From e164ca8c992dde681223c0e54d96a024b0410320 Mon Sep 17 00:00:00 2001 From: VG Doc Bot Date: Thu, 18 Jul 2024 03:51:20 +0000 Subject: [PATCH] Commit new auto-generated docs --- ...vg_1_1MultipathAlignmentGraph-members.html | 6 +- classvg_1_1MultipathAlignmentGraph.html | 46 ++++++++++---- classvg_1_1Surjector-members.html | 61 ++++++++++--------- classvg_1_1Surjector.html | 19 ++++++ functions_a.html | 4 +- functions_func_a.html | 4 +- functions_m.html | 19 +++--- functions_vars_m.html | 1 + search/all_1.js | 4 +- search/all_d.js | 2 +- search/functions_1.js | 4 +- search/variables_d.js | 2 +- 12 files changed, 107 insertions(+), 65 deletions(-) diff --git a/classvg_1_1MultipathAlignmentGraph-members.html b/classvg_1_1MultipathAlignmentGraph-members.html index adbe7f66ac8..cc5507bac16 100644 --- a/classvg_1_1MultipathAlignmentGraph-members.html +++ b/classvg_1_1MultipathAlignmentGraph-members.html @@ -75,9 +75,9 @@ - - - + + + diff --git a/classvg_1_1MultipathAlignmentGraph.html b/classvg_1_1MultipathAlignmentGraph.html index 38a8f5ab390..5e2e6472abb 100644 --- a/classvg_1_1MultipathAlignmentGraph.html +++ b/classvg_1_1MultipathAlignmentGraph.html @@ -128,10 +128,10 @@ - - - - + + + + @@ -184,8 +184,8 @@ - - + +
add_decomposed_tail_alignments(const Alignment &alignment, const HandleGraph &align_graph, multipath_alignment_t &multipath_aln_out, unordered_set< size_t > &prohibited_merges, vector< pair< path_t, int32_t >> &shared_tail_alns, vector< vector< pair< path_t, int32_t >>> &unshared_tail_alns, size_t attachment_idx, bool to_left, size_t unmergeable_len, const GSSWAligner *aligner, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr)vg::MultipathAlignmentGraphprotected
add_reachability_edges(const HandleGraph &vg, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, vector< size_t > *path_node_provenance=nullptr)vg::MultipathAlignmentGraph
align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, unordered_map< handle_t, bool > *left_align_strand=nullptr)vg::MultipathAlignmentGraph
align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, function< size_t(const Alignment &, const HandleGraph &)> band_padding_function, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, unordered_map< handle_t, bool > *left_align_strand=nullptr)vg::MultipathAlignmentGraph
align_tails(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t min_paths, unordered_set< size_t > *sources=nullptr)vg::MultipathAlignmentGraphprotected
align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, unordered_map< handle_t, bool > *left_align_strand=nullptr)vg::MultipathAlignmentGraph
align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length, bool simplify_topologies, size_t unmergeable_len, function< size_t(const Alignment &, const HandleGraph &)> band_padding_function, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, unordered_map< handle_t, bool > *left_align_strand=nullptr)vg::MultipathAlignmentGraph
align_tails(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t min_paths, size_t max_tail_length, unordered_set< size_t > *sources=nullptr)vg::MultipathAlignmentGraphprotected
clear_reachability_edges()vg::MultipathAlignmentGraph
collapse_order_length_runs(const HandleGraph &graph, gcsa::GCSA *gcsa, vector< size_t > &path_node_provenance)vg::MultipathAlignmentGraphprotected
count_reachability_edges() constvg::MultipathAlignmentGraph
void add_reachability_edges (const HandleGraph &vg, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, vector< size_t > *path_node_provenance=nullptr)
 Add edges between reachable nodes and split nodes at overlaps. More...
 
void align (const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, unordered_map< handle_t, bool > *left_align_strand=nullptr)
 
void align (const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, function< size_t(const Alignment &, const HandleGraph &)> band_padding_function, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, unordered_map< handle_t, bool > *left_align_strand=nullptr)
 
void align (const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, unordered_map< handle_t, bool > *left_align_strand=nullptr)
 
void align (const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length, bool simplify_topologies, size_t unmergeable_len, function< size_t(const Alignment &, const HandleGraph &)> band_padding_function, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, unordered_map< handle_t, bool > *left_align_strand=nullptr)
 
void to_dot (ostream &out, const Alignment *alignment=nullptr) const
 
vector< vector< id_t > > get_connected_components () const
vector< pair< size_t, size_t > > get_cut_segments (path_t &path, SnarlManager *cutting_snarls, SnarlDistanceIndex *dist_index, const function< pair< id_t, bool >(id_t)> &project, int64_t max_snarl_cut_size) const
 Returns the intervals of the path that lie inside of snarls. More...
 
