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

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::NGSSimulatorprivate
advance_by_distance(size_t &offset, bool &is_reverse, pos_t &pos, size_t distance, const string &source_path)vg::NGSSimulatorprivate
advance_on_graph(pos_t &pos, char &graph_char)vg::NGSSimulatorprivate
advance_on_graph_by_distance(pos_t &pos, size_t distance)vg::NGSSimulatorprivate
advance_on_path(size_t &offset, bool &is_reverse, pos_t &pos, char &graph_char, const string &source_path)vg::NGSSimulatorprivate
advance_on_path_by_distance(size_t &offset, bool &is_reverse, pos_t &pos, size_t distance, const string &source_path)vg::NGSSimulatorprivate
alphabetvg::NGSSimulatorprivatestatic
apply_aligned_base(Alignment &aln, const pos_t &pos, char graph_char, char read_char)vg::NGSSimulatorprivate
apply_deletion(Alignment &aln, const pos_t &pos)vg::NGSSimulatorprivate
apply_insertion(Alignment &aln, const pos_t &pos)vg::NGSSimulatorprivate
apply_N_mask(string &sequence, const vector< bool > &n_mask)vg::NGSSimulatorprivate
background_samplervg::NGSSimulatorprivate
edge_cachevg::NGSSimulatorprivate
finalize()vg::NGSSimulatorprivate
get_read_name()vg::NGSSimulatorprivate
graphvg::NGSSimulatorprivate
indel_error_propvg::NGSSimulatorprivate
indel_poly_ratevg::NGSSimulatorprivate
insert_meanvg::NGSSimulatorprivate
insert_samplervg::NGSSimulatorprivate
insert_sdvg::NGSSimulatorprivate
joint_initial_distrvg::NGSSimulatorprivate
mut_samplervg::NGSSimulatorprivate
mutation_alphabetsvg::NGSSimulatorprivate
NGSSimulator(PathPositionHandleGraph &graph, const string &ngs_fastq_file, bool interleaved_fastq=false, const vector< string > &source_paths={}, const vector< pair< string, double >> &transcript_expressions={}, double substition_polymorphism_rate=0.001, double indel_polymorphism_rate=0.0002, double indel_error_proportion=0.01, double insert_length_mean=1000.0, double insert_length_stdev=75.0, double error_multiplier=1.0, bool retry_on_Ns=true, size_t seed=0)vg::NGSSimulator
NGSSimulator(void)=deletevg::NGSSimulatorprivate
node_cachevg::NGSSimulatorprivate
path_samplervg::NGSSimulatorprivate
phred_probvg::NGSSimulatorprivate
prngvg::NGSSimulatorprivate
prob_samplervg::NGSSimulatorprivate
record_read_pair_quality(const Alignment &aln_1, const Alignment &aln_2)vg::NGSSimulatorprivate
record_read_quality(const Alignment &aln, bool read_2=false)vg::NGSSimulatorprivate
retry_on_Nsvg::NGSSimulatorprivate
sample_countervg::NGSSimulatorprivate
sample_read()vg::NGSSimulator
sample_read_internal(Alignment &aln, size_t &offset, bool &is_reverse, pos_t &curr_pos, const string &source_path)vg::NGSSimulatorprivate
sample_read_pair()vg::NGSSimulator
sample_read_quality()vg::NGSSimulatorprivate
sample_read_quality_internal(pair< uint8_t, bool > first, bool transitions_1)vg::NGSSimulatorprivate
sample_read_quality_pair()vg::NGSSimulatorprivate
sample_start_graph_pos()vg::NGSSimulatorprivate
sample_start_path_pos()vg::NGSSimulatorprivate
sample_start_pos(size_t &offset, bool &is_reverse, pos_t &pos, string &source_path)vg::NGSSimulatorprivate
seedvg::NGSSimulatorprivate
source_pathsvg::NGSSimulatorprivate
start_pos_samplersvg::NGSSimulatorprivate
strand_samplervg::NGSSimulatorprivate
sub_poly_ratevg::NGSSimulatorprivate
total_seq_lengthvg::NGSSimulatorprivate
transition_distrs_1vg::NGSSimulatorprivate
transition_distrs_2vg::NGSSimulatorprivate
walk_backwards(const Path &path, size_t distance)vg::NGSSimulatorprivate