| genotype(const Snarl &snarl, const vector< SnarlTraversal > &traversals, int ref_trav_idx, int ploidy, const string &ref_path_name, pair< size_t, size_t > ref_range) | vg::RatioSupportSnarlCaller | virtual |
| get_best_support(const vector< Support > &supports, const vector< int > &skips) | vg::SupportBasedSnarlCaller | protectedstatic |
| get_bias(const vector< int > &traversal_sizes, int best_trav, int second_best_trav, int ref_trav_idx) const | vg::RatioSupportSnarlCaller | protected |
| get_min_total_support_for_call() const | vg::SupportBasedSnarlCaller | virtual |
| get_ref_offsets(const SnarlTraversal &ref_trav) const | vg::RatioSupportSnarlCaller | protected |
| get_skip_allele_fn() const | vg::SupportBasedSnarlCaller | virtual |
| get_support_finder() const | vg::SupportBasedSnarlCaller | |
| graph | vg::SupportBasedSnarlCaller | protected |
| max_het_bias | vg::RatioSupportSnarlCaller | protected |
| max_indel_het_bias | vg::RatioSupportSnarlCaller | protected |
| max_ma_bias | vg::RatioSupportSnarlCaller | protected |
| max_ref_het_bias | vg::RatioSupportSnarlCaller | protected |
| min_ad_log_likelihood_for_filter | vg::RatioSupportSnarlCaller | protected |
| min_alt_path_support | vg::SupportBasedSnarlCaller | protected |
| min_mad_for_filter | vg::SupportBasedSnarlCaller | protected |
| min_site_depth | vg::SupportBasedSnarlCaller | protected |
| min_total_support_for_call | vg::SupportBasedSnarlCaller | protected |
| RatioSupportSnarlCaller(const PathHandleGraph &graph, SnarlManager &snarl_manager, TraversalSupportFinder &support_finder) | vg::RatioSupportSnarlCaller | |
| set_het_bias(double het_bias, double ref_het_bias=0.) | vg::RatioSupportSnarlCaller | |
| set_min_supports(double min_mad_for_call, double min_support_for_call, double min_site_support) | vg::SupportBasedSnarlCaller | |
| snarl_manager | vg::SupportBasedSnarlCaller | protected |
| support_finder | vg::SupportBasedSnarlCaller | protected |
| support_val(const Support &support) | vg::SupportBasedSnarlCaller | inlineprotectedstatic |
| SupportBasedSnarlCaller(const PathHandleGraph &graph, SnarlManager &snarl_manager, TraversalSupportFinder &support_finder) | vg::SupportBasedSnarlCaller | |
| update_vcf_header(string &header) const | vg::RatioSupportSnarlCaller | virtual |
| update_vcf_info(const Snarl &snarl, const vector< SnarlTraversal > &traversals, const vector< int > &genotype, const unique_ptr< CallInfo > &call_info, const string &sample_name, vcflib::Variant &variant) | vg::RatioSupportSnarlCaller | virtual |
| ~RatioSupportSnarlCaller() | vg::RatioSupportSnarlCaller | virtual |
| ~SnarlCaller() | vg::SnarlCaller | virtual |
| ~SupportBasedSnarlCaller() | vg::SupportBasedSnarlCaller | virtual |
