diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm index 0592367991ff071366ce2d568ec21df5f92f69d1..4c82faa8610ddda17bac6c841bee85edff559ead 100644 --- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm +++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm @@ -429,11 +429,11 @@ sub fetch_by_chr_name{ =cut sub fetch_by_mapfrag{ - my ($self,$mapfrag,$flag,$size) = @_; + my ($self,$mymapfrag,$flag,$size) = @_; $flag ||= 'fixed-width'; # alt.. 'context' $size ||= $flag eq 'fixed-width' ? 200000 : 0; - unless( $mapfrag ) { + unless( $mymapfrag ) { $self->throw("Mapfrag name argument required"); } @@ -441,7 +441,7 @@ sub fetch_by_mapfrag{ #set the end of the slice to the end of the chromosome my $ca = $self->db()->get_MapFragAdaptor(); - my $mapfrag = $ca->fetch_by_synonym($mapfrag); + my $mapfrag = $ca->fetch_by_synonym($mymapfrag); return undef unless defined $mapfrag; if( $flag eq 'fixed-width' ) {