From e5fa1001559c2ded9b8efc97d7b7d2721ff0d9bf Mon Sep 17 00:00:00 2001
From: at7 <anja@ebi.ac.uk>
Date: Wed, 20 Nov 2019 16:54:51 +0000
Subject: [PATCH] remove deprecated status for get_all__VariationFeatures
methods
---
modules/Bio/EnsEMBL/Slice.pm | 8 --------
1 file changed, 8 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index d4c94eb210..d786e6b79b 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -1850,7 +1850,6 @@ sub get_all_VariationFeatures{
}
=head2 get_all_somatic_VariationFeatures
- Deprecated. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_by_Slice_SO_terms instead.
Args [1] : (optional) ArrayRef $so_terms
SequenceOntology terms to limit the fetch to
Args [2] : (optional) boolean $without_children
@@ -1877,7 +1876,6 @@ sub get_all_VariationFeatures{
sub get_all_somatic_VariationFeatures {
my ($self, $so_terms, $without_children, $included_so, $dbtype) = @_;
- deprecate('get_all_somatic_VariationFeatures is deprecated and will be removed in e95. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_by_Slice_SO_terms instead.');
if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) {
return $vf_adaptor->fetch_all_somatic_by_Slice_SO_terms($self, $so_terms, $without_children, $included_so);
}
@@ -1885,7 +1883,6 @@ sub get_all_somatic_VariationFeatures {
}
=head2 get_all_somatic_VariationFeatures_by_source
- Deprecated. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_by_Slice_Source instead.
Arg [1] : string $source [optional]
The name of the source to query for
Arg [2] : string $dbtype [optional]
@@ -1903,7 +1900,6 @@ sub get_all_somatic_VariationFeatures {
sub get_all_somatic_VariationFeatures_by_source {
my ($self, $source, $dbtype) = @_;
- deprecate('get_all_somatic_VariationFeatures_by_source is deprecated and will be removed in e95. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_by_Slice_Source instead.');
my $constraint = (defined($source)) ? " s.name='$source' " : undef;
if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) {
return $vf_adaptor->fetch_all_somatic_by_Slice_constraint($self, $constraint);
@@ -1912,7 +1908,6 @@ sub get_all_somatic_VariationFeatures_by_source {
}
=head2 get_all_somatic_VariationFeatures_with_phenotype
- Deprecated. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_with_phenotype_by_Slice instead.
Arg [1] : $variation_feature_source [optional]
Arg [2] : $phenotype_source [optional]
Arg [3] : $phenotype_name [optional]
@@ -1930,7 +1925,6 @@ sub get_all_somatic_VariationFeatures_by_source {
sub get_all_somatic_VariationFeatures_with_phenotype {
my ($self, $source, $p_source, $phenotype, $dbtype) = @_;
- deprecate('get_all_somatic_VariationFeatures_with_phenotype is deprecated and will be removed in e95. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_with_phenotype_by_Slice instead.');
if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) {
return $vf_adaptor->fetch_all_somatic_with_phenotype_by_Slice($self, $source, $p_source, $phenotype);
}
@@ -1939,7 +1933,6 @@ sub get_all_somatic_VariationFeatures_with_phenotype {
=head2 get_all_VariationFeatures_by_Population
- Deprecated. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Slice_Population instead.
Arg [1] : Bio::EnsEMBL::Variation::Population
Arg [2] : $minimum_frequency [optional]
Arg [3] : string $dbtype [optional]
@@ -1961,7 +1954,6 @@ sub get_all_somatic_VariationFeatures_with_phenotype {
sub get_all_VariationFeatures_by_Population {
my ($self, $minimum_frequency, $dbtype) = @_;
- deprecate('get_all_VariationFeatures_by_Population is deprecated and will be removed in e95. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Slice_Population instead.');
if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) {
return $vf_adaptor->fetch_all_by_Slice_Population($self, $minimum_frequency);
}
--
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