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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.
| AbstractReadSampler(PathPositionHandleGraph &graph) | vg::AbstractReadSampler | inline |
| advance(int64_t &offset, bool &is_reverse, pos_t &pos, char &graph_char, const string &source_path) | vg::NGSSimulator | private |
| advance_by_distance(int64_t &offset, bool &is_reverse, pos_t &pos, int64_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, int64_t distance) | vg::NGSSimulator | private |
| advance_on_path(int64_t &offset, bool &is_reverse, pos_t &pos, char &graph_char, const string &source_path) | vg::NGSSimulator | private |
| advance_on_path_by_distance(int64_t &offset, bool &is_reverse, pos_t &pos, int64_t distance, const string &source_path) | vg::NGSSimulator | private |
| alphabet | vg::NGSSimulator | privatestatic |
| annotate_with_path_positions(Alignment &aln) | vg::AbstractReadSampler | protected |
| annotation_path_filter | vg::AbstractReadSampler | |
| 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 |
| connect_to_position_file(const string &filename) | vg::NGSSimulator | |
| finalize() | vg::NGSSimulator | private |
| fragment_mean | vg::NGSSimulator | private |
| fragment_sd | vg::NGSSimulator | private |
| get_read_name() | vg::NGSSimulator | private |
| graph | vg::AbstractReadSampler | protected |
| indel_error_prop | vg::NGSSimulator | private |
| indel_poly_rate | vg::NGSSimulator | private |
| joint_initial_distr | vg::NGSSimulator | private |
| max_tries | vg::AbstractReadSampler | |
| multi_position_annotations | vg::AbstractReadSampler | |
| 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< double > &source_path_ploidies={}, 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 fragment_length_mean=300.0, double fragment_length_stdev=50.0, double error_multiplier=1.0, bool retry_on_Ns=true, bool sample_unsheared_paths=false, uint64_t seed=0) | vg::NGSSimulator | |
| NGSSimulator(void)=delete | vg::NGSSimulator | private |
| path_sampler | vg::NGSSimulator | private |
| phred_prob | vg::NGSSimulator | private |
| position_file | vg::NGSSimulator | private |
| prng() | vg::NGSSimulator | private |
| prngs | 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 |
| register_sampled_position(const Alignment &aln, const string &path_name, size_t offset, bool is_reverse) | vg::NGSSimulator | private |
| retry_on_Ns | vg::NGSSimulator | private |
| sample_counter | vg::NGSSimulator | private |
| sample_path() | vg::NGSSimulator | private |
| sample_read() | vg::NGSSimulator | |
| sample_read_internal(Alignment &aln, int64_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(const size_t &source_path_idx, const int64_t &fragment_length) | vg::NGSSimulator | private |
| sample_start_pos(const size_t &source_path_idx, const int64_t &fragment_length, int64_t &offset, bool &is_reverse, pos_t &pos) | vg::NGSSimulator | private |
| sample_unsheared_paths | 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(int64_t &offset, bool &is_reverse, pos_t &pos, int64_t distance, const string &source_path, const Path &path) | vg::NGSSimulator | private |
| walk_backwards_along_alignment(const Path &path, int64_t distance, pos_t &pos) | vg::NGSSimulator | private |
| ~AbstractReadSampler()=default | vg::AbstractReadSampler | virtual |
1.8.17