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vg
tools for working with variation graphs
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#include <stdio.h>#include <vector>#include <list>#include <unordered_map>#include <algorithm>#include <vg/vg.pb.h>#include "path.hpp"#include "alignment.hpp"#include "utility.hpp"#include "handle.hpp"Namespaces | |
| haplo | |
| vg | |
Functions | |
| void | vg::topologically_order_subpaths (MultipathAlignment &multipath_aln) |
| Put subpaths in topological order (assumed to be true for other algorithms) More... | |
| void | vg::identify_start_subpaths (MultipathAlignment &multipath_aln) |
| void | vg::optimal_alignment (const MultipathAlignment &multipath_aln, Alignment &aln_out, bool subpath_global) |
| int32_t | vg::optimal_alignment_score (const MultipathAlignment &multipath_aln, bool subpath_global) |
| vector< Alignment > | vg::optimal_alignments (const MultipathAlignment &multipath_aln, size_t count) |
| vector< Alignment > | vg::optimal_alignments_with_disjoint_subpaths (const MultipathAlignment &multipath_aln, size_t count) |
| vector< Alignment > | vg::haplotype_consistent_alignments (const MultipathAlignment &multipath_aln, const haplo::ScoreProvider &score_provider, size_t soft_count, size_t hard_count, bool optimal_first) |
| void | vg::rev_comp_multipath_alignment (const MultipathAlignment &multipath_aln, const function< int64_t(int64_t)> &node_length, MultipathAlignment &rev_comp_out) |
| void | vg::rev_comp_multipath_alignment_in_place (MultipathAlignment *multipath_aln, const function< int64_t(int64_t)> &node_length) |
| void | vg::to_multipath_alignment (const Alignment &aln, MultipathAlignment &multipath_aln_out) |
| void | vg::transfer_read_metadata (const Alignment &from, MultipathAlignment &to) |
| void | vg::transfer_read_metadata (const MultipathAlignment &from, Alignment &to) |
| void | vg::transfer_read_metadata (const MultipathAlignment &from, MultipathAlignment &to) |
| void | vg::transfer_read_metadata (const Alignment &from, Alignment &to) |
| void | vg::merge_non_branching_subpaths (MultipathAlignment &multipath_aln) |
| Merges non-branching paths in a multipath alignment in place. More... | |
| vector< vector< int64_t > > | vg::connected_components (const MultipathAlignment &multipath_aln) |
| void | vg::extract_sub_multipath_alignment (const MultipathAlignment &multipath_aln, const vector< int64_t > &subpath_indexes, MultipathAlignment &sub_multipath_aln) |
| bool | vg::validate_multipath_alignment (const MultipathAlignment &multipath_aln, const HandleGraph &handle_graph) |
| void | vg::view_multipath_alignment (ostream &out, const MultipathAlignment &multipath_aln, const HandleGraph &handle_graph) |
| Send a formatted string representation of the MultipathAlignment into the ostream. More... | |
| void | vg::view_multipath_alignment_as_dot (ostream &out, const MultipathAlignment &multipath_aln, bool show_graph=false) |
| Converts a MultipathAlignment to a GraphViz Dot representation, output to the given ostream. More... | |
utility functions for the MultipathAlignment protobuf object
1.8.16