unordered_map< bool, unordered_map< size_t, vector< Alignment > > > align_tails (const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t min_paths, unordered_set< size_t > *sources=nullptr)
 
unordered_map< bool, unordered_map< size_t, vector< Alignment > > > align_tails (const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t min_paths, size_t max_tail_length, unordered_set< size_t > *sources=nullptr)
 
void add_decomposed_tail_alignments (const Alignment &alignment, const HandleGraph &align_graph, multipath_alignment_t &multipath_aln_out, unordered_set< size_t > &prohibited_merges, vector< pair< path_t, int32_t >> &shared_tail_alns, vector< vector< pair< path_t, int32_t >>> &unshared_tail_alns, size_t attachment_idx, bool to_left, size_t unmergeable_len, const GSSWAligner *aligner, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr)
 
@@ -920,8 +920,8 @@

-

◆ align() [1/2]

+ +

◆ align() [1/2]

@@ -974,6 +974,12 @@

double 

+ + + + + + @@ -1040,8 +1046,8 @@

-

◆ align() [2/2]

+ +

◆ align() [2/2]

@@ -1094,6 +1100,12 @@

double 

+ + + + + + @@ -1160,8 +1172,8 @@

-

◆ align_tails()

+ +

◆ align_tails()

@@ -1217,6 +1229,12 @@

size_t 

+ + + + + + @@ -1235,7 +1253,9 @@

-

Generate alignments of the tails of the query sequence, beyond the sources and sinks. The Alignment passed must be the one that owns the sequence we are working on. Returns a map from tail (left=false, right=true), to a map from subpath number to all the Alignments of the tail off of that subpath. Also computes the source subpaths and adds their numbers to the given set if not null. If dynamic alignment count is also selected, can indicate a minimum number of paths that must be in the extending graph in order to do an alignment

+

Generate alignments of the tails of the query sequence, beyond the sources and sinks. The Alignment passed must be the one that owns the sequence we are working on. Returns a map from tail (left=false, right=true), to a map from subpath number to all the Alignments of the tail off of that subpath. Also computes the source subpaths and adds their numbers to the given set if not null.

+

If a tail is longer than max_tail_length, produces an alignment softclipping it.

+

If dynamic alignment count is also selected, can indicate a minimum number of paths that must be in the extending graph in order to do an alignment

diff --git a/classvg_1_1Surjector-members.html b/classvg_1_1Surjector-members.html index 542fa610bae..f66d7913ae1 100644 --- a/classvg_1_1Surjector-members.html +++ b/classvg_1_1Surjector-members.html @@ -101,36 +101,37 @@

