vg
tools for working with variation graphs
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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 |