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| vector< size_t > | vg::subpath_topological_order (const multipath_alignment_t &multipath_aln, bool do_index) |
| | Return either the vector of topological order by index or the vector of indexes within the topological order. More...
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| void | vg::topologically_order_subpaths (multipath_alignment_t &multipath_aln) |
| | Put subpaths in topological order (assumed to be true for other algorithms) More...
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| void | vg::remove_empty_alignment_sections (multipath_alignment_t &multipath_aln) |
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| void | vg::identify_start_subpaths (multipath_alignment_t &multipath_aln) |
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| void | vg::clear_alignment (multipath_alignment_t &multipath_aln) |
| | Clear all of the field associated with the alignment. More...
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| tuple< MultipathProblem, int64_t, int32_t > | vg::run_multipath_dp (const multipath_alignment_t &multipath_aln, bool subpath_global=false, bool forward=true) |
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| template<typename TracebackIterator > |
| void | vg::populate_path_from_traceback (const multipath_alignment_t &multipath_aln, const MultipathProblem &problem, TracebackIterator traceback_start, TracebackIterator traceback_end, Path *output) |
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| int32_t | vg::optimal_alignment_internal (const multipath_alignment_t &multipath_aln, Alignment *aln_out, bool subpath_global) |
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| void | vg::optimal_alignment (const multipath_alignment_t &multipath_aln, Alignment &aln_out, bool subpath_global) |
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| int32_t | vg::optimal_alignment_score (const multipath_alignment_t &multipath_aln, bool subpath_global) |
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| int32_t | vg::worst_alignment_score (const multipath_alignment_t &multipath_aln) |
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| void | vg::remove_low_scoring_sections (multipath_alignment_t &multipath_aln, int32_t max_score_diff) |
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| vector< Alignment > | vg::optimal_alignments (const multipath_alignment_t &multipath_aln, size_t count) |
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| vector< Alignment > | vg::optimal_alignments_with_disjoint_subpaths (const multipath_alignment_t &multipath_aln, size_t count) |
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| vector< Alignment > | vg::haplotype_consistent_alignments (const multipath_alignment_t &multipath_aln, const haplo::ScoreProvider &score_provider, size_t soft_count, size_t hard_count, bool optimal_first) |
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| pair< int64_t, int64_t > | vg::aligned_interval (const multipath_alignment_t &multipath_aln) |
| | The indexes on the read sequence of the portion of the read that is aligned outside of soft clips. More...
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| void | vg::rev_comp_subpath (const subpath_t &subpath, const function< int64_t(int64_t)> &node_length, subpath_t &rev_comp_out) |
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| void | vg::rev_comp_multipath_alignment (const multipath_alignment_t &multipath_aln, const function< int64_t(int64_t)> &node_length, multipath_alignment_t &rev_comp_out) |
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| void | vg::rev_comp_multipath_alignment_in_place (multipath_alignment_t *multipath_aln, const function< int64_t(int64_t)> &node_length) |
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| void | vg::convert_multipath_alignment_char (multipath_alignment_t &multipath_aln, char from, char to) |
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| void | vg::convert_Us_to_Ts (multipath_alignment_t &multipath_aln) |
| | Replaces all U's in the sequence and the aligned Paths with T's. More...
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| void | vg::convert_Ts_to_Us (multipath_alignment_t &multipath_aln) |
| | Replaces all T's in the sequence and the aligned Paths with U's. More...
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| template<class ProtoAlignment > |
| void | vg::transfer_from_proto_annotation (const ProtoAlignment &from, multipath_alignment_t &to) |
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| template<class ProtoAlignment > |
| void | vg::transfer_to_proto_annotation (const multipath_alignment_t &from, ProtoAlignment &to) |
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| template<class ProtoAlignment1 , class ProtoAlignment2 > |
| void | vg::transfer_between_proto_annotation (const ProtoAlignment1 &from, ProtoAlignment2 &to) |
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| template<class Alignment1 , class Alignment2 > |
| void | vg::transfer_uniform_metadata (const Alignment1 &from, Alignment2 &to) |
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| void | vg::to_proto_multipath_alignment (const multipath_alignment_t &multipath_aln, MultipathAlignment &proto_multipath_aln_out) |
| | Convert an STL-based multipath_alignment_t to a protobuf MultipathAlignment. More...
