vg::BaseMapper Member List

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

accelerate_mem_query(string::const_iterator begin, string::const_iterator &cursor) const	vg::BaseMapper
accelerator	vg::BaseMapper
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
fanout_length_threshold	vg::BaseMapper
fast_reseed	vg::BaseMapper
fast_reseed_length_diff	vg::BaseMapper
filter_short_mems	vg::BaseMapper
find_fanout_mems(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator qual_begin, int max_fans_out, char max_fanout_base_quality, vector< deque< pair< string::const_iterator, char >>> *mem_fanout_breaks=nullptr)	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_stripped_matches(string::const_iterator seq_begin, string::const_iterator seq_end, size_t strip_length, size_t max_match_length, size_t target_count)	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
greedy_restart_assume_substitution	vg::BaseMapper
greedy_restart_max_count	vg::BaseMapper
greedy_restart_max_lcp	vg::BaseMapper
greedy_restart_min_length	vg::BaseMapper
haplo_score_provider	vg::BaseMapper
haplotype_consistency_exponent	vg::BaseMapper
hard_hit_max	vg::BaseMapper
has_fixed_fragment_length_distr()	vg::PairedEndMapper
hit_max	vg::BaseMapper
lcp	vg::BaseMapper
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
parse_matrix(std::istream &matrix_stream)	vg::AlignerClient	static
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, double haplotype_consistency_exponent=1)	vg::BaseMapper
set_alignment_scores(istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, 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)	vg::AlignerClient	virtual
vg::AlignerClient::set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)	vg::AlignerClient	virtual
vg::AlignerClient::set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)	vg::AlignerClient	virtual
set_fragment_length_distr_params(size_t maximum_sample_size=1000, size_t reestimation_frequency=1000, double robust_estimation_fraction=0.95)	vg::PairedEndMapper
short_mem_filter_factor	vg::BaseMapper
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
use_greedy_mem_restarts	vg::BaseMapper
walk_fanout_path(string::const_iterator begin, string::const_iterator end, const deque< pair< string::const_iterator, char >> &fanout_breaks, gcsa::node_type pos)	vg::BaseMapper
xindex	vg::BaseMapper