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Ensembl Variation Deprecated Methods

This file contains the list of methods deprecated in the Ensembl Variation API. A method is deprecated when it is not functional anymore (schema/data change) or has been replaced by a better one. Backwards compatibility is provided whenever possible. When a method is deprecated, a deprecation warning is thrown whenever the method is used. The warning also contains instructions on replacing the deprecated method and when it will be removed. A year after deprecation (4 Ensembl releases), the method is removed from the API.

Removed in Ensembl Release 101 (deprecated from Ensembl Release 95)

  • Bio::EnsEMBL::Variation::VariationFeature::add_consequence_type()
  • Bio::EnsEMBL::Variation::VariationFeature::get_consequence_type()

Removed in Ensembl Release 100 (deprecated from Ensembl Release 96)

  • Bio::EnsEMBL::Variation::ancestral_allele()

Removed in Ensembl Release 98

  • Bio::EnsEMBL::Variation::OverlapConsequence::get_all_parent_SO_terms()

Removed in Ensembl Release 91 (deprecated from Ensembl Release 87)

  • Bio::EnsEMBL::Variation::Utils::Sequence::array_to_bitval()
  • Bio::EnsEMBL::Variation::Utils::Sequence::bitval_to_array()

Removed in Ensembl Release 89 (deprecated from Ensembl Release 85)

  • Bio::EnsEMBL::Variation::DBSQL::PopulationAdaptor::fetch_tagged_Population()
  • Bio::EnsEMBL::Variation::DBSQL::PopulationAdaptor::fetch_tag_Population()
  • Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_tagged_by_VariationFeature()
  • Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_tags_by_VariationFeature()
  • Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_tags_and_tagged_by_VariationFeature()
  • Bio::EnsEMBL::Variation::VariationFeature::is_tag()
  • Bio::EnsEMBL::Variation::VariationFeature::is_tagged()
  • Bio::EnsEMBL::Variation::VariationFeature::get_all_tag_VariationFeatures()
  • Bio::EnsEMBL::Variation::VariationFeature::get_all_tagged_VariationFeatures()
  • Bio::EnsEMBL::Variation::VariationFeature::get_all_tag_and_tagged_VariationFeatures()

Removed in Ensembl Release 87 (deprecated from Ensembl Release 83)

Deprecated methods related to the validation_status data:####

  • Bio::EnsEMBL::Variation::Variation::get_all_validation_states()
  • Bio::EnsEMBL::Variation::Variation::add_validation_state()
  • Bio::EnsEMBL::Variation::VariationFeature::get_all_validation_states()
  • Bio::EnsEMBL::Variation::VariationFeature::add_validation_state()
  • Bio::EnsEMBL::Variation::Utils::Sequence::get_all_validation_states()
  • Bio::EnsEMBL::Variation::Utils::Sequence::get_validation_code()
  • Bio::EnsEMBL::Variation::Utils::Sequence::add_validation_state()

Deprecated method source_object() in various objects:####

  • Bio::EnsEMBL::Variation::Variation::source_object()
  • Bio::EnsEMBL::Variation::VariationFeature::source_object()
  • Bio::EnsEMBL::Variation::PhenotypeFeature::source_object()
  • Bio::EnsEMBL::Variation::BaseStructuralVariation::source_object()
  • Bio::EnsEMBL::Variation::StructuralVariationFeature::source_object()
  • Bio::EnsEMBL::Variation::Study::source_object()