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
pessimistic_tail_gap_multiplier,
size_t max_tail_length,
pessimistic_tail_gap_multiplier,
size_t max_tail_length,
min_paths,
size_t max_tail_length,
max_low_complexity_anchor_prunevg::Surjector
max_subgraph_basesvg::Surjector
max_tail_anchor_prunevg::Surjector
min_fold_coverage_for_downsamplevg::Surjector
min_shift_for_prunevg::Surjector
min_splice_lengthvg::Surjector
min_splice_repair_lengthvg::Surjector
multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) constvg::Surjector
multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) constvg::Surjector
multi_surject(const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) constvg::Surjector
parse_matrix(std::istream &matrix_stream)vg::AlignerClientstatic
path_chunk_t typedefvg::Surjector
path_score_annotations(const unordered_map< pair< path_handle_t, bool >, pair< AlnType, pair< step_handle_t, step_handle_t >>> &surjections) constvg::Surjectorprotected
prune_suspicious_anchorsvg::Surjector
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) constvg::Surjectorprotected
qual_adj_alignervg::AlignerClientprivate
realigning_surject(const PathPositionHandleGraph *graph, const Alignment &source, const path_handle_t &path_handle, bool rev_strand, const vector< path_chunk_t > &path_chunks, const vector< pair< step_handle_t, step_handle_t >> &ref_chunks, pair< step_handle_t, step_handle_t > &path_range_out, bool allow_negative_scores, bool preserve_N_alignments=false, bool sinks_are_anchors=false, bool sources_are_anchors=false, vector< pair< step_handle_t, step_handle_t >> *all_path_ranges_out=nullptr) constvg::Surjectorprotected
regular_alignervg::AlignerClientprivate
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) constvg::Surjectorprotected
reverse_adjacencies(const vector< vector< size_t >> &adj) constvg::Surjectorprotected
set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)vg::AlignerClientvirtual
set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)vg::AlignerClientvirtual
set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)vg::AlignerClientvirtual
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, bool rev_strand, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out) constvg::Surjectorprotected
shift_prune_diffvg::Surjector
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, bool rev_strand, 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) constvg::Surjectorprotected
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) constvg::Surjector
surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) constvg::Surjector
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) constvg::Surjector
surject_internal(const Alignment *source_aln, const multipath_alignment_t *source_mp_aln, vector< Alignment > *alns_out, vector< multipath_alignment_t > *mp_alns_out, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool all_paths, bool allow_negative_scores, bool preserve_deletions) constvg::Surjectorprotected
Surjector(const PathPositionHandleGraph *graph)vg::Surjector
transitive_reduction(const vector< vector< size_t >> &adj) constvg::Surjectorprotected
warned_about_subgraph_sizevg::Surjectormutable
max_tail_lengthvg::Surjector
min_fold_coverage_for_downsamplevg::Surjector
min_shift_for_prunevg::Surjector
min_splice_lengthvg::Surjector
min_splice_repair_lengthvg::Surjector
multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) constvg::Surjector
multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) constvg::Surjector
multi_surject(const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) constvg::Surjector
parse_matrix(std::istream &matrix_stream)vg::AlignerClientstatic
path_chunk_t typedefvg::Surjector
path_score_annotations(const unordered_map< pair< path_handle_t, bool >, pair< AlnType, pair< step_handle_t, step_handle_t >>> &surjections) constvg::Surjectorprotected
prune_suspicious_anchorsvg::Surjector
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) constvg::Surjectorprotected
qual_adj_alignervg::AlignerClientprivate
realigning_surject(const PathPositionHandleGraph *graph, const Alignment &source, const path_handle_t &path_handle, bool rev_strand, const vector< path_chunk_t > &path_chunks, const vector< pair< step_handle_t, step_handle_t >> &ref_chunks, pair< step_handle_t, step_handle_t > &path_range_out, bool allow_negative_scores, bool preserve_N_alignments=false, bool sinks_are_anchors=false, bool sources_are_anchors=false, vector< pair< step_handle_t, step_handle_t >> *all_path_ranges_out=nullptr) constvg::Surjectorprotected
regular_alignervg::AlignerClientprivate
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) constvg::Surjectorprotected
reverse_adjacencies(const vector< vector< size_t >> &adj) constvg::Surjectorprotected
set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)vg::AlignerClientvirtual
set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)vg::AlignerClientvirtual
set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)vg::AlignerClientvirtual
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, bool rev_strand, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out) constvg::Surjectorprotected
shift_prune_diffvg::Surjector
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, bool rev_strand, 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) constvg::Surjectorprotected
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) constvg::Surjector
surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) constvg::Surjector
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) constvg::Surjector
surject_internal(const Alignment *source_aln, const multipath_alignment_t *source_mp_aln, vector< Alignment > *alns_out, vector< multipath_alignment_t > *mp_alns_out, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool all_paths, bool allow_negative_scores, bool preserve_deletions) constvg::Surjectorprotected
Surjector(const PathPositionHandleGraph *graph)vg::Surjector
transitive_reduction(const vector< vector< size_t >> &adj) constvg::Surjectorprotected
warned_about_subgraph_sizevg::Surjectormutable
diff --git a/classvg_1_1Surjector.html b/classvg_1_1Surjector.html index 2904ce14952..50fe48339c7 100644 --- a/classvg_1_1Surjector.html +++ b/classvg_1_1Surjector.html @@ -140,6 +140,9 @@ int64_t min_splice_repair_length = 250  the minimum length apparent intron that we will try to repair More...
  +size_t max_tail_length = 10000 + the maximum length of a tail that we will try to align More...
+  size_t max_subgraph_bases = 100 * 1024  How big of a graph in bp should we ever try to align against for realigning surjection? More...
  @@ -1833,6 +1836,22 @@

