|
| Surjector (const PathPositionHandleGraph *graph) |
|
Alignment | surject (const Alignment &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const |
|
Alignment | surject (const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const |
|
multipath_alignment_t | surject (const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const |
|
void | set_alignment_scores (int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) |
| Set all the aligner scoring parameters and create the stored aligner instances. More...
|
|
void | set_alignment_scores (std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) |
|
void | set_alignment_scores (const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) |
|
|
void | surject_internal (const Alignment *source_aln, const multipath_alignment_t *source_mp_aln, Alignment *aln_out, multipath_alignment_t *mp_aln_out, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores, bool preserve_deletions) const |
|
Alignment | realigning_surject (const PathPositionHandleGraph *graph, const Alignment &source, const path_handle_t &path_handle, const vector< path_chunk_t > &path_chunks, pair< step_handle_t, step_handle_t > &path_range_out, bool allow_negative_scores, bool preserve_N_alignments=false, bool preserve_tail_indel_anchors=false) const |
|
multipath_alignment_t | spliced_surject (const PathPositionHandleGraph *path_position_graph, const string &src_sequence, const string &src_quality, const int32_t src_mapping_quality, const path_handle_t &path_handle, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections, pair< step_handle_t, step_handle_t > &path_range_out, bool allow_negative_scores, bool deletions_as_splices) const |
|
unordered_map< path_handle_t, pair< vector< path_chunk_t >, vector< pair< step_handle_t, step_handle_t > > > > | extract_overlapping_paths (const PathPositionHandleGraph *graph, const Alignment &source, const unordered_set< path_handle_t > &surjection_paths) const |
| get the chunks of the alignment path that follow the given reference paths More...
|
|
unordered_map< path_handle_t, pair< vector< path_chunk_t >, vector< pair< step_handle_t, step_handle_t > > > > | extract_overlapping_paths (const PathPositionHandleGraph *graph, const multipath_alignment_t &source, const unordered_set< path_handle_t > &surjection_paths, unordered_map< path_handle_t, vector< tuple< size_t, size_t, int32_t >>> &connections_out) const |
| same semantics except for a multipath alignment More...
|
|
void | filter_redundant_path_chunks (vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections) const |
|
pair< size_t, size_t > | compute_path_interval (const PathPositionHandleGraph *graph, const Alignment &source, path_handle_t path_handle, const vector< path_chunk_t > &path_chunks) const |
| compute the widest interval of path positions that the realigned sequence could align to More...
|
|
unordered_map< id_t, pair< id_t, bool > > | extract_linearized_path_graph (const PathPositionHandleGraph *graph, MutableHandleGraph *into, path_handle_t path_handle, size_t first, size_t last) const |
| make a linear graph that corresponds to a path interval, possibly duplicating nodes in case of cycles More...
|
|
void | set_path_position (const PathPositionHandleGraph *graph, const pos_t &init_surj_pos, const pos_t &final_surj_pos, const step_handle_t &range_begin, const step_handle_t &range_end, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out) const |
| use the graph position bounds and the path range bounds to assign a path position to a surjected read More...
|
|
vector< vector< size_t > > | reverse_adjacencies (const vector< vector< size_t >> &adj) const |
| reverses an adjacency list More...
|
|
vector< size_t > | connected_components (const vector< vector< size_t >> &adj, const vector< vector< size_t >> &rev_adj, size_t *num_comps_out) const |
|
vector< vector< size_t > > | transitive_reduction (const vector< vector< size_t >> &adj) const |
| returns the transitive reduction of a topologically sorted DAG's adjacency list More...
|
|
vector< vector< size_t > > | remove_dominated_chunks (const string &src_sequence, const vector< vector< size_t >> &adj, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections) const |
| eliminate any path chunks that have the exact same colinearities as another but are much shorter More...
|
|
vector< pair< vector< size_t >, vector< size_t > > > | find_constriction_bicliques (const vector< vector< size_t >> &adj, const string &src_sequence, const vector< path_chunk_t > &path_chunks, const vector< tuple< size_t, size_t, int32_t >> &connections) const |
|
void | prune_unconnectable (vector< vector< size_t >> &adj, vector< vector< tuple< size_t, int32_t, bool >>> &splice_adj, vector< size_t > &component, vector< vector< size_t >> &comp_groups, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks) const |
|
| AlignerClient (double gc_content_estimate=vg::default_gc_content) |
|
const GSSWAligner * | get_aligner (bool have_qualities=true) const |
|
const QualAdjAligner * | get_qual_adj_aligner () const |
|
const Aligner * | get_regular_aligner () const |
|