vg
tools for working with variation graphs
vg::QualAdjAligner Member List

This is the complete list of members for vg::QualAdjAligner, including all inherited members.

align(Alignment &alignment, const HandleGraph &g, bool traceback_aln, bool print_score_matrices) constvg::QualAdjAlignervirtual
align(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &topological_order, bool traceback_aln, bool print_score_matrices) constvg::QualAdjAlignervirtual
align_global_banded(Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true) constvg::QualAdjAlignervirtual
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) constvg::QualAdjAlignervirtual
align_internal(Alignment &alignment, vector< Alignment > *multi_alignments, const HandleGraph &g, const vector< handle_t > *topological_order, bool pinned, bool pin_left, int32_t max_alt_alns, bool traceback_aln, bool print_score_matrices) constvg::QualAdjAlignerprivate
align_pinned(Alignment &alignment, const HandleGraph &g, bool pin_left) constvg::QualAdjAlignervirtual
align_pinned(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &topological_order, bool pin_left) constvg::QualAdjAlignervirtual
align_pinned_multi(Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, bool pin_left, int32_t max_alt_alns) constvg::QualAdjAlignervirtual
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) constvg::QualAdjAlignervirtual
align_xdrop(Alignment &alignment, Graph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented) constvg::QualAdjAlignervirtual
align_xdrop_multi(Alignment &alignment, Graph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented, int32_t max_alt_alns) constvg::QualAdjAlignervirtual
compute_group_mapping_quality(vector< double > &scores, vector< size_t > &group) constvg::GSSWAligner
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) constvg::GSSWAligner
compute_mapping_quality(vector< double > &scores, bool fast_approximation) constvg::GSSWAligner
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) constvg::GSSWAligner
create_gssw_graph(const HandleGraph &g) constvg::GSSWAlignerprotected
create_gssw_graph(const HandleGraph &g, const vector< handle_t > &topological_order) constvg::GSSWAlignerprotected
estimate_max_possible_mapping_quality(int length, double min_diffs, double next_min_diffs) constvg::GSSWAligner
estimate_next_best_score(int length, double min_diffs) constvg::GSSWAlignerprotected
full_length_bonusvg::GSSWAligner
gap_extensionvg::GSSWAligner
gap_openvg::GSSWAligner
get_xdrop() constvg::QualAdjAlignervirtual
graph_cigar(gssw_graph_mapping *gm) constvg::GSSWAlignerprotected
group_mapping_quality_exact(vector< double > &scaled_scores, vector< size_t > &group) constvg::GSSWAlignerprotected
gssw_mapping_to_alignment(gssw_graph *graph, gssw_graph_mapping *gm, Alignment &alignment, bool pinned, bool pin_left, bool print_score_matrices=false) constvg::GSSWAlignerprotected
GSSWAligner()=defaultvg::GSSWAlignerprotected
identify_pinning_points(const HandleGraph &graph) constvg::GSSWAlignerprotected
init_mapping_quality(double gc_content)vg::QualAdjAligner
load_scoring_matrix(std::istream &matrix_stream)vg::GSSWAlignervirtual
log_basevg::GSSWAligner
longest_detectable_gap(const Alignment &alignment, const string::const_iterator &read_pos) constvg::GSSWAligner
longest_detectable_gap(size_t read_length, size_t read_pos) constvg::GSSWAligner
longest_detectable_gap(const Alignment &alignment) constvg::GSSWAligner
mapping_quality_score_diff(double mapping_quality) constvg::GSSWAligner
matchvg::GSSWAligner
max_possible_mapping_quality(int length) constvg::GSSWAligner
max_qual_scorevg::QualAdjAligner
maximum_mapping_quality_approx(vector< double > &scaled_scores, size_t *max_idx_out)vg::GSSWAlignerstatic
maximum_mapping_quality_exact(vector< double > &scaled_scores, size_t *max_idx_out)vg::GSSWAlignerstatic
mismatchvg::GSSWAligner
nt_tablevg::GSSWAligner
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)vg::QualAdjAligner
remove_bonuses(const Alignment &aln, bool pinned=false, bool pin_left=false) constvg::GSSWAlignervirtual
scale_factorvg::QualAdjAligner
score_exact_match(const Alignment &aln, size_t read_offset, size_t length) constvg::QualAdjAlignervirtual
score_exact_match(const string &sequence, const string &base_quality) constvg::QualAdjAlignervirtual
score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) constvg::QualAdjAlignervirtual
score_gap(size_t gap_length) constvg::GSSWAligner
score_gappy_alignment(const Alignment &aln, const function< size_t(pos_t, pos_t, size_t)> &estimate_distance, bool strip_bonuses=false) constvg::GSSWAlignervirtual
score_matrixvg::GSSWAligner
score_partial_alignment(const Alignment &alignment, const HandleGraph &graph, const Path &path, string::const_iterator seq_begin) constvg::QualAdjAlignervirtual
score_to_unnormalized_likelihood_ln(double score) constvg::GSSWAligner
score_ungapped_alignment(const Alignment &aln, bool strip_bonuses=false) constvg::GSSWAlignervirtual
unreverse_graph(gssw_graph *graph) constvg::GSSWAlignerprotected
unreverse_graph_mapping(gssw_graph_mapping *gm) constvg::GSSWAlignerprotected
~GSSWAligner()vg::GSSWAlignerprotected
~QualAdjAligner(void)=defaultvg::QualAdjAligner