+ + + +

◆ max_tail_length

+ +
+
+ + + + +
size_t vg::Surjector::max_tail_length = 10000
+
+ +

the maximum length of a tail that we will try to align

+
diff --git a/functions_a.html b/functions_a.html index 865200fba1b..5ed2f7509e0 100644 --- a/functions_a.html +++ b/functions_a.html @@ -341,7 +341,7 @@

- a -

    , vg::DeletionAligner , vg::DozeuInterface , vg::Mapper -, vg::MultipathAlignmentGraph +, vg::MultipathAlignmentGraph , vg::QualAdjAligner , vg::SSWAligner , vg::VG @@ -409,7 +409,7 @@

    - a -

      : vg::MinimizerMapper
    • align_tails() -: vg::MultipathAlignmentGraph +: vg::MultipathAlignmentGraph
    • align_to_cluster_graph_pairs() : vg::MultipathMapper diff --git a/functions_func_a.html b/functions_func_a.html index 350f0100b18..2c477fd0f32 100644 --- a/functions_func_a.html +++ b/functions_func_a.html @@ -278,7 +278,7 @@

      - a -

        , vg::DeletionAligner , vg::DozeuInterface , vg::Mapper -, vg::MultipathAlignmentGraph +, vg::MultipathAlignmentGraph , vg::QualAdjAligner , vg::SSWAligner , vg::VG @@ -343,7 +343,7 @@

        - a -

          : vg::MinimizerMapper
        • align_tails() -: vg::MultipathAlignmentGraph +: vg::MultipathAlignmentGraph
        • align_to_cluster_graph_pairs() : vg::MultipathMapper diff --git a/functions_m.html b/functions_m.html index 987010e7248..483cd4d2c66 100644 --- a/functions_m.html +++ b/functions_m.html @@ -712,6 +712,7 @@

          - m -

          • max_tail_length : vg::MinimizerMapper +, vg::Surjector
          • max_tail_merge_supress_length : vg::MultipathMapper @@ -812,13 +813,13 @@

            - m -

              : vg::BaseMapper
            • MEMAccelerator() -: vg::MEMAccelerator +: vg::MEMAccelerator
            • MEMChainModel() : vg::MEMChainModel
            • MEMChainModelVertex() -: vg::MEMChainModelVertex +: vg::MEMChainModelVertex
            • memcluster_t : vg::MultipathMapper @@ -833,7 +834,7 @@

              - m -

                : vg::MEMAccelerator
              • MemoizingGraph() -: vg::MemoizingGraph +: vg::MemoizingGraph
              • memory_high_water_kb : vg::Watchdog @@ -845,7 +846,7 @@

                - m -

                  : GBWTConfig , vg::Funnel , vg::IntegratedSnarlFinder::MergedAdjacencyGraph -, vg::VG +, vg::VG
                • merge_fast : GBWTConfig @@ -1303,7 +1304,7 @@

                  - m -

                    : vg::AbstractReadSampler
                  • multi_surject() -: vg::Surjector +: vg::Surjector
                  • multiallelic_sv_warned : vg::Constructor @@ -1312,7 +1313,7 @@

                    - m -

                      : vg::MultipathMapper
                    • multipath_alignment_t() -: vg::multipath_alignment_t +: vg::multipath_alignment_t
                    • multipath_map() : vg::MultipathMapper @@ -1324,7 +1325,7 @@

                      - m -

                        : vg::MultipathAlignmentEmitter
                      • MultipathAlignmentGraph() -: vg::MultipathAlignmentGraph +: vg::MultipathAlignmentGraph
                      • MultipathMapper() : vg::MultipathMapper @@ -1345,13 +1346,13 @@

                        - m -

                          : vg::NGSSimulator
                        • mutable_connection() -: vg::subpath_t +: vg::subpath_t
                        • mutable_edit() : vg::path_mapping_t
                        • mutable_mapping() -: vg::path_t +: vg::path_t
                        • mutable_next() : vg::subpath_t diff --git a/functions_vars_m.html b/functions_vars_m.html index fb27a38163c..b0917ba9eda 100644 --- a/functions_vars_m.html +++ b/functions_vars_m.html @@ -492,6 +492,7 @@

                          - m -

                          • max_tail_length : vg::MinimizerMapper +, vg::Surjector
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