Index _ | A | B | C | D | E | G | H | I | L | M | N | P | R | S | T _ __init__() (pygrgl.Mutation method) A add_individual_id() (pygrgl.GRG method) add_mutation() (pygrgl.GRG method) add_population() (pygrgl.GRG method) allele (pygrgl.Mutation property) B bp_range (pygrgl.GRG property) C clear_individual_ids() (pygrgl.GRG method) connect() (pygrgl.MutableGRG method) D disconnect() (pygrgl.MutableGRG method) dot_product() (in module pygrgl) E ensure_unique_mutations() (pygrgl.MutableGRG method) G get_bfs_order() (in module pygrgl) get_dfs_order() (in module pygrgl) get_down_edges() (pygrgl.GRG method) get_individual_id() (pygrgl.GRG method) get_mutation_by_id() (pygrgl.GRG method) get_mutation_node_miss() (pygrgl.GRG method) get_mutation_node_pairs() (pygrgl.GRG method) get_mutations_for_node() (pygrgl.GRG method) get_muts_and_miss_for_node() (pygrgl.GRG method) get_node_mutation_miss() (pygrgl.GRG method) get_node_mutation_pairs() (pygrgl.GRG method) get_num_individual_coals() (pygrgl.GRG method) get_population_id() (pygrgl.GRG method) get_populations() (pygrgl.GRG method) get_root_nodes() (pygrgl.GRG method) get_sample_nodes() (pygrgl.GRG method) get_topo_order() (in module pygrgl) get_up_edges() (pygrgl.GRG method) GRG (class in pygrgl) grg_from_trees() (in module pygrgl) grg_to_cyto() (in module pygrgl.display) grg_to_cyto_json() (in module pygrgl) grgl::ApiMisuseFailure (C++ class) grgl::BadInputFileFailure (C++ class) grgl::convertTreeSeqToGRG (C++ function) grgl::DfsPass (C++ enum) grgl::DfsPass::DFS_PASS_BACK_AGAIN (C++ enumerator) grgl::DfsPass::DFS_PASS_NONE (C++ enumerator) grgl::DfsPass::DFS_PASS_THERE (C++ enumerator) grgl::GRG (C++ class) grgl::GRG::addIndividualId (C++ function) grgl::GRG::addMutation (C++ function) grgl::GRG::addPopulation (C++ function) grgl::GRG::clearIndividualIds (C++ function) grgl::GRG::edgesAreOrdered (C++ function) grgl::GRG::getBPRange (C++ function) grgl::GRG::getDownEdges (C++ function) grgl::GRG::getIndividualId (C++ function) grgl::GRG::getMutationsForNode (C++ function) grgl::GRG::getMutationsToNodeOrdered (C++ function) grgl::GRG::getNodesAndMutations (C++ function) grgl::GRG::getNumIndividualCoals (C++ function) grgl::GRG::getPloidy (C++ function) grgl::GRG::getPopulationId (C++ function) grgl::GRG::getPopulations (C++ function) grgl::GRG::getRootNodes (C++ function) grgl::GRG::getSampleNodes (C++ function) grgl::GRG::getSpecifiedBPRange (C++ function) grgl::GRG::getUnmappedMutations (C++ function) grgl::GRG::getUpEdges (C++ function) grgl::GRG::hasIndividualCoals (C++ function) grgl::GRG::hasIndividualIds (C++ function) grgl::GRG::hasMissingData (C++ function) grgl::GRG::hasUpEdges (C++ function) grgl::GRG::isPhased (C++ function) grgl::GRG::isSample (C++ function) grgl::GRG::matMul (C++ function) grgl::GRG::MutAndNode (C++ type) grgl::GRG::mutationsAreOrdered (C++ function) grgl::GRG::mutationsAreUnique (C++ function) grgl::GRG::MutNodeMiss (C++ type) grgl::GRG::NodeAndMut (C++ type) grgl::GRG::NodeAndMutIterator (C++ class) grgl::GRG::NodeAndMutIterator::begin (C++ function) grgl::GRG::NodeAndMutIterator::end (C++ function) grgl::GRG::NodeAndMutIterator::size (C++ function) grgl::GRG::NodeAndMutIterator::VectIter3 (C++ class) grgl::GRG::nodeHasMutations (C++ function) grgl::GRG::NodeMutMiss (C++ type) grgl::GRG::nodesAreOrdered (C++ function) grgl::GRG::numDownEdges (C++ function) grgl::GRG::numEdges (C++ function) grgl::GRG::numNodes (C++ function) grgl::GRG::numUpEdges (C++ function) grgl::GRG::removeMutation (C++ function) grgl::GRG::setNumIndividualCoals (C++ function) grgl::GRG::setNumIndividualCoalsGrow (C++ function) grgl::GRG::setPopulationId (C++ function) grgl::GRG::setSpecifiedBPRange (C++ function) grgl::GRG::sortMutations (C++ function) grgl::GRG::visitBfs (C++ function) grgl::GRG::visitDfs (C++ function) grgl::GRGVisitor (C++ class) grgl::GRGVisitor::visit (C++ function) grgl::MutableGRG (C++ class) grgl::MutableGRG::compact (C++ function) grgl::MutableGRG::connect (C++ function) grgl::MutableGRG::disconnect (C++ function) grgl::MutableGRG::edgesAreOrdered (C++ function) grgl::MutableGRG::ensureUniqueMutations (C++ function) grgl::MutableGRG::getDownEdges (C++ function) grgl::MutableGRG::getNode (C++ function) grgl::MutableGRG::getUpEdges (C++ function) grgl::MutableGRG::hasUpEdges (C++ function) grgl::MutableGRG::makeNode (C++ function) grgl::MutableGRG::merge (C++ function) grgl::MutableGRG::MutableGRG (C++ function) grgl::MutableGRG::nodesAreOrdered (C++ function) grgl::MutableGRG::numDownEdges (C++ function) grgl::MutableGRG::numEdges (C++ function) grgl::MutableGRG::numNodes (C++ function) grgl::MutableGRG::numUpEdges (C++ function) grgl::Mutation (C++ class) grgl::Mutation::alleleStorageString (C++ function) grgl::Mutation::getAltIndex (C++ function) grgl::Mutation::getBothAlleles (C++ function) grgl::Mutation::setAlleleStorageString (C++ function) grgl::readImmutableGrg (C++ function) grgl::readMutableGrg (C++ function) grgl::SerializationFailure (C++ class) grgl::simplifyAndSerialize (C++ function) grgl::TraversalDirection (C++ enum) grgl::TraversalDirection::DIRECTION_DOWN (C++ enumerator) grgl::TraversalDirection::DIRECTION_UP (C++ enumerator) grgl::writeGrg (C++ function) H haploid_shape (pygrgl.GRG property) has_individual_coals (pygrgl.GRG property) has_individual_ids (pygrgl.GRG property) I is_sample() (pygrgl.GRG method) L load_immutable_grg() (in module pygrgl) load_mutable_grg() (in module pygrgl) M make_node() (pygrgl.MutableGRG method) matmul() (in module pygrgl) merge() (pygrgl.MutableGRG method) module pygrgl pygrgl.display MutableGRG (class in pygrgl) Mutation (class in pygrgl) mutations_are_ordered (pygrgl.GRG property) mutations_are_unique() (pygrgl.GRG method) N node_has_mutations() (pygrgl.GRG method) nodes_are_ordered (pygrgl.GRG property) num_down_edges() (pygrgl.GRG method) num_edges (pygrgl.GRG property) num_individuals (pygrgl.GRG property) num_mutations (pygrgl.GRG property) num_nodes (pygrgl.GRG property) num_samples (pygrgl.GRG property) num_up_edges() (pygrgl.GRG method) P ploidy (pygrgl.GRG property) position (pygrgl.Mutation property) pygrgl module pygrgl.display module R ref_allele (pygrgl.Mutation property) remove_mutation() (pygrgl.GRG method) S save_grg() (in module pygrgl) save_subset() (in module pygrgl) set_mutation_by_id() (pygrgl.GRG method) set_num_individual_coals() (pygrgl.GRG method) set_population_id() (pygrgl.GRG method) shape (pygrgl.GRG property) shared_frontier() (in module pygrgl) sort_mutations() (pygrgl.GRG method) specified_bp_range (pygrgl.GRG property) T time (pygrgl.Mutation property) TraversalDirection (class in pygrgl)