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vg
tools for working with variation graphs
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This is the complete list of members for vg::LegacyCaller, including all inherited members.
| add_allele_path_to_info(const HandleGraph *graph, vcflib::Variant &v, int allele, const Traversal &trav, bool reversed, bool one_based) const | vg::VCFOutputCaller | protected |
| add_allele_path_to_info(vcflib::Variant &v, int allele, const SnarlTraversal &trav, bool reversed, bool one_based) const | vg::VCFOutputCaller | protected |
| add_variant(vcflib::Variant &var) const | vg::VCFOutputCaller | |
| break_chain(const HandleGraph &graph, const Chain &chain, size_t max_edges, size_t max_trivial) | vg::GraphCaller | protected |
| call_snarl(const Snarl &snarl) | vg::LegacyCaller | virtual |
| call_top_level_chains(const HandleGraph &graph, size_t max_edges, size_t max_trivial, RecurseType recurise_type=RecurseOnFail) | vg::GraphCaller | virtual |
| call_top_level_snarls(const HandleGraph &graph, RecurseType recurse_type=RecurseOnFail) | vg::GraphCaller | virtual |
| emit_variant(const PathPositionHandleGraph &graph, SnarlCaller &snarl_caller, const Snarl &snarl, const vector< SnarlTraversal > &called_traversals, const vector< int > &genotype, int ref_trav_idx, const unique_ptr< SnarlCaller::CallInfo > &call_info, const string &ref_path_name, int ref_offset, bool genotype_snarls, int ploidy, function< string(const vector< SnarlTraversal > &, const vector< int > &, int, int, int)> trav_to_string=nullptr) | vg::VCFOutputCaller | protected |
| find_index(const Snarl &snarl, const vector< PathIndex * > path_indexes) const | vg::LegacyCaller | protected |
| flatten_common_allele_ends(vcflib::Variant &variant, bool backward, size_t len_override) const | vg::VCFOutputCaller | protected |
| get_ref_interval(const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name) const | vg::VCFOutputCaller | protected |
| get_ref_position(const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name, int64_t ref_path_offset) const | vg::VCFOutputCaller | protected |
| get_reference_traversal(const Snarl &snarl, TraversalFinder &trav_finder) const | vg::LegacyCaller | protected |
| graph | vg::LegacyCaller | protected |
| GraphCaller(SnarlCaller &snarl_caller, SnarlManager &snarl_manager) | vg::GraphCaller | |
| include_nested | vg::VCFOutputCaller | protected |
| is_traversable(const Snarl &snarl) | vg::LegacyCaller | protected |
| is_vg | vg::LegacyCaller | protected |
| LegacyCaller(const PathPositionHandleGraph &graph, SupportBasedSnarlCaller &snarl_caller, SnarlManager &snarl_manager, const string &sample_name, const vector< string > &ref_paths={}, const vector< size_t > &ref_path_offsets={}, const vector< int > &ref_path_ploidies={}) | vg::LegacyCaller | |
| max_bubble_paths | vg::LegacyCaller | protected |
| max_search_depth | vg::LegacyCaller | protected |
| max_search_width | vg::LegacyCaller | protected |
| max_uncalled_alleles | vg::VCFOutputCaller | protected |
| max_vcf_line_length | vg::VCFOutputCaller | protectedstatic |
| output_variants | vg::VCFOutputCaller | mutableprotected |
| output_vcf | vg::VCFOutputCaller | mutableprotected |
| path_indexes | vg::LegacyCaller | protected |
| print_snarl(const HandleGraph *grpah, const handle_t &snarl_start, const handle_t &snarl_end, bool in_brackets=false) const | vg::VCFOutputCaller | protected |
| print_snarl(const Snarl &snarl, bool in_brackets=false) const | vg::VCFOutputCaller | protected |
| re_genotype(const Snarl &snarl, TraversalFinder &trav_finder, const vector< SnarlTraversal > &in_traversals, const vector< int > &in_genotype, int ploidy, const string &ref_path_name, pair< size_t, size_t > ref_interval) const | vg::LegacyCaller | protected |
| RecurseAlways enum value | vg::GraphCaller | |
| RecurseNever enum value | vg::GraphCaller | |
| RecurseOnFail enum value | vg::GraphCaller | |
| RecurseType enum name | vg::GraphCaller | |
| ref_offsets | vg::LegacyCaller | protected |
| ref_paths | vg::LegacyCaller | protected |
| ref_ploidies | vg::LegacyCaller | protected |
| sample_name | vg::VCFOutputCaller | protected |
| scan_snarl(const string &allele_string, function< void(const string &, Snarl &)> callback) const | vg::VCFOutputCaller | protected |
| set_nested(bool nested) | vg::VCFOutputCaller | |
| set_show_progress(bool show_progress) | vg::GraphCaller | |
| set_translation(const unordered_map< nid_t, pair< string, size_t >> *translation) | vg::VCFOutputCaller | |
| show_progress | vg::GraphCaller | protected |
| snarl_caller | vg::GraphCaller | protected |
| snarl_manager | vg::GraphCaller | protected |
| top_down_genotype(const Snarl &snarl, TraversalFinder &trav_finder, int ploidy, const string &ref_path_name, pair< size_t, size_t > ref_interval) const | vg::LegacyCaller | protected |
| translation | vg::VCFOutputCaller | protected |
| trav_string(const HandleGraph &graph, const SnarlTraversal &trav) const | vg::VCFOutputCaller | protected |
| traversal_finder | vg::LegacyCaller | protected |
| update_nesting_info_tags(const SnarlManager *snarl_manager) | vg::VCFOutputCaller | protected |
| vcf_fixup(vcflib::Variant &var) const | vg::VCFOutputCaller | |
| vcf_header(const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides={}) const | vg::LegacyCaller | virtual |
| VCFOutputCaller(const string &sample_name) | vg::VCFOutputCaller | |
| write_variants(ostream &out_stream, const SnarlManager *snarl_manager=nullptr) | vg::VCFOutputCaller | |
| ~GraphCaller() | vg::GraphCaller | virtual |
| ~LegacyCaller() | vg::LegacyCaller | virtual |
| ~VCFOutputCaller() | vg::VCFOutputCaller | virtual |
1.8.17