- genogrove::data_type::flanking_query_result (C++ class)
- genogrove::data_type::flanking_query_result::flanking_query_result (C++ function)
- genogrove::data_type::flanking_query_result::get_predecessor (C++ function)
- genogrove::data_type::flanking_query_result::get_successor (C++ function)
- genogrove::data_type::flanking_query_result::set_predecessor (C++ function)
- genogrove::data_type::flanking_query_result::set_successor (C++ function)
- genogrove::data_type::genomic_coordinate (C++ class)
- genogrove::data_type::genomic_coordinate::aggregate (C++ function)
- genogrove::data_type::genomic_coordinate::deserialize (C++ function)
- genogrove::data_type::genomic_coordinate::genomic_coordinate (C++ function), [1]
- genogrove::data_type::genomic_coordinate::get_end (C++ function)
- genogrove::data_type::genomic_coordinate::get_start (C++ function)
- genogrove::data_type::genomic_coordinate::get_strand (C++ function)
- genogrove::data_type::genomic_coordinate::is_interval (C++ member)
- genogrove::data_type::genomic_coordinate::operator< (C++ function)
- genogrove::data_type::genomic_coordinate::operator== (C++ function)
- genogrove::data_type::genomic_coordinate::operator> (C++ function)
- genogrove::data_type::genomic_coordinate::overlaps (C++ function)
- genogrove::data_type::genomic_coordinate::serialize (C++ function)
- genogrove::data_type::genomic_coordinate::set_range (C++ function)
- genogrove::data_type::genomic_coordinate::set_strand (C++ function)
- genogrove::data_type::genomic_coordinate::to_string (C++ function)
- genogrove::data_type::genomic_coordinate::~genomic_coordinate (C++ function)
- genogrove::data_type::interval (C++ class)
- genogrove::data_type::interval::aggregate (C++ function)
- genogrove::data_type::interval::deserialize (C++ function)
- genogrove::data_type::interval::get_end (C++ function)
- genogrove::data_type::interval::get_start (C++ function)
- genogrove::data_type::interval::interval (C++ function), [1]
- genogrove::data_type::interval::INVALID_POSITION (C++ member)
- genogrove::data_type::interval::is_interval (C++ member)
- genogrove::data_type::interval::operator< (C++ function)
- genogrove::data_type::interval::operator== (C++ function)
- genogrove::data_type::interval::operator> (C++ function)
- genogrove::data_type::interval::overlaps (C++ function)
- genogrove::data_type::interval::serialize (C++ function)
- genogrove::data_type::interval::set_range (C++ function)
- genogrove::data_type::interval::to_string (C++ function)
- genogrove::data_type::interval::~interval (C++ function)
- genogrove::data_type::key (C++ class)
- genogrove::data_type::key::deserialize (C++ function)
- genogrove::data_type::key::get_data (C++ function), [1]
- genogrove::data_type::key::get_value (C++ function)
- genogrove::data_type::key::has_data (C++ function)
- genogrove::data_type::key::key (C++ function), [1], [2], [3], [4], [5]
- genogrove::data_type::key::operator< (C++ function)
- genogrove::data_type::key::operator= (C++ function), [1]
- genogrove::data_type::key::operator== (C++ function)
- genogrove::data_type::key::operator> (C++ function)
- genogrove::data_type::key::serialize (C++ function)
- genogrove::data_type::key::set_data (C++ function)
- genogrove::data_type::key::set_value (C++ function)
- genogrove::data_type::key::to_string (C++ function)
- genogrove::data_type::key::~key (C++ function)
- genogrove::data_type::kmer (C++ class)
- genogrove::data_type::kmer::aggregate (C++ function)
- genogrove::data_type::kmer::BASE_MASK (C++ member)
- genogrove::data_type::kmer::decode_base (C++ function)
- genogrove::data_type::kmer::deserialize (C++ function)
