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void | vg::augment (MutablePathMutableHandleGraph *graph, const string &gam_path, const string &aln_format, vector< Translation > *out_translations, const string &gam_out_path, bool embed_paths, bool break_at_ends, bool remove_softclips, bool filter_out_of_graph_alignments, double min_baseq, double min_mapq, Packer *packer, size_t min_bp_coverage, double max_frac_n, bool edges_only) |
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void | vg::augment (MutablePathMutableHandleGraph *graph, vector< Path > &path_vector, const string &aln_format, vector< Translation > *out_translations, const string &gam_out_path, bool embed_paths, bool break_at_ends, bool remove_softclips, bool filter_out_of_graph_alignments, double min_baseq, double min_mapq, Packer *packer, size_t min_bp_coverage, double max_frac_n, bool edges_only) |
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void | vg::augment_impl (MutablePathMutableHandleGraph *graph, function< void(function< void(Alignment &)>, bool, bool)> iterate_gam, const string &aln_format, vector< Translation > *out_translation, const string &gam_out_path, bool embed_paths, bool break_at_ends, bool remove_soft_clips, bool filter_out_of_graph_alignments, double min_baseq, double min_mapq, Packer *packer, size_t min_bp_coverage, double max_frac_n, bool edges_only) |
| Generic version used to implement the above three methods.
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double | vg::get_avg_baseq (const Edit &edit, const string &base_quals, size_t position_in_read) |
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void | vg::find_breakpoints (const Path &path, unordered_map< id_t, set< pos_t > > &breakpoints, bool break_ends, const string &base_quals, double min_baseq, double max_frac_n) |
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unordered_map< id_t, set< pos_t > > | vg::forwardize_breakpoints (const HandleGraph *graph, const unordered_map< id_t, set< pos_t > > &breakpoints) |
| Flips the breakpoints onto the forward strand.
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void | vg::find_packed_breakpoints (const Path &path, Packer &packed_breakpoints, bool break_ends=true, const string &base_quals="", double min_baseq=0, double max_frac_n=1.) |
| Like "find_breakpoints", but store in packed structure (better for large gams and enables coverage filter)
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unordered_map< id_t, set< pos_t > > | vg::filter_breakpoints_by_coverage (const Packer &packed_breakpoints, size_t min_bp_coverage) |
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path_handle_t | vg::add_path_to_graph (MutablePathHandleGraph *graph, const Path &path) |
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map< pos_t, id_t > | vg::ensure_breakpoints (MutableHandleGraph *graph, const unordered_map< id_t, set< pos_t > > &breakpoints) |
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bool | vg::simplify_filtered_edits (HandleGraph *graph, Alignment &aln, Path &path, const map< pos_t, id_t > &node_translation, const unordered_map< id_t, size_t > &orig_node_sizes, double min_baseq, double max_frac_n) |
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Path | vg::add_nodes_and_edges (MutableHandleGraph *graph, const Path &path, const map< pos_t, id_t > &node_translation, unordered_map< pair< pos_t, string >, vector< id_t > > &added_seqs, unordered_map< id_t, Path > &added_nodes, const unordered_map< id_t, size_t > &orig_node_sizes, size_t max_node_size=1024) |
| This version doesn't require a set of dangling sides to populate
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Path | vg::add_nodes_and_edges (MutableHandleGraph *graph, const Path &path, const map< pos_t, id_t > &node_translation, unordered_map< pair< pos_t, string >, vector< id_t > > &added_seqs, unordered_map< id_t, Path > &added_nodes, const unordered_map< id_t, size_t > &orig_node_sizes, set< NodeSide > &dangling, size_t max_node_size) |
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vector< Translation > | vg::make_translation (const HandleGraph *graph, const map< pos_t, id_t > &node_translation, const unordered_map< id_t, Path > &added_nodes, const unordered_map< id_t, size_t > &orig_node_sizes) |
| Produce a graph Translation object from information about the editing process.
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void | vg::add_edges_only (MutableHandleGraph *graph, function< void(function< void(Alignment &)>, bool, bool)> iterate_gam, double min_mapq, size_t min_bp_coverage) |
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