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| void | vg::from_proto_multipath_alignment (const MultipathAlignment &proto_multipath_aln, multipath_alignment_t &multipath_aln_out) |
| | Convert a protobuf MultipathAlignment to an STL-based multipath_alignment_t. More...
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| void | vg::to_multipath_alignment (const Alignment &aln, multipath_alignment_t &multipath_aln_out) |
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| void | vg::transfer_read_metadata (const MultipathAlignment &from, multipath_alignment_t &to) |
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| void | vg::transfer_read_metadata (const multipath_alignment_t &from, MultipathAlignment &to) |
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| void | vg::transfer_read_metadata (const multipath_alignment_t &from, multipath_alignment_t &to) |
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| void | vg::transfer_read_metadata (const Alignment &from, multipath_alignment_t &to) |
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| void | vg::transfer_read_metadata (const multipath_alignment_t &from, Alignment &to) |
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| void | vg::transfer_read_metadata (const Alignment &from, Alignment &to) |
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| void | vg::transfer_proto_metadata (const Alignment &from, MultipathAlignment &to) |
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| void | vg::transfer_proto_metadata (const MultipathAlignment &from, Alignment &to) |
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| void | vg::merge_non_branching_subpaths (multipath_alignment_t &multipath_aln, const unordered_set< size_t > *prohibited_merges) |
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| void | vg::connected_comps_do (const multipath_alignment_t &multipath_aln, function< void(void)> &on_new_component, function< void(size_t)> &on_new_node) |
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| size_t | vg::num_connected_components (const multipath_alignment_t &multipath_aln) |
| | Returns the number of connected components in the multipath alignment. More...
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| vector< vector< int64_t > > | vg::connected_components (const multipath_alignment_t &multipath_aln) |
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| void | vg::extract_sub_multipath_alignment (const multipath_alignment_t &multipath_aln, const vector< int64_t > &subpath_indexes, multipath_alignment_t &sub_multipath_aln) |
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| void | vg::append_multipath_alignment (multipath_alignment_t &multipath_aln, const multipath_alignment_t &to_append) |
| | Add the subpaths of one multipath alignment onto another. More...
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| bool | vg::contains_connection (const multipath_alignment_t &multipath_aln) |
| | Returns true if any subpath has a connection adjacency. More...
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| vector< tuple< int64_t, int64_t, int64_t, int64_t > > | vg::search_multipath_alignment (const multipath_alignment_t &multipath_aln, const pos_t &graph_pos, int64_t seq_pos) |
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| pair< tuple< int64_t, int64_t, int64_t >, vector< tuple< int64_t, int64_t, int64_t, int64_t > > > | vg::trace_path (const multipath_alignment_t &multipath_aln, const Path &path, int64_t subpath_idx, int64_t mapping_idx, int64_t edit_idx, int64_t base_idx, bool search_left, int64_t search_limit) |
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| bool | vg::contains_match (const multipath_alignment_t &multipath_aln, const pos_t &pos, int64_t read_pos, int64_t match_length) |
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| vector< pair< int, char > > | vg::cigar_against_path (const multipath_alignment_t &multipath_aln, const string &path_name, bool rev, int64_t path_pos, const PathPositionHandleGraph &graph, int64_t min_splice_length) |
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| bool | vg::validate_multipath_alignment (const multipath_alignment_t &multipath_aln, const HandleGraph &handle_graph) |
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| void | vg::view_multipath_alignment (ostream &out, const multipath_alignment_t &multipath_aln, const HandleGraph &handle_graph) |
| | Send a formatted string representation of the multipath_alignment_t into the ostream. More...
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| void | vg::view_multipath_alignment_as_dot (ostream &out, const multipath_alignment_t &multipath_aln, bool show_graph=false) |
| | Converts a multipath_alignment_t to a GraphViz Dot representation, output to the given ostream. More...
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| string | vg::debug_string (const connection_t &connection) |
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| string | vg::debug_string (const subpath_t &subpath) |
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| string | vg::debug_string (const multipath_alignment_t &multipath_aln) |
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