- genogrove::data_type::kmer::encode_base (C++ function)
- genogrove::data_type::kmer::get_encoding (C++ function)
- genogrove::data_type::kmer::get_k (C++ function)
- genogrove::data_type::kmer::is_valid (C++ function)
- genogrove::data_type::kmer::kmer (C++ function), [1], [2]
- genogrove::data_type::kmer::max_k (C++ member)
- genogrove::data_type::kmer::operator< (C++ function)
- genogrove::data_type::kmer::operator== (C++ function)
- genogrove::data_type::kmer::operator> (C++ function)
- genogrove::data_type::kmer::overlaps (C++ function)
- genogrove::data_type::kmer::serialize (C++ function)
- genogrove::data_type::kmer::to_string (C++ function)
- genogrove::data_type::kmer::~kmer (C++ function)
- genogrove::data_type::numeric (C++ class)
- genogrove::data_type::numeric::aggregate (C++ function)
- genogrove::data_type::numeric::deserialize (C++ function)
- genogrove::data_type::numeric::get_value (C++ function)
- genogrove::data_type::numeric::numeric (C++ function), [1]
- genogrove::data_type::numeric::operator< (C++ function)
- genogrove::data_type::numeric::operator== (C++ function)
- genogrove::data_type::numeric::operator> (C++ function)
- genogrove::data_type::numeric::overlaps (C++ function)
- genogrove::data_type::numeric::serialize (C++ function)
- genogrove::data_type::numeric::set_value (C++ function)
- genogrove::data_type::numeric::to_string (C++ function)
- genogrove::data_type::numeric::~numeric (C++ function)
- genogrove::data_type::query_result (C++ class)
- genogrove::data_type::query_result::add_key (C++ function)
- genogrove::data_type::query_result::get_keys (C++ function)
- genogrove::data_type::query_result::get_query (C++ function)
- genogrove::data_type::query_result::query_result (C++ function)
- genogrove::data_type::registry (C++ class)
- genogrove::data_type::registry::clear (C++ function)
- genogrove::data_type::registry::contains (C++ function)
- genogrove::data_type::registry::deserialize (C++ function)
- genogrove::data_type::registry::empty (C++ function)
- genogrove::data_type::registry::find (C++ function)
- genogrove::data_type::registry::get (C++ function)
- genogrove::data_type::registry::id_type (C++ type)
- genogrove::data_type::registry::instance (C++ function)
- genogrove::data_type::registry::intern (C++ function), [1]
- genogrove::data_type::registry::key_is_payload (C++ member)
- genogrove::data_type::registry::null_id (C++ member)
- genogrove::data_type::registry::operator= (C++ function), [1]
- genogrove::data_type::registry::registry (C++ function), [1]
- genogrove::data_type::registry::reset (C++ function)
- genogrove::data_type::registry::serialize (C++ function)
- genogrove::data_type::registry::size (C++ function)
- genogrove::data_type::registry::~registry (C++ function)
- genogrove::data_type::serialization_traits (C++ struct)
- genogrove::data_type::serialization_traits::deserialize (C++ function)
- genogrove::data_type::serialization_traits::serialize (C++ function)
- genogrove::data_type::serializer (C++ struct)
- genogrove::data_type::serializer::read (C++ function)
- genogrove::data_type::serializer::write (C++ function)
- genogrove::io::alignment_flags (C++ class)
- genogrove::io::alignment_flags::alignment_flags (C++ function), [1]
- genogrove::io::alignment_flags::has_flag (C++ function)
- genogrove::io::alignment_flags::is_duplicate (C++ function)
- genogrove::io::alignment_flags::is_mate_reverse (C++ function)
- genogrove::io::alignment_flags::is_mate_unmapped (C++ function)
- genogrove::io::alignment_flags::is_paired (C++ function)
- genogrove::io::alignment_flags::is_proper_pair (C++ function)
