vg
tools for working with variation graphs
vg::Deconstructor Member List

This is the complete list of members for vg::Deconstructor, 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) constvg::VCFOutputCallerprotected
add_allele_path_to_info(vcflib::Variant &v, int allele, const SnarlTraversal &trav, bool reversed, bool one_based) constvg::VCFOutputCallerprotected
add_contigs_to_vcf_header(const string &vcf_header) constvg::Deconstructorprivate
add_star_traversals(vector< Traversal > &travs, vector< string > &trav_names, vector< vector< int >> &trav_clusters, vector< pair< double, int64_t >> &trav_cluster_info, const unordered_map< string, vector< int >> &parent_haplotypes) constvg::Deconstructorprivate
add_variant(vcflib::Variant &var) constvg::VCFOutputCaller
choose_traversals(const string &sample_name, const vector< int > &travs, const vector< int > &trav_to_allele, const vector< string > &trav_to_name, const vector< int > &gbwt_phases) constvg::Deconstructorprivate
cluster_thresholdvg::Deconstructorprivate
deconstruct(vector< string > refpaths, const PathPositionHandleGraph *graph, SnarlManager *snarl_manager, bool include_nested, int context_jaccard_window, bool untangle_traversals, bool keep_conflicted, bool strict_conflicts, bool long_ref_contig, double cluster_threshold=1.0, gbwt::GBWT *gbwt=nullptr, bool nested_decomposition=false, bool star_allele=false)vg::Deconstructor
deconstruct_graph(SnarlManager *snarl_manager)vg::Deconstructorprivate
deconstruct_graph_top_down(SnarlManager *snarl_manager)vg::Deconstructorprivate
deconstruct_site(const handle_t &snarl_start, const handle_t &snarl_end, const NestingInfo *in_nesting_info=nullptr, vector< NestingInfo > *out_nesting_infos=nullptr) constvg::Deconstructorprivate
Deconstructor()vg::Deconstructor
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::VCFOutputCallerprotected
flatten_common_allele_ends(vcflib::Variant &variant, bool backward, size_t len_override) constvg::VCFOutputCallerprotected
gbwtvg::Deconstructorprivate
gbwt_reference_samplesvg::Deconstructorprivate
gbwt_sample_to_phase_rangevg::Deconstructorprivate
gbwt_trav_findervg::Deconstructorprivate
get_alleles(vcflib::Variant &v, const vector< Traversal > &travs, const vector< pair< step_handle_t, step_handle_t >> &trav_steps, int ref_path_idx, const vector< vector< int >> &trav_clusters, char prev_char, bool use_start) constvg::Deconstructorprivate
get_context(step_handle_t start_step, step_handle_t end_step) constvg::Deconstructorprivate
get_genotypes(vcflib::Variant &v, const vector< string > &names, const vector< int > &trav_to_allele, const vector< pair< double, int64_t >> &trav_to_cluster_info) constvg::Deconstructorprivate
get_ref_interval(const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name) constvg::VCFOutputCallerprotected
get_ref_position(const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name, int64_t ref_path_offset) constvg::VCFOutputCallerprotected
get_traversals(const handle_t &snarl_start, const handle_t &snarl_end, vector< Traversal > &out_travs, vector< string > &out_trav_path_names, vector< pair< step_handle_t, step_handle_t >> &out_trav_steps) constvg::Deconstructorprivate
get_vcf_header()vg::Deconstructorprivate
graphvg::Deconstructorprivate
include_nestedvg::VCFOutputCallerprotected
keep_conflicted_genotypesvg::Deconstructorprivate
long_ref_contigvg::Deconstructorprivate
max_uncalled_allelesvg::VCFOutputCallerprotected
max_vcf_line_lengthvg::VCFOutputCallerprotectedstatic
nested_decompositionvg::Deconstructorprivate
off_ref_pathsvg::Deconstructormutableprivate
output_variantsvg::VCFOutputCallermutableprotected
output_vcfvg::VCFOutputCallermutableprotected
path_jaccard_windowvg::Deconstructorprivate
path_to_sample_phasevg::Deconstructorprivate
path_trav_findervg::Deconstructorprivate
print_snarl(const HandleGraph *grpah, const handle_t &snarl_start, const handle_t &snarl_end, bool in_brackets=false) constvg::VCFOutputCallerprotected
print_snarl(const Snarl &snarl, bool in_brackets=false) constvg::VCFOutputCallerprotected
ref_pathsvg::Deconstructorprivate
ref_samplesvg::Deconstructorprivate
sample_namevg::VCFOutputCallerprotected
sample_namesvg::Deconstructorprivate
sample_ploidysvg::Deconstructorprivate
scan_snarl(const string &allele_string, function< void(const string &, Snarl &)> callback) constvg::VCFOutputCallerprotected
set_nested(bool nested)vg::VCFOutputCaller
set_translation(const unordered_map< nid_t, pair< string, size_t >> *translation)vg::VCFOutputCaller
show_path_infovg::Deconstructorprivate
star_allelevg::Deconstructorprivate
strict_conflict_checkingvg::Deconstructorprivate
translationvg::VCFOutputCallerprotected
trav_string(const HandleGraph &graph, const SnarlTraversal &trav) constvg::VCFOutputCallerprotected
untangle_allele_traversalsvg::Deconstructorprivate
update_nesting_info_tags(const SnarlManager *snarl_manager)vg::VCFOutputCallerprotected
vcf_fixup(vcflib::Variant &var) constvg::VCFOutputCaller
vcf_header(const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides) constvg::VCFOutputCallervirtual
VCFOutputCaller(const string &sample_name)vg::VCFOutputCaller
write_variants(ostream &out_stream, const SnarlManager *snarl_manager=nullptr)vg::VCFOutputCaller
~Deconstructor()vg::Deconstructor
~VCFOutputCaller()vg::VCFOutputCallervirtual
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