {
sub _load_mapper {
my $transcript = shift;
my $start_phase = shift;
my $mapper = Bio::EnsEMBL::Mapper->new( 'cdna', 'genomic');
......@@ -138,7 +140,6 @@ sub _load_mapper {
my $cdna_start = undef;
# Take possible N-padding at beginning of CDS into account.
my $start_phase = $self->{'start_phase'};
my $cdna_end = ( $start_phase > 0 ) ? $start_phase : 0;;
foreach my $ex (@{$transcript->get_all_Exons}) {
......
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