- genogrove::io::alignment_flags::is_qc_fail (C++ function)
- genogrove::io::alignment_flags::is_read1 (C++ function)
- genogrove::io::alignment_flags::is_read2 (C++ function)
- genogrove::io::alignment_flags::is_reverse (C++ function)
- genogrove::io::alignment_flags::is_secondary (C++ function)
- genogrove::io::alignment_flags::is_supplementary (C++ function)
- genogrove::io::alignment_flags::is_unmapped (C++ function)
- genogrove::io::alignment_flags::value (C++ function)
- genogrove::io::bam_reader (C++ class)
- genogrove::io::bam_reader::bam_reader (C++ function), [1], [2], [3]
- genogrove::io::bam_reader::get_current_line (C++ function)
- genogrove::io::bam_reader::get_error_message (C++ function)
- genogrove::io::bam_reader::get_header (C++ function)
- genogrove::io::bam_reader::get_reference_names (C++ function)
- genogrove::io::bam_reader::has_next (C++ function)
- genogrove::io::bam_reader::operator= (C++ function), [1]
- genogrove::io::bam_reader::read_next (C++ function)
- genogrove::io::bam_reader::~bam_reader (C++ function)
- genogrove::io::bam_reader_options (C++ struct)
- genogrove::io::bam_reader_options::defaults (C++ function)
- genogrove::io::bam_reader_options::high_quality (C++ function)
- genogrove::io::bam_reader_options::include_all (C++ function)
- genogrove::io::bam_reader_options::min_mapq (C++ member)
- genogrove::io::bam_reader_options::primary_only (C++ function)
- genogrove::io::bam_reader_options::skip_duplicates (C++ member)
- genogrove::io::bam_reader_options::skip_qc_fail (C++ member)
- genogrove::io::bam_reader_options::skip_secondary (C++ member)
- genogrove::io::bam_reader_options::skip_supplementary (C++ member)
- genogrove::io::bam_reader_options::skip_unmapped (C++ member)
- genogrove::io::bed_entry (C++ class)
- genogrove::io::bed_entry::bed_entry (C++ function), [1]
- genogrove::io::bed_entry::blocks (C++ member)
- genogrove::io::bed_entry::chrom (C++ member)
- genogrove::io::bed_entry::deserialize (C++ function)
- genogrove::io::bed_entry::end (C++ member)
- genogrove::io::bed_entry::item_rgb (C++ member)
- genogrove::io::bed_entry::name (C++ member)
- genogrove::io::bed_entry::score (C++ member)
- genogrove::io::bed_entry::serialize (C++ function)
- genogrove::io::bed_entry::start (C++ member)
- genogrove::io::bed_entry::strand (C++ member)
- genogrove::io::bed_entry::thickness (C++ member)
- genogrove::io::bed_reader (C++ class)
- genogrove::io::bed_reader::bed_reader (C++ function), [1], [2], [3]
- genogrove::io::bed_reader::get_current_line (C++ function)
- genogrove::io::bed_reader::get_error_message (C++ function)
- genogrove::io::bed_reader::has_next (C++ function)
- genogrove::io::bed_reader::operator= (C++ function), [1]
- genogrove::io::bed_reader::read_next (C++ function)
- genogrove::io::bed_reader::~bed_reader (C++ function)
- genogrove::io::bed_reader_options (C++ struct)
- genogrove::io::bed_reader_options::defaults (C++ function)
- genogrove::io::bed_reader_options::skip_invalid_lines (C++ member)
- genogrove::io::block_info (C++ struct)
- genogrove::io::block_info::block_info (C++ function), [1]
- genogrove::io::block_info::count (C++ member)
- genogrove::io::block_info::deserialize (C++ function)
- genogrove::io::block_info::serialize (C++ function)
- genogrove::io::block_info::sizes (C++ member)
- genogrove::io::block_info::starts (C++ member)
- genogrove::io::cigar_element (C++ struct)
- genogrove::io::cigar_element::cigar_element (C++ function), [1]
- genogrove::io::cigar_element::consumes_query (C++ function)
- genogrove::io::cigar_element::consumes_reference (C++ function)
- genogrove::io::cigar_element::length (C++ member)
