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| 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) |
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Alignment | sample_read () |
| Sample an individual read and alignment. More...
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pair< Alignment, Alignment > | sample_read_pair () |
| Sample a pair of reads an alignments. More...
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| NGSSimulator (void)=delete |
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void | record_read_quality (const Alignment &aln, bool read_2=false) |
| Add a quality string to the training data. More...
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void | record_read_pair_quality (const Alignment &aln_1, const Alignment &aln_2) |
| Add a pair of quality strings to the training data. More...
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void | finalize () |
| Indicate that there is no more training data. More...
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pair< string, vector< bool > > | sample_read_quality () |
| Get a quality string and a vector of 'N'-masks that mimics the training data. More...
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pair< pair< string, vector< bool > >, pair< string, vector< bool > > > | sample_read_quality_pair () |
| Get a pair of quality strings and vectors of 'N'-masks that mimic the training data. More...
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pair< string, vector< bool > > | sample_read_quality_internal (pair< uint8_t, bool > first, bool transitions_1) |
| Wrapped internal function for quality sampling. More...
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void | sample_read_internal (Alignment &aln, size_t &offset, bool &is_reverse, pos_t &curr_pos, const string &source_path) |
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void | sample_start_pos (size_t &offset, bool &is_reverse, pos_t &pos, string &source_path) |
| Sample an appropriate starting position according to the mode. Updates the arguments. More...
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pos_t | sample_start_graph_pos () |
| Get a random position in the graph. More...
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tuple< size_t, bool, pos_t, string > | sample_start_path_pos () |
| Get a random position along the source path. More...
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string | get_read_name () |
| Get an unclashing read name. More...
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bool | advance (size_t &offset, bool &is_reverse, pos_t &pos, char &graph_char, const string &source_path) |
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bool | advance_by_distance (size_t &offset, bool &is_reverse, pos_t &pos, size_t distance, const string &source_path) |
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bool | advance_on_path (size_t &offset, bool &is_reverse, pos_t &pos, char &graph_char, const string &source_path) |
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bool | advance_on_path_by_distance (size_t &offset, bool &is_reverse, pos_t &pos, size_t distance, const string &source_path) |
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bool | advance_on_graph (pos_t &pos, char &graph_char) |
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bool | advance_on_graph_by_distance (pos_t &pos, size_t distance) |
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void | apply_N_mask (string &sequence, const vector< bool > &n_mask) |
| Mask out bases with 'N's if the mask is true. More...
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pos_t | walk_backwards (const Path &path, size_t distance) |
| Returns the position a given distance from the end of the path, walking backwards. More...
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void | apply_deletion (Alignment &aln, const pos_t &pos) |
| Add a deletion to the alignment. More...
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void | apply_insertion (Alignment &aln, const pos_t &pos) |
| Add an insertion to the alignment. More...
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void | apply_aligned_base (Alignment &aln, const pos_t &pos, char graph_char, char read_char) |
| Add a match/mismatch to the alignment. More...
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unordered_map< char, string > | mutation_alphabets |
| Remainder of the alphabet after removing a given character. More...
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size_t | total_seq_length = 0 |
| The total sequence length in our graph. More...
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vector< double > | phred_prob |
| Memo for Phred -> probability conversion. More...
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vector< MarkovDistribution< pair< uint8_t, bool >, pair< uint8_t, bool > > > | transition_distrs_1 |
| A Markov distribution for each read position indicating quality and whether the base is an 'N'. More...
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vector< MarkovDistribution< pair< uint8_t, bool >, pair< uint8_t, bool > > > | transition_distrs_2 |
| A second set of Markov distributions for the second read in a pair. More...
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MarkovDistribution< pair< uint8_t, bool >, pair< pair< uint8_t, bool >, pair< uint8_t, bool > > > | joint_initial_distr |
| A distribution for the joint initial qualities of a read pair. More...
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PathPositionHandleGraph & | graph |
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LRUCache< id_t, Node > | node_cache |
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LRUCache< id_t, vector< Edge > > | edge_cache |
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default_random_engine | prng |
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vg::discrete_distribution | path_sampler |
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vector< vg::uniform_int_distribution< size_t > > | start_pos_samplers |
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vg::uniform_int_distribution< uint8_t > | strand_sampler |
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vg::uniform_int_distribution< size_t > | background_sampler |
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vg::uniform_int_distribution< size_t > | mut_sampler |
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vg::uniform_real_distribution< double > | prob_sampler |
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vg::normal_distribution< double > | insert_sampler |
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const double | sub_poly_rate |
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const double | indel_poly_rate |
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const double | indel_error_prop |
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const double | insert_mean |
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const double | insert_sd |
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size_t | sample_counter = 0 |
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size_t | seed |
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const bool | retry_on_Ns |
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vector< string > | source_paths |
| Restrict reads to just these paths (path-only mode) if nonempty. More...
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Class that simulates reads with alignments to a graph that mimic the error profile of NGS sequencing data.