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| Mapper (PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr) |
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| Mapper (void) |
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| ~Mapper (void) |
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bool | alignments_consistent (const map< string, double > &pos1, const map< string, double > &pos2, int fragment_size_bound) |
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bool | pair_consistent (Alignment &aln1, Alignment &aln2, double pval) |
| use the fragment length annotations to assess if the pair is consistent or not More...
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pair< bool, bool > | pair_rescue (Alignment &mate1, Alignment &mate2, bool &tried1, bool &tried2, int match_score, int full_length_bonus, bool traceback, bool xdrop_alignment) |
| use the fragment configuration statistics to rescue more precisely More...
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vector< Alignment > | mems_id_clusters_to_alignments (const Alignment &alignment, vector< MaximalExactMatch > &mems, int additional_multimaps) |
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set< const vector< MaximalExactMatch > * > | clusters_to_drop (const vector< vector< MaximalExactMatch > > &clusters) |
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int32_t | score_alignment (const Alignment &aln, bool use_approx_distance=false) |
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void | remove_full_length_bonuses (Alignment &aln) |
| Given an alignment scored with full length bonuses on, subtract out the full length bonus if it was applied. More...
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Alignment | patch_alignment (const Alignment &aln, int max_patch_length, bool trim_internal_deletions=true, bool xdrop_alignment=false) |
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Alignment | align_cluster (const Alignment &aln, const vector< MaximalExactMatch > &mems, bool traceback, bool xdrop_alignment=false) |
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double | compute_uniqueness (const Alignment &aln, const vector< MaximalExactMatch > &mems) |
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Alignment | align_maybe_flip (const Alignment &base, HandleGraph &graph, bool flip, bool traceback, bool banded_global=false, bool xdrop_alignment=false) |
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Alignment | align_maybe_flip (const Alignment &base, HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool flip, bool traceback, bool banded_global=false, bool xdrop_alignment=false) |
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bool | adjacent_positions (const Position &pos1, const Position &pos2) |
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int64_t | get_node_length (int64_t node_id) |
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bool | check_alignment (const Alignment &aln) |
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Alignment | align (const string &seq, int kmer_size=0, int stride=0, int max_mem_length=0, int band_width=1000, int band_overlap=500, bool xdrop_alignment=false) |
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Alignment | align (const Alignment &read, int kmer_size=0, int stride=0, int max_mem_length=0, int band_width=1000, int band_overlap=500, bool xdrop_alignment=false) |
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vector< Alignment > | align_multi (const Alignment &aln, int kmer_size=0, int stride=0, int max_mem_length=0, int band_width=1000, int band_overlap=500, bool xdrop_alignment=false) |
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pair< vector< Alignment >, vector< Alignment > > | align_paired_multi (const Alignment &read1, const Alignment &read2, bool &queued_resolve_later, int max_mem_length=0, bool only_top_scoring_pair=false, bool retrying=false, bool xdrop_alignment=false) |
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double | compute_cluster_mapping_quality (const vector< vector< MaximalExactMatch > > &clusters, int read_length) |
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double | estimate_max_possible_mapping_quality (int length, double min_diffs, double next_min_diffs) |
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double | max_possible_mapping_quality (int length) |
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int64_t | graph_mixed_distance_estimate (pos_t pos1, pos_t pos2, int64_t maximum) |
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int64_t | approx_distance (pos_t pos1, pos_t pos2) |
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int64_t | approx_position (pos_t pos) |
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int64_t | approx_alignment_position (const Alignment &aln) |
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Position | alignment_end_position (const Alignment &aln) |
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int64_t | approx_fragment_length (const Alignment &aln1, const Alignment &aln2) |
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vector< pos_t > | likely_mate_positions (const Alignment &aln, bool is_first) |
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unordered_map< path_handle_t, int64_t > | min_pair_fragment_length (const Alignment &aln1, const Alignment &aln2) |
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| BaseMapper (PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr) |
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| BaseMapper (void) |
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int | random_match_length (double chance_random) |
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void | set_alignment_scores (int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, uint32_t xdrop_max_gap_length=default_xdrop_max_gap_length, double haplotype_consistency_exponent=1) |
| Override alignment score setting to support haplotype consistency exponent. More...