- genogrove::io::cigar_element::op (C++ member)
- genogrove::io::cigar_element::to_char (C++ function)
- genogrove::io::cigar_op (C++ enum)
- genogrove::io::cigar_op::DEL (C++ enumerator)
- genogrove::io::cigar_op::HARD_CLIP (C++ enumerator)
- genogrove::io::cigar_op::INS (C++ enumerator)
- genogrove::io::cigar_op::MATCH (C++ enumerator)
|
- genogrove::io::cigar_op::PAD (C++ enumerator)
- genogrove::io::cigar_op::REF_SKIP (C++ enumerator)
- genogrove::io::cigar_op::SEQ_MATCH (C++ enumerator)
- genogrove::io::cigar_op::SEQ_MISMATCH (C++ enumerator)
- genogrove::io::cigar_op::SOFT_CLIP (C++ enumerator)
- genogrove::io::compression_type (C++ enum)
- genogrove::io::compression_type::BZIP2 (C++ enumerator)
- genogrove::io::compression_type::GZIP (C++ enumerator)
- genogrove::io::compression_type::LZ4 (C++ enumerator)
- genogrove::io::compression_type::NONE (C++ enumerator)
- genogrove::io::compression_type::UNKNOWN (C++ enumerator)
- genogrove::io::compression_type::XZ (C++ enumerator)
- genogrove::io::compression_type::ZSTD (C++ enumerator)
- genogrove::io::fasta_entry (C++ struct)
- genogrove::io::fasta_entry::comment (C++ member)
- genogrove::io::fasta_entry::fasta_entry (C++ function), [1]
- genogrove::io::fasta_entry::name (C++ member)
- genogrove::io::fasta_entry::quality (C++ member)
- genogrove::io::fasta_entry::sequence (C++ member)
- genogrove::io::fasta_index (C++ class)
- genogrove::io::fasta_index::fasta_index (C++ function), [1], [2]
- genogrove::io::fasta_index::fetch (C++ function), [1]
- genogrove::io::fasta_index::has_sequence (C++ function)
- genogrove::io::fasta_index::operator= (C++ function), [1]
- genogrove::io::fasta_index::sequence_count (C++ function)
- genogrove::io::fasta_index::sequence_length (C++ function)
- genogrove::io::fasta_index::sequence_name (C++ function)
- genogrove::io::fasta_index::~fasta_index (C++ function)
- genogrove::io::fasta_reader (C++ class)
- genogrove::io::fasta_reader::fasta_reader (C++ function), [1], [2], [3]
- genogrove::io::fasta_reader::get_current_line (C++ function)
- genogrove::io::fasta_reader::get_error_message (C++ function)
- genogrove::io::fasta_reader::has_next (C++ function)
- genogrove::io::fasta_reader::operator= (C++ function), [1]
- genogrove::io::fasta_reader::read_next (C++ function)
- genogrove::io::fasta_reader::~fasta_reader (C++ function)
- genogrove::io::fasta_reader_options (C++ struct)
- genogrove::io::fasta_reader_options::defaults (C++ function)
- genogrove::io::fasta_reader_options::skip_empty_sequences (C++ member)
- genogrove::io::filetype (C++ enum)
- genogrove::io::filetype::BAM (C++ enumerator)
- genogrove::io::filetype::BED (C++ enumerator)
- genogrove::io::filetype::BEDGRAPH (C++ enumerator)
- genogrove::io::filetype::FASTA (C++ enumerator)
- genogrove::io::filetype::FASTQ (C++ enumerator)
- genogrove::io::filetype::GFF (C++ enumerator)
- genogrove::io::filetype::GG (C++ enumerator)
- genogrove::io::filetype::GTF (C++ enumerator)
- genogrove::io::filetype::SAM (C++ enumerator)
- genogrove::io::filetype::UNKNOWN (C++ enumerator)
- genogrove::io::filetype::VCF (C++ enumerator)
- genogrove::io::filetype_detector (C++ class)
- genogrove::io::filetype_detector::detect_filetype (C++ function)
- genogrove::io::gff_entry (C++ struct)
- genogrove::io::gff_entry::attributes (C++ member)
- genogrove::io::gff_entry::end (C++ member)
- genogrove::io::gff_entry::format (C++ member)
- genogrove::io::gff_entry::get_attribute (C++ function)
- genogrove::io::gff_entry::get_exon_number (C++ function)
- genogrove::io::gff_entry::get_gene_biotype (C++ function)
- genogrove::io::gff_entry::get_gene_id (C++ function)
- genogrove::io::gff_entry::get_gene_name (C++ function)
