diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm index 3f6cf6b1b2b82a85743d07d8c3178af092bc4b07..64fb5603c26d3aff4cc1a43271d64c966218062b 100644 --- a/modules/Bio/EnsEMBL/Mapper.pm +++ b/modules/Bio/EnsEMBL/Mapper.pm @@ -357,10 +357,10 @@ sub map_coordinates { # new mapping Coordinate, the IndelCoordinate. $target_start = $target_coord->{'start'}; $target_end = $target_coord->{'end'}; - + #original coordinates - $ori_start = $self_coord->{'start'}; - $ori_end = $self_coord->{'end'}; + $ori_start = $self_coord->{'start'}; + $ori_end = $self_coord->{'end'}; #create a Gap object my $gap = Bio::EnsEMBL::Mapper::Gap->new( $start, diff --git a/modules/Bio/EnsEMBL/TranscriptMapper.pm b/modules/Bio/EnsEMBL/TranscriptMapper.pm index 1538574680da3b5082849fe5adb03716d3dded96..3def4ab8347fdcd8ccf9cd9dce42000f5ab31118 100644 --- a/modules/Bio/EnsEMBL/TranscriptMapper.pm +++ b/modules/Bio/EnsEMBL/TranscriptMapper.pm @@ -248,7 +248,7 @@ sub _load_mapper { sub cdna2genomic { - my ($self,$start,$end, $include_original_region, $cdna_coding_start) = @_; + my ($self, $start, $end, $include_original_region, $cdna_coding_start) = @_; if( !defined $end ) { throw("Must call with start/end"); @@ -257,7 +257,7 @@ sub cdna2genomic { $cdna_coding_start = defined $cdna_coding_start ? $cdna_coding_start : 1; my $mapper = $self->{'exon_coord_mapper'}; - return $mapper->map_coordinates( 'cdna', $start, $end, 1, "cdna", $include_original_region, $cdna_coding_start); + return $mapper->map_coordinates('cdna', $start, $end, 1, "cdna", $include_original_region, $cdna_coding_start); }