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

This is the complete list of members for vg::BaseMapper, including all inherited members.

adaptive_diff_exponentvg::BaseMapper
adaptive_reseed_diffvg::BaseMapper
adaptive_reseed_length_memovg::BaseMapperstatic
adjust_alignments_for_base_qualityvg::AlignerClient
AlignerClient(double gc_content_estimate=vg::default_gc_content)vg::AlignerClientprotected
apply_haplotype_consistency_scores(const vector< Alignment * > &alns)vg::BaseMapper
assume_acyclicvg::BaseMapper
avg_node_lengthvg::BaseMapper
BaseMapper(PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr)vg::BaseMapper
BaseMapper(void)vg::BaseMapper
debugvg::BaseMapper
estimate_gc_content(const gcsa::GCSA *gcsa)vg::BaseMapperstatic
exclude_unalignedvg::BaseMapper
fast_reseedvg::BaseMapper
fast_reseed_length_diffvg::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::BaseMapper
fragment_length_distrvg::BaseMapper
gc_content_estimatevg::AlignerClientprivate
gcsavg::BaseMapper
get_adaptive_min_reseed_length(size_t parent_mem_length)vg::BaseMapper
get_aligner(bool have_qualities=true) constvg::AlignerClientprotected
get_qual_adj_aligner() constvg::AlignerClientprotected
get_regular_aligner() constvg::AlignerClientprotected
haplo_score_providervg::BaseMapper
haplotype_consistency_exponentvg::BaseMapper
has_fixed_fragment_length_distr()vg::BaseMapper
hit_maxvg::BaseMapper
lcpvg::BaseMapper
load_scoring_matrix(std::ifstream &matrix_stream)vg::AlignerClient
mapping_quality_methodvg::BaseMapper
max_mapping_qualityvg::BaseMapper
max_sub_mem_recursion_depthvg::BaseMapper
mem_reseed_lengthvg::BaseMapper
min_mem_lengthvg::BaseMapper
precollapse_order_length_hitsvg::BaseMapper
precollapse_order_length_runs(string::const_iterator seq_begin, vector< MaximalExactMatch > &mems)vg::BaseMapper
prefilter_redundant_hitsvg::BaseMapper
prefilter_redundant_sub_mems(vector< MaximalExactMatch > &mems, vector< pair< int, vector< size_t >>> &sub_mem_containment_graph)vg::BaseMapper
qual_adj_alignervg::AlignerClientprivate
random_match_length(double chance_random)vg::BaseMapper
recombination_penaltyvg::BaseMapper
regular_alignervg::AlignerClientprivate
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::BaseMapper
strip_bonusesvg::BaseMapper
sub_mem_count_thinningvg::BaseMapper
sub_mem_thinning_burn_invg::BaseMapper
total_seq_lengthvg::BaseMapper
unpaired_penaltyvg::BaseMapper
use_approx_sub_mem_countvg::BaseMapper
xindexvg::BaseMapper