Commit 61c95c0b authored by Andy Yates's avatar Andy Yates
Browse files

Merge from HEAD. Deprecating the fetch_nearest_Gene_by_Feature() method. It is...

Merge from HEAD. Deprecating the fetch_nearest_Gene_by_Feature() method. It is unreliable and a replacement is being developed
parent b6b91c04
......@@ -1939,10 +1939,11 @@ sub fetch_all_by_transcript_supporting_evidence {
Arg [1] : Feature object
Example : $genes = $gene_adaptor->fetch_nearest_Gene_by_Feature($feat);
Description: Gets the nearest gene to the feature
Description: DEPRECATED; BE AWARE THE RESULTS OF THIS METHOD ARE UNRELIABLE
ESPECIALLY WRT STRANDED AND STREAM.
Returntype : Listref of Bio::EnsEMBL::Gene, EMPTY list if no nearest
Caller : general
Status : UnStable
Status : DEPRECATED
=cut
......@@ -1950,6 +1951,8 @@ sub fetch_nearest_Gene_by_Feature {
my $self = shift;
my $feat = shift;
deprecate("fetch_nearest_Gene_by_Feature() is a deprecated method. Strand and stream implementations are unreliable. Please use with caution");
my $stranded = shift;
my $stream = shift; # 1 up stream -1 downstream
my @genes;
......
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