- genogrove::io::gff_entry::get_transcript_id (C++ function)
- genogrove::io::gff_entry::gff_entry (C++ function), [1]
- genogrove::io::gff_entry::is_gff3 (C++ function)
- genogrove::io::gff_entry::is_gtf (C++ function)
- genogrove::io::gff_entry::phase (C++ member)
- genogrove::io::gff_entry::score (C++ member)
- genogrove::io::gff_entry::seqid (C++ member)
- genogrove::io::gff_entry::source (C++ member)
- genogrove::io::gff_entry::start (C++ member)
- genogrove::io::gff_entry::strand (C++ member)
- genogrove::io::gff_entry::type (C++ member)
- genogrove::io::gff_format (C++ enum)
- genogrove::io::gff_format::GFF3 (C++ enumerator)
- genogrove::io::gff_format::GTF (C++ enumerator)
- genogrove::io::gff_format::UNKNOWN (C++ enumerator)
- genogrove::io::gff_reader (C++ class)
- genogrove::io::gff_reader::get_current_line (C++ function)
- genogrove::io::gff_reader::get_error_message (C++ function)
- genogrove::io::gff_reader::gff_reader (C++ function), [1], [2], [3]
- genogrove::io::gff_reader::has_next (C++ function)
- genogrove::io::gff_reader::operator= (C++ function), [1]
- genogrove::io::gff_reader::read_next (C++ function)
- genogrove::io::gff_reader::~gff_reader (C++ function)
- genogrove::io::gff_reader_options (C++ struct)
- genogrove::io::gff_reader_options::defaults (C++ function)
- genogrove::io::gff_reader_options::skip_invalid_lines (C++ member)
- genogrove::io::gff_reader_options::validate_gtf (C++ member)
- genogrove::io::mate_info (C++ struct)
- genogrove::io::mate_info::chrom (C++ member)
- genogrove::io::mate_info::insert_size (C++ member)
- genogrove::io::mate_info::mate_info (C++ function), [1]
- genogrove::io::mate_info::position (C++ member)
- genogrove::io::rgb_color (C++ struct)
- genogrove::io::rgb_color::blue (C++ member)
- genogrove::io::rgb_color::green (C++ member)
- genogrove::io::rgb_color::red (C++ member)
- genogrove::io::rgb_color::rgb_color (C++ function), [1]
- genogrove::io::sam_entry (C++ struct)
- genogrove::io::sam_entry::chrom (C++ member)
- genogrove::io::sam_entry::cigar (C++ member)
- genogrove::io::sam_entry::cigar_string_repr (C++ function)
- genogrove::io::sam_entry::consumes_reference (C++ function)
- genogrove::io::sam_entry::end (C++ member)
- genogrove::io::sam_entry::flags (C++ member)
- genogrove::io::sam_entry::get_strand (C++ function)
- genogrove::io::sam_entry::is_mapped (C++ function)
- genogrove::io::sam_entry::is_primary (C++ function)
- genogrove::io::sam_entry::mapq (C++ member)
- genogrove::io::sam_entry::mate (C++ member)
- genogrove::io::sam_entry::qname (C++ member)
- genogrove::io::sam_entry::quality (C++ member)
- genogrove::io::sam_entry::sam_entry (C++ function)
- genogrove::io::sam_entry::sequence (C++ member)
- genogrove::io::sam_entry::start (C++ member)
- genogrove::io::sam_entry::tags (C++ member)
- genogrove::io::sam_flags (C++ struct)
- genogrove::io::sam_flags::DUPLICATE (C++ member)
- genogrove::io::sam_flags::MATE_REVERSE (C++ member)
- genogrove::io::sam_flags::MATE_UNMAPPED (C++ member)
- genogrove::io::sam_flags::PAIRED (C++ member)
- genogrove::io::sam_flags::PROPER_PAIR (C++ member)
- genogrove::io::sam_flags::QCFAIL (C++ member)
- genogrove::io::sam_flags::READ1 (C++ member)
- genogrove::io::sam_flags::READ2 (C++ member)
- genogrove::io::sam_flags::REVERSE (C++ member)
- genogrove::io::sam_flags::SECONDARY (C++ member)
- genogrove::io::sam_flags::SUPPLEMENTARY (C++ member)
- genogrove::io::sam_flags::UNMAPPED (C++ member)
- genogrove::io::sam_tag (C++ struct)
- genogrove::io::sam_tag::key (C++ member)
- genogrove::io::sam_tag::sam_tag (C++ function), [1]
- genogrove::io::sam_tag::value (C++ member)
