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vg
tools for working with variation graphs
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This is the complete list of members for vg::BaseMapper, including all inherited members.
| adaptive_diff_exponent | vg::BaseMapper | |
| adaptive_reseed_diff | vg::BaseMapper | |
| adaptive_reseed_length_memo | vg::BaseMapper | static |
| adjust_alignments_for_base_quality | vg::AlignerClient | |
| AlignerClient(double gc_content_estimate=vg::default_gc_content) | vg::AlignerClient | protected |
| apply_haplotype_consistency_scores(const vector< Alignment * > &alns) | vg::BaseMapper | |
| assume_acyclic | vg::BaseMapper | |
| avg_node_length | vg::BaseMapper | |
| BaseMapper(PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr) | vg::BaseMapper | |
| BaseMapper(void) | vg::BaseMapper | |
| debug | vg::BaseMapper | |
| estimate_gc_content(const gcsa::GCSA *gcsa) | vg::BaseMapper | static |
| exclude_unaligned | vg::BaseMapper | |
| fast_reseed | vg::BaseMapper | |
| fast_reseed_length_diff | vg::BaseMapper | |
| find_mems_deep(string::const_iterator seq_begin, string::const_iterator seq_end, double &lcp_avg, double &fraction_filtered, int max_mem_length=0, int min_mem_length=1, int reseed_length=0, bool use_lcp_reseed_heuristic=false, bool use_diff_based_fast_reseed=false, bool include_parent_in_sub_mem_count=false, bool record_max_lcp=false, int reseed_below_count=0) | vg::BaseMapper | |
| find_mems_simple(string::const_iterator seq_begin, string::const_iterator seq_end, int max_mem_length=0, int min_mem_length=1, int reseed_length=0) | vg::BaseMapper | |
| find_sub_mems(const vector< MaximalExactMatch > &mems, int parent_layer_begin, int parent_layer_end, int mem_idx, string::const_iterator next_mem_end, int min_mem_length, vector< pair< MaximalExactMatch, vector< size_t >>> &sub_mems_out) | vg::BaseMapper | |
| find_sub_mems_fast(const vector< MaximalExactMatch > &mems, int parent_layer_begin, int parent_layer_end, int mem_idx, string::const_iterator leftmost_guaranteed_disjoint_bound, string::const_iterator leftmost_seeding_bound, int min_sub_mem_length, vector< pair< MaximalExactMatch, vector< size_t >>> &sub_mems_out) | vg::BaseMapper | |
| force_fragment_length_distr(double mean, double stddev) | vg::PairedEndMapper | |
| fragment_length_distr | vg::PairedEndMapper | protected |
| gc_content_estimate | vg::AlignerClient | private |
| gcsa | vg::BaseMapper | |
| get_adaptive_min_reseed_length(size_t parent_mem_length) | vg::BaseMapper | |
| get_aligner(bool have_qualities=true) const | vg::AlignerClient | protected |
| get_qual_adj_aligner() const | vg::AlignerClient | protected |
| get_regular_aligner() const | vg::AlignerClient | protected |
| haplo_score_provider | vg::BaseMapper | |
| haplotype_consistency_exponent | vg::BaseMapper | |
| has_fixed_fragment_length_distr() | vg::PairedEndMapper | |
| hit_max | vg::BaseMapper | |
| lcp | vg::BaseMapper | |
| load_scoring_matrix(std::ifstream &matrix_stream) | vg::AlignerClient | |
| mapping_quality_method | vg::BaseMapper | |
| max_mapping_quality | vg::BaseMapper | |
| max_sub_mem_recursion_depth | vg::BaseMapper | |
| mem_reseed_length | vg::BaseMapper | |
| min_mem_length | vg::BaseMapper | |
| precollapse_order_length_hits | vg::BaseMapper | |
| precollapse_order_length_runs(string::const_iterator seq_begin, vector< MaximalExactMatch > &mems) | vg::BaseMapper | |
| prefilter_redundant_hits | vg::BaseMapper | |
| prefilter_redundant_sub_mems(vector< MaximalExactMatch > &mems, vector< pair< int, vector< size_t >>> &sub_mem_containment_graph) | vg::BaseMapper | |
| qual_adj_aligner | vg::AlignerClient | private |
| random_match_length(double chance_random) | vg::BaseMapper | |
| recombination_penalty | vg::BaseMapper | |
| regular_aligner | vg::AlignerClient | private |
| rescue_high_count_order_length_mems(vector< MaximalExactMatch > &mems, size_t max_rescue_hit_count) | vg::BaseMapper | |
| sequence_positions(const string &seq) | vg::BaseMapper | |
| set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, uint32_t xdrop_max_gap_length=default_xdrop_max_gap_length, double haplotype_consistency_exponent=1) | vg::BaseMapper | |
| vg::AlignerClient::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, uint32_t xdrop_max_gap_length=default_xdrop_max_gap_length) | vg::AlignerClient | |
| set_cache_size(int new_cache_size) | vg::BaseMapper | |
| set_fragment_length_distr_params(size_t maximum_sample_size=1000, size_t reestimation_frequency=1000, double robust_estimation_fraction=0.95) | vg::PairedEndMapper | |
| strip_bonuses | vg::BaseMapper | |
| sub_mem_count_thinning | vg::BaseMapper | |
| sub_mem_thinning_burn_in | vg::BaseMapper | |
| total_seq_length | vg::BaseMapper | |
| unpaired_penalty | vg::BaseMapper | |
| use_approx_sub_mem_count | vg::BaseMapper | |
| xindex | vg::BaseMapper |
1.8.16