| add(const Alignment &aln, int min_mapq=0, int min_baseq=0, int trim_ends=0) | vg::Packer | |
| as_edge_table(ostream &out, vector< vg::id_t > node_ids) | vg::Packer | |
| as_quality_table(ostream &out, vector< vg::id_t > node_ids) | vg::Packer | |
| as_table(ostream &out, bool show_edits, vector< vg::id_t > node_ids) | vg::Packer | |
| average_node_quality(size_t i) const | vg::Packer | |
| base_locks | vg::Packer | private |
| bin_for_position(size_t i) const | vg::Packer | private |
| bin_size | vg::Packer | private |
| clear() | vg::Packer | |
| close_edit_tmpfiles(void) | vg::Packer | private |
| collect_coverage(const vector< Packer * > &packers) | vg::Packer | |
| combine_qualities(int map_quality, int base_quality) const | vg::Packer | private |
| compute_quality(const Alignment &aln, size_t position_in_read) const | vg::Packer | private |
| cov_bin_size | vg::Packer | private |
| coverage_at_position(size_t i) const | vg::Packer | |
| coverage_bin_offset(size_t i) const | vg::Packer | private |
| coverage_bin_size(size_t i) const | vg::Packer | private |
| coverage_civ | vg::Packer | private |
| coverage_dynamic | vg::Packer | private |
| coverage_size(void) const | vg::Packer | |
| data_width | vg::Packer | private |
| delim1 | vg::Packer | private |
| delim2 | vg::Packer | private |
| edge_cov_bin_size | vg::Packer | private |
| edge_coverage(Edge &e) const | vg::Packer | |
| edge_coverage(size_t i) const | vg::Packer | |
| edge_coverage_bin_offset(size_t i) const | vg::Packer | private |
| edge_coverage_bin_size(size_t i) const | vg::Packer | private |
| edge_coverage_civ | vg::Packer | private |
| edge_coverage_dynamic | vg::Packer | private |
| edge_index(const Edge &e) const | vg::Packer | |
| edge_locks | vg::Packer | private |
| edge_vector_size(void) const | vg::Packer | |
| edit_count | vg::Packer | private |
| edit_csas | vg::Packer | private |
| edit_length | vg::Packer | private |
| edit_tmpfile_names | vg::Packer | private |
| edit_value(const Edit &edit, bool revcomp) const | vg::Packer | |
| edits_at_position(size_t i) const | vg::Packer | |
| ensure_edit_tmpfiles_open(void) | vg::Packer | private |
| escape_delim(const string &s, char d) const | vg::Packer | private |
| escape_delims(const string &s) const | vg::Packer | private |
| estimate_batch_size(size_t num_threads) | vg::Packer | static |
| estimate_bin_count(size_t num_threads) | vg::Packer | static |
| estimate_data_width(size_t expected_coverage) | vg::Packer | static |
| get_bin_size(void) const | vg::Packer | |
| get_graph() const | vg::Packer | |
| get_n_bins(void) const | vg::Packer | |
| graph | vg::Packer | private |
| has_qualities() const | vg::Packer | |
| increment_coverage(size_t i) | vg::Packer | |
| increment_coverage(size_t i, size_t v) | vg::Packer | |
| increment_edge_coverage(size_t i) | vg::Packer | |
| increment_edge_coverage(size_t i, size_t v) | vg::Packer | |
| increment_node_quality(size_t i, size_t v) | vg::Packer | |
| index_to_node(size_t i) const | vg::Packer | |
| init_coverage_bin(size_t i) | vg::Packer | private |
| init_edge_coverage_bin(size_t i) | vg::Packer | private |
| init_node_quality_bin(size_t i) | vg::Packer | private |
| is_compacted | vg::Packer | private |
| is_dynamic(void) const | vg::Packer | |
| load(istream &in) | vg::Packer | |
| load_from_file(const string &file_name) | vg::Packer | |
| lru_cache_size | vg::Packer | privatestatic |
| make_compact(void) | vg::Packer | |
| make_dynamic(void) | vg::Packer | |
| maximum_quality | vg::Packer | privatestatic |
| merge_from_dynamic(vector< Packer * > &packers) | vg::Packer | |
| merge_from_files(const vector< string > &file_names) | vg::Packer | |
| n_bins | vg::Packer | private |
| node_index(nid_t node_id) const | vg::Packer | |
| node_qual_bin_size | vg::Packer | private |
| node_quality_bin_offset(size_t i) const | vg::Packer | private |
| node_quality_bin_size(size_t i) const | vg::Packer | private |
| node_quality_civ | vg::Packer | private |
| node_quality_dynamic | vg::Packer | private |
| node_quality_locks | vg::Packer | private |
| node_quality_vector_size(void) const | vg::Packer | |
| num_bases_dynamic | vg::Packer | private |
| num_edges_dynamic | vg::Packer | private |
| num_nodes_dynamic | vg::Packer | private |
| Packer(const HandleGraph *graph=nullptr) | vg::Packer | |
| Packer(const HandleGraph *graph, bool record_bases, bool record_edges, bool record_edits, bool record_qualities, size_t bin_size=0, size_t coverage_bins=1, size_t data_width=8) | vg::Packer | |
| pos_key(size_t i) const | vg::Packer | |
| position_in_basis(const Position &pos) const | vg::Packer | |
| quality_cache | vg::Packer | mutableprivate |
| record_bases | vg::Packer | private |
| record_edges | vg::Packer | private |
| record_edits | vg::Packer | private |
| record_qualities | vg::Packer | private |
| remove_edit_tmpfiles(void) | vg::Packer | private |
| save_to_file(const string &file_name) | vg::Packer | |
| serialize(std::ostream &out, sdsl::structure_tree_node *s=NULL, std::string name="") | vg::Packer | |
| show_structure(ostream &out) | vg::Packer | |
| tmpfstream_locks | vg::Packer | private |
| tmpfstreams | vg::Packer | private |
| total_node_quality(size_t i) const | vg::Packer | |
| unescape_delim(const string &s, char d) const | vg::Packer | private |
| unescape_delims(const string &s) const | vg::Packer | private |
| write_edits(vector< ofstream * > &out) const | vg::Packer | |
| write_edits(ostream &out, size_t bin) const | vg::Packer | |
| ~Packer() | vg::Packer | |