- genogrove::io::thick_info (C++ struct)
- genogrove::io::thick_info::end (C++ member)
- genogrove::io::thick_info::start (C++ member)
- genogrove::io::thick_info::thick_info (C++ function), [1]
- genogrove::structure::bulk_t (C++ struct)
- genogrove::structure::graph_overlay (C++ class)
- genogrove::structure::graph_overlay::add_edge (C++ function), [1]
- genogrove::structure::graph_overlay::clear (C++ function)
- genogrove::structure::graph_overlay::edge (C++ struct)
- genogrove::structure::graph_overlay::edge::edge (C++ function), [1]
- genogrove::structure::graph_overlay::edge::metadata (C++ member)
- genogrove::structure::graph_overlay::edge::target (C++ member)
- genogrove::structure::graph_overlay::edge_count (C++ function)
- genogrove::structure::graph_overlay::empty (C++ function)
- genogrove::structure::graph_overlay::get_edge_list (C++ function)
- genogrove::structure::graph_overlay::get_edges (C++ function)
- genogrove::structure::graph_overlay::get_neighbors (C++ function)
- genogrove::structure::graph_overlay::get_neighbors_if (C++ function)
- genogrove::structure::graph_overlay::graph_overlay (C++ function)
- genogrove::structure::graph_overlay::has_edge (C++ function)
- genogrove::structure::graph_overlay::out_degree (C++ function)
- genogrove::structure::graph_overlay::remap_keys (C++ function)
- genogrove::structure::graph_overlay::remove_all_edges (C++ function)
- genogrove::structure::graph_overlay::remove_edge (C++ function)
- genogrove::structure::graph_overlay::remove_edges_from (C++ function)
- genogrove::structure::graph_overlay::remove_edges_if (C++ function)
- genogrove::structure::graph_overlay::remove_edges_to (C++ function)
- genogrove::structure::graph_overlay::vertex_count_with_edges (C++ function)
- genogrove::structure::grove (C++ class)
- genogrove::structure::grove::get_order (C++ function)
- genogrove::structure::grove::get_rightmost_node (C++ function)
- genogrove::structure::grove::get_root_nodes (C++ function)
- genogrove::structure::grove::grove (C++ function), [1], [2], [3]
- genogrove::structure::grove::operator= (C++ function), [1]
- genogrove::structure::grove::~grove (C++ function)
- genogrove::structure::node (C++ class)
- genogrove::structure::node::add_child (C++ function)
- genogrove::structure::node::calc_keys_aggregate (C++ function)
- genogrove::structure::node::calc_subtree_range (C++ function)
- genogrove::structure::node::deserialize (C++ function)
- genogrove::structure::node::get_child (C++ function), [1]
- genogrove::structure::node::get_children (C++ function), [1]
- genogrove::structure::node::get_is_leaf (C++ function)
- genogrove::structure::node::get_keys (C++ function), [1]
- genogrove::structure::node::get_next (C++ function)
- genogrove::structure::node::get_order (C++ function)
- genogrove::structure::node::get_parent (C++ function)
- genogrove::structure::node::insert_key_ptr (C++ function), [1]
- genogrove::structure::node::node (C++ function), [1], [2]
- genogrove::structure::node::operator= (C++ function), [1]
- genogrove::structure::node::print_keys (C++ function)
- genogrove::structure::node::serialize (C++ function)
- genogrove::structure::node::set_is_leaf (C++ function)
- genogrove::structure::node::set_next (C++ function)
- genogrove::structure::node::set_parent (C++ function)
- genogrove::structure::node::~node (C++ function)
- genogrove::structure::sorted_t (C++ struct)
- genogrove::structure::string_hash (C++ struct)
- genogrove::structure::string_hash::is_transparent (C++ type)
- genogrove::structure::string_hash::operator() (C++ function)
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