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| QualAdjAligner (int8_t _match=default_match, int8_t _mismatch=default_mismatch, int8_t _gap_open=default_gap_open, int8_t _gap_extension=default_gap_extension, int8_t _full_length_bonus=default_full_length_bonus, int8_t _max_scaled_score=default_max_scaled_score, uint8_t _max_qual_score=default_max_qual_score, double gc_content=default_gc_content) |
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| ~QualAdjAligner (void)=default |
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void | align (Alignment &alignment, const HandleGraph &g, bool traceback_aln, bool print_score_matrices) const |
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void | align (Alignment &alignment, const HandleGraph &g, const vector< handle_t > &topological_order, bool traceback_aln, bool print_score_matrices) const |
| Same as previous, but takes advantage of a pre-computed topological order. More...
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void | align_global_banded (Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true) const |
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void | align_pinned (Alignment &alignment, const HandleGraph &g, bool pin_left) const |
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void | align_pinned (Alignment &alignment, const HandleGraph &g, const vector< handle_t > &topological_order, bool pin_left) const |
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void | align_global_banded_multi (Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, int32_t max_alt_alns, int32_t band_padding=0, bool permissive_banding=true) const |
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void | align_pinned_multi (Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, bool pin_left, int32_t max_alt_alns) const |
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void | align_pinned_multi (Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, const vector< handle_t > &topological_order, bool pin_left, int32_t max_alt_alns) const |
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void | align_xdrop (Alignment &alignment, const HandleGraph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented) const |
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void | align_xdrop_multi (Alignment &alignment, const HandleGraph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented, int32_t max_alt_alns) const |
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const XdropAligner & | get_xdrop () const |
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void | init_mapping_quality (double gc_content) |
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int32_t | score_exact_match (const Alignment &aln, size_t read_offset, size_t length) const |
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int32_t | score_exact_match (const string &sequence, const string &base_quality) const |
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int32_t | score_exact_match (string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const |
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int32_t | score_partial_alignment (const Alignment &alignment, const HandleGraph &graph, const Path &path, string::const_iterator seq_begin) const |
| Compute the score of a path against the given range of subsequence with the given qualities. More...
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double | max_possible_mapping_quality (int length) const |
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double | estimate_max_possible_mapping_quality (int length, double min_diffs, double next_min_diffs) const |
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int32_t | score_gap (size_t gap_length) const |
| Returns the score of an insert or deletion of the given length. More...
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void | compute_mapping_quality (vector< Alignment > &alignments, int max_mapping_quality, bool fast_approximation, double cluster_mq, bool use_cluster_mq, int overlap_count, double mq_estimate, double maybe_mq_threshold, double identity_weight) const |
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void | compute_paired_mapping_quality (pair< vector< Alignment >, vector< Alignment >> &alignment_pairs, const vector< double > &frag_weights, int max_mapping_quality1, int max_mapping_quality2, bool fast_approximation, double cluster_mq, bool use_cluster_mq, int overlap_count1, int overlap_count2, double mq_estimate1, double mq_estimate2, double maybe_mq_threshold, double identity_weight) const |
| same function for paired reads, mapping qualities are stored in both alignments in the pair More...
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int32_t | compute_mapping_quality (const vector< double > &scores, bool fast_approximation, const vector< double > *multiplicities=nullptr) const |
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int32_t | compute_group_mapping_quality (const vector< double > &scores, const vector< size_t > &group, const vector< double > *multiplicities=nullptr) const |
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double | mapping_quality_score_diff (double mapping_quality) const |
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double | score_to_unnormalized_likelihood_ln (double score) const |
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size_t | longest_detectable_gap (const Alignment &alignment, const string::const_iterator &read_pos) const |
| The longest gap detectable from a read position without soft-clipping. More...
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size_t | longest_detectable_gap (size_t read_length, size_t read_pos) const |
| The longest gap detectable from a read position without soft-clipping, for a generic read. More...
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size_t | longest_detectable_gap (const Alignment &alignment) const |
| The longest gap detectable from any read position without soft-clipping. More...
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virtual int32_t | score_gappy_alignment (const Alignment &aln, const function< size_t(pos_t, pos_t, size_t)> &estimate_distance, bool strip_bonuses=false) const |
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virtual int32_t | score_ungapped_alignment (const Alignment &aln, bool strip_bonuses=false) const |
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virtual void | load_scoring_matrix (std::istream &matrix_stream) |
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virtual int32_t | remove_bonuses (const Alignment &aln, bool pinned=false, bool pin_left=false) const |
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static double | maximum_mapping_quality_exact (const vector< double > &scaled_scores, size_t *max_idx_out, const vector< double > *multiplicities=nullptr) |
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static double | maximum_mapping_quality_approx (const vector< double > &scaled_scores, size_t *max_idx_out, const vector< double > *multiplicities=nullptr) |
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| GSSWAligner ()=default |
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| ~GSSWAligner () |
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gssw_graph * | create_gssw_graph (const HandleGraph &g) const |
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gssw_graph * | create_gssw_graph (const HandleGraph &g, const vector< handle_t > &topological_order) const |
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unordered_set< id_t > | identify_pinning_points (const HandleGraph &graph) const |
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void | unreverse_graph_mapping (gssw_graph_mapping *gm) const |
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void | unreverse_graph (gssw_graph *graph) const |
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void | gssw_mapping_to_alignment (gssw_graph *graph, gssw_graph_mapping *gm, Alignment &alignment, bool pinned, bool pin_left, bool print_score_matrices=false) const |
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string | graph_cigar (gssw_graph_mapping *gm) const |
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double | group_mapping_quality_exact (const vector< double > &scaled_scores, const vector< size_t > &group, const vector< double > *multiplicities=nullptr) const |
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double | estimate_next_best_score (int length, double min_diffs) const |
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void | init_mapping_quality (double gc_content) |
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An aligner that uses read base qualities to adjust its scores and alignments.