From 34b9ecce53cce6a2feed059b4aa4ac96910295cb Mon Sep 17 00:00:00 2001
From: Laurent Gil <lgil@ebi.ac.uk>
Date: Tue, 5 Nov 2013 13:17:07 +0000
Subject: [PATCH] Add an new option in the method
"get_all_StructuralVariationFeatures_by_Study"
---
modules/Bio/EnsEMBL/Slice.pm | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index b93ac2b0ca..dfd1ecac8f 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -2096,12 +2096,16 @@ sub get_all_StructuralVariationFeatures_by_VariationSet {
=head2 get_all_StructuralVariationFeatures_by_Study
Arg [1] : Bio::EnsEMBL:Variation::Study $study
- Arg [2] : (optional) string $dbtype
+ Arg [2] : (optional) int $include_evidence
+ Arg [3] : (optional) string $dbtype
The dbtype of structural variation to obtain (i.e. can be different from the "variation" type).
This assumes that the extra db has been added to the DBAdaptor under this name (using the
DBConnection::add_db_adaptor method).
Description : returns all structural variation features on this slice associated with a
given study.
+ If $include_evidence is set (i.e. $include_evidence=1), structural variation features from
+ both structural variation (SV) and their supporting structural variations (SSV) will be
+ returned. By default, it only returns features from structural variations (SV).
This function will only work correctly if the variation database has been
attached to the core database.
ReturnType : listref of Bio::EnsEMBL::Variation::StructuralVariationFeature
@@ -2114,10 +2118,11 @@ sub get_all_StructuralVariationFeatures_by_VariationSet {
sub get_all_StructuralVariationFeatures_by_Study {
my $self = shift;
my $study = shift;
+ my $include_evidence = shift;
my $dbtype = shift;
if (my $svf_adaptor = $self->_get_StructuralVariationFeatureAdaptor($dbtype)) {
- return $svf_adaptor->fetch_all_by_Slice_Study($self, $study);
+ return $svf_adaptor->fetch_all_by_Slice_Study($self, $study, $include_evidence);
}
return [];
}
--
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