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void | set_cache_size (int new_cache_size) |
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vector< MaximalExactMatch > | find_mems_deep (string::const_iterator seq_begin, string::const_iterator seq_end, double &lcp_avg, double &fraction_filtered, int max_mem_length=0, int min_mem_length=1, int reseed_length=0, bool use_lcp_reseed_heuristic=false, bool use_diff_based_fast_reseed=false, bool include_parent_in_sub_mem_count=false, bool record_max_lcp=false, int reseed_below_count=0) |
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vector< MaximalExactMatch > | find_mems_simple (string::const_iterator seq_begin, string::const_iterator seq_end, int max_mem_length=0, int min_mem_length=1, int reseed_length=0) |
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void | rescue_high_count_order_length_mems (vector< MaximalExactMatch > &mems, size_t max_rescue_hit_count) |
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void | precollapse_order_length_runs (string::const_iterator seq_begin, vector< MaximalExactMatch > &mems) |
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void | prefilter_redundant_sub_mems (vector< MaximalExactMatch > &mems, vector< pair< int, vector< size_t >>> &sub_mem_containment_graph) |
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void | find_sub_mems (const vector< MaximalExactMatch > &mems, int parent_layer_begin, int parent_layer_end, int mem_idx, string::const_iterator next_mem_end, int min_mem_length, vector< pair< MaximalExactMatch, vector< size_t >>> &sub_mems_out) |
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void | find_sub_mems_fast (const vector< MaximalExactMatch > &mems, int parent_layer_begin, int parent_layer_end, int mem_idx, string::const_iterator leftmost_guaranteed_disjoint_bound, string::const_iterator leftmost_seeding_bound, int min_sub_mem_length, vector< pair< MaximalExactMatch, vector< size_t >>> &sub_mems_out) |
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set< pos_t > | sequence_positions (const string &seq) |
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size_t | get_adaptive_min_reseed_length (size_t parent_mem_length) |
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void | apply_haplotype_consistency_scores (const vector< Alignment * > &alns) |
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void | set_alignment_scores (int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, uint32_t xdrop_max_gap_length=default_xdrop_max_gap_length) |
| Set all the aligner scoring parameters and create the stored aligner instances. More...
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void | load_scoring_matrix (std::ifstream &matrix_stream) |
| Load a scoring amtrix from a file to set scores. More...
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void | set_fragment_length_distr_params (size_t maximum_sample_size=1000, size_t reestimation_frequency=1000, double robust_estimation_fraction=0.95) |
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bool | has_fixed_fragment_length_distr () |
| Returns true if fragment length distribution has been fixed. More...
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void | force_fragment_length_distr (double mean, double stddev) |
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vector< Alignment > | align_multi_internal (bool compute_unpaired_qualities, const Alignment &aln, int kmer_size, int stride, int max_mem_length, int band_width, int band_overlap, double &cluster_mq, int keep_multimaps=0, int additional_multimaps=0, vector< MaximalExactMatch > *restricted_mems=nullptr, bool xdrop_alignment=false) |
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void | compute_mapping_qualities (vector< Alignment > &alns, double cluster_mq, double mq_estimate, double mq_cap) |
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void | compute_mapping_qualities (pair< vector< Alignment >, vector< Alignment >> &pair_alns, double cluster_mq, double mq_estmate1, double mq_estimate2, double mq_cap1, double mq_cap2) |
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vector< Alignment > | score_sort_and_deduplicate_alignments (vector< Alignment > &all_alns, const Alignment &original_alignment) |
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void | filter_and_process_multimaps (vector< Alignment > &all_alns, int total_multimaps) |
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vector< Alignment > | align_banded (const Alignment &read, int kmer_size=0, int stride=0, int max_mem_length=0, int band_width=1000, int band_overlap=500, bool xdrop_alignment=false) |
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vector< Alignment > | align_mem_multi (const Alignment &aln, vector< MaximalExactMatch > &mems, double &cluster_mq, double lcp_avg, double fraction_filtered, int max_mem_length, int keep_multimaps, int additional_multimaps, bool xdrop_alignment=false) |
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