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

advance(size_t &offset, bool &is_reverse, pos_t &pos, char &graph_char, const string &source_path)	vg::NGSSimulator	private
advance_by_distance(size_t &offset, bool &is_reverse, pos_t &pos, size_t distance, const string &source_path)	vg::NGSSimulator	private
advance_on_graph(pos_t &pos, char &graph_char)	vg::NGSSimulator	private
advance_on_graph_by_distance(pos_t &pos, size_t distance)	vg::NGSSimulator	private
advance_on_path(size_t &offset, bool &is_reverse, pos_t &pos, char &graph_char, const string &source_path)	vg::NGSSimulator	private
advance_on_path_by_distance(size_t &offset, bool &is_reverse, pos_t &pos, size_t distance, const string &source_path)	vg::NGSSimulator	private
alphabet	vg::NGSSimulator	privatestatic
apply_aligned_base(Alignment &aln, const pos_t &pos, char graph_char, char read_char)	vg::NGSSimulator	private
apply_deletion(Alignment &aln, const pos_t &pos)	vg::NGSSimulator	private
apply_insertion(Alignment &aln, const pos_t &pos)	vg::NGSSimulator	private
apply_N_mask(string &sequence, const vector< bool > &n_mask)	vg::NGSSimulator	private
background_sampler	vg::NGSSimulator	private
edge_cache	vg::NGSSimulator	private
finalize()	vg::NGSSimulator	private
get_read_name()	vg::NGSSimulator	private
graph	vg::NGSSimulator	private
indel_error_prop	vg::NGSSimulator	private
indel_poly_rate	vg::NGSSimulator	private
insert_mean	vg::NGSSimulator	private
insert_sampler	vg::NGSSimulator	private
insert_sd	vg::NGSSimulator	private
joint_initial_distr	vg::NGSSimulator	private
mut_sampler	vg::NGSSimulator	private
mutation_alphabets	vg::NGSSimulator	private
NGSSimulator(PathPositionHandleGraph &graph, const string &ngs_fastq_file, const string &ngs_paired_fastq_file="", bool interleaved_fastq=false, const vector< string > &source_paths={}, const vector< pair< string, double >> &transcript_expressions={}, const vector< tuple< string, string, size_t >> &haplotype_transcripts={}, double substition_polymorphism_rate=0.001, double indel_polymorphism_rate=0.0002, double indel_error_proportion=0.01, double insert_length_mean=300.0, double insert_length_stdev=50.0, double error_multiplier=1.0, bool retry_on_Ns=true, size_t seed=0)	vg::NGSSimulator
NGSSimulator(void)=delete	vg::NGSSimulator	private
node_cache	vg::NGSSimulator	private
path_sampler	vg::NGSSimulator	private
phred_prob	vg::NGSSimulator	private
prng	vg::NGSSimulator	private
prob_sampler	vg::NGSSimulator	private
record_read_pair_quality(const Alignment &aln_1, const Alignment &aln_2)	vg::NGSSimulator	private
record_read_quality(const Alignment &aln, bool read_2=false)	vg::NGSSimulator	private
retry_on_Ns	vg::NGSSimulator	private
sample_counter	vg::NGSSimulator	private
sample_read()	vg::NGSSimulator
sample_read_internal(Alignment &aln, size_t &offset, bool &is_reverse, pos_t &curr_pos, const string &source_path)	vg::NGSSimulator	private
sample_read_pair()	vg::NGSSimulator
sample_read_quality()	vg::NGSSimulator	private
sample_read_quality_internal(pair< uint8_t, bool > first, bool transitions_1)	vg::NGSSimulator	private
sample_read_quality_pair()	vg::NGSSimulator	private
sample_start_graph_pos()	vg::NGSSimulator	private
sample_start_path_pos()	vg::NGSSimulator	private
sample_start_pos(size_t &offset, bool &is_reverse, pos_t &pos, string &source_path)	vg::NGSSimulator	private
seed	vg::NGSSimulator	private
source_paths	vg::NGSSimulator	private
start_pos_samplers	vg::NGSSimulator	private
strand_sampler	vg::NGSSimulator	private
sub_poly_rate	vg::NGSSimulator	private
total_seq_length	vg::NGSSimulator	private
transition_distrs_1	vg::NGSSimulator	private
transition_distrs_2	vg::NGSSimulator	private
walk_backwards(const Path &path, size_t distance)	vg::NGSSimulator	private