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vg
tools for working with variation graphs
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This is the complete list of members for vg::VCFGenotyper, 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::VCFGenotyper | 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_gaf_traversals(const PathHandleGraph &graph, const string &snarl_name, const vector< SnarlTraversal > &travs, int64_t ref_trav_idx, const string &ref_path_name, int64_t ref_path_position, const TraversalSupportFinder *support_finder=nullptr) | vg::GAFOutputCaller | |
| emit_gaf_variant(const PathHandleGraph &graph, const string &snarl_name, const vector< SnarlTraversal > &travs, const vector< int > &genotype, int64_t ref_trav_idx, const string &ref_path_name, int64_t ref_path_position, const TraversalSupportFinder *support_finder=nullptr) | vg::GAFOutputCaller | |
| 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 |
| emitter | vg::GAFOutputCaller | protected |
| flatten_common_allele_ends(vcflib::Variant &variant, bool backward, size_t len_override) const | vg::VCFOutputCaller | protected |
| gaf_output | vg::VCFGenotyper | protected |
| gaf_sample_name | vg::GAFOutputCaller | protected |
| GAFOutputCaller(AlignmentEmitter *emitter, const string &sample_name, const vector< string > &ref_paths, size_t trav_padding) | vg::GAFOutputCaller | |
| 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_ref_positions(const vector< vcflib::Variant * > &variants) const | vg::VCFGenotyper | protected |
| graph | vg::VCFGenotyper | protected |
| GraphCaller(SnarlCaller &snarl_caller, SnarlManager &snarl_manager) | vg::GraphCaller | |
| include_nested | vg::VCFOutputCaller | protected |
| input_vcf | vg::VCFGenotyper | protected |
| max_uncalled_alleles | vg::VCFOutputCaller | protected |
| max_vcf_line_length | vg::VCFOutputCaller | protectedstatic |
| output_variants | vg::VCFOutputCaller | mutableprotected |
| output_vcf | vg::VCFOutputCaller | mutableprotected |
| pad_traversal(const PathHandleGraph &graph, const SnarlTraversal &trav) const | vg::GAFOutputCaller | |
| path_to_ploidy | vg::VCFGenotyper | 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 |
| RecurseAlways enum value | vg::GraphCaller | |
| RecurseNever enum value | vg::GraphCaller | |
| RecurseOnFail enum value | vg::GraphCaller | |
| RecurseType enum name | vg::GraphCaller | |
| ref_paths | vg::GAFOutputCaller | protected |
| sample_name | vg::VCFOutputCaller | protected |
| scan_contig_lengths() const | vg::VCFGenotyper | protectedvirtual |
| 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 |
| translation | vg::VCFOutputCaller | protected |
| trav_padding | vg::GAFOutputCaller | protected |
| trav_string(const HandleGraph &graph, const SnarlTraversal &trav) const | vg::VCFOutputCaller | protected |
| traversal_finder | vg::VCFGenotyper | protected |
| traversals_only | vg::VCFGenotyper | 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::VCFGenotyper | virtual |
| VCFGenotyper(const PathHandleGraph &graph, SnarlCaller &snarl_caller, SnarlManager &snarl_manager, vcflib::VariantCallFile &variant_file, const string &sample_name, const vector< string > &ref_paths, const vector< int > &ref_path_ploidies, FastaReference *ref_fasta, FastaReference *ins_fasta, AlignmentEmitter *aln_emitter, bool traversals_only, bool gaf_output, size_t trav_padding) | vg::VCFGenotyper | |
| VCFOutputCaller(const string &sample_name) | vg::VCFOutputCaller | |
| write_variants(ostream &out_stream, const SnarlManager *snarl_manager=nullptr) | vg::VCFOutputCaller | |
| ~GAFOutputCaller() | vg::GAFOutputCaller | virtual |
| ~GraphCaller() | vg::GraphCaller | virtual |
| ~VCFGenotyper() | vg::VCFGenotyper | virtual |
| ~VCFOutputCaller() | vg::VCFOutputCaller | virtual |
1.8.17