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vg
tools for working with variation graphs
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This is the complete list of members for vg::Genotyper, including all inherited members.
| Adaptive enum value | vg::Genotyper | |
| alg2name | vg::Genotyper | |
| alignment_qual_score(VG &graph, const Snarl *snarl, const Alignment &alignment) | vg::Genotyper | |
| all_snarls | vg::Genotyper | |
| allele_ambiguity_log_probs(const VG &graph, const Snarl *snarl, const vector< list< NodeTraversal >> &superbubble_paths, const unordered_map< pair< NodeTraversal, NodeTraversal >, unordered_set< size_t >, hash_oriented_edge > &edge_allele_sets, vector< unordered_map< vector< size_t >, double, hash_ambiguous_allele_set >> *out_allele_ambiguity_probs) | vg::Genotyper | |
| dagify_steps | vg::Genotyper | |
| default_sequence_quality | vg::Genotyper | |
| deleted_prior_logprob | vg::Genotyper | |
| diploid_prior_logprob | vg::Genotyper | |
| edge_allele_labels(const VG &graph, const Snarl *snarl, const vector< list< NodeTraversal >> &superbubble_paths, unordered_map< pair< NodeTraversal, NodeTraversal >, unordered_set< size_t >, hash_oriented_edge > *out_edge_allele_sets) | vg::Genotyper | |
| Exhaustive enum value | vg::Genotyper | |
| genotype_snarl(VG &graph, const Snarl *snarl, const vector< SnarlTraversal > &superbubble_paths, const map< const Alignment *, vector< Affinity >> &affinities) | vg::Genotyper | |
| get_affinities(AugmentedGraph &aug, const map< string, const Alignment * > &reads_by_name, const Snarl *snarl, const pair< unordered_set< id_t >, unordered_set< edge_t > > &contents, const SnarlManager &manager, const vector< SnarlTraversal > &superbubble_paths) | vg::Genotyper | |
| get_affinities_fast(AugmentedGraph &aug, const map< string, const Alignment * > &reads_by_name, const Snarl *snarl, const pair< unordered_set< id_t >, unordered_set< edge_t > > &contents, const SnarlManager &manager, const vector< SnarlTraversal > &superbubble_paths, bool allow_internal_alignments=false) | vg::Genotyper | |
| get_genotype_log_likelihood(VG &graph, const Snarl *snarl, const vector< int > &genotype, const vector< pair< const Alignment *, vector< Affinity >>> &alignment_consistency) | vg::Genotyper | |
| get_genotype_log_prior(const vector< int > &genotype) | vg::Genotyper | |
| get_qualities_in_snarl(VG &graph, const Snarl *snarl, const Alignment &alignment) | vg::Genotyper | |
| get_snarl_reference_bounds(const Snarl *snarl, const PathIndex &index, const HandleGraph *graph) | vg::Genotyper | |
| get_snarl_traversals(AugmentedGraph &augmented_graph, SnarlManager &manager, map< string, const Alignment * > &reads_by_name, const Snarl *snarl, const pair< unordered_set< id_t >, unordered_set< edge_t > > &contents, PathIndex *reference_index, TraversalAlg use_traversal_alg) | vg::Genotyper | |
| haploid_prior_logprob | vg::Genotyper | |
| het_prior_logprob | vg::Genotyper | |
| is_snarl_smaller_than_reads(AugmentedGraph &augmented_graph, const Snarl *snarl, const pair< unordered_set< id_t >, unordered_set< edge_t > > &contents, map< string, const Alignment * > &reads_by_name) | vg::Genotyper | static |
| locus_to_variant(VG &graph, const Snarl *snarl, const pair< unordered_set< id_t >, unordered_set< edge_t > > &contents, const SnarlManager &manager, const PathIndex &index, vcflib::VariantCallFile &vcf, const Locus &locus, const string &sample_name="SAMPLE") | vg::Genotyper | |
| make_subset_graph(VG &graph, const string &ref_path_name, map< string, const Alignment * > &reads_by_name) | vg::Genotyper | |
| mapping_enters_side(const Mapping &mapping, const handle_t &side, const HandleGraph *graph) | vg::Genotyper | static |
| mapping_exits_side(const Mapping &mapping, const handle_t &side, const HandleGraph *graph) | vg::Genotyper | static |
| max_het_bias | vg::Genotyper | |
| max_path_search_steps | vg::Genotyper | |
| min_recurrence | vg::Genotyper | |
| min_score_per_base | vg::Genotyper | |
| min_unique_per_strand | vg::Genotyper | |
| normal_aligners | vg::Genotyper | |
| polyploid_prior_success_logprob | vg::Genotyper | |
| print_statistics(ostream &out) | vg::Genotyper | |
| quality_aligners | vg::Genotyper | |
| Reads enum value | vg::Genotyper | |
| realign_indels | vg::Genotyper | |
| report_affinities(map< const Alignment *, vector< Genotyper::Affinity >> &affinities, vector< SnarlTraversal > &paths, VG &graph) | vg::Genotyper | |
| report_snarl(const Snarl *snarl, const SnarlManager &manager, const PathIndex *index, VG &graph, PathIndex *reference_index) | vg::Genotyper | |
| report_snarl_traversal(const Snarl *snarl, const SnarlManager &manager, VG &graph) | vg::Genotyper | |
| Representative enum value | vg::Genotyper | |
| run(AugmentedGraph &graph, ostream &out, string ref_path_name, string contig_name="", string sample_name="", string augmented_file_name="", bool output_vcf=false, bool output_json=false, int length_override=0, int variant_offset=0) | vg::Genotyper | |
| show_progress | vg::Genotyper | |
| snarl_reference_length_histogram | vg::Genotyper | |
| snarl_traversals | vg::Genotyper | |
| start_vcf(std::ostream &stream, const PathIndex &index, const string &sample_name, const string &contig_name, size_t contig_size) | vg::Genotyper | |
| translator | vg::Genotyper | |
| traversal_alg | vg::Genotyper | |
| TraversalAlg enum name | vg::Genotyper | |
| unfold_max_length | vg::Genotyper | |
| use_mapq | vg::Genotyper | |
| write_variant() | vg::Genotyper | |
| write_vcf_header(std::ostream &stream, const std::string &sample_name, const std::string &contig_name, size_t contig_size) | vg::Genotyper |
1.8.17