vg
tools for working with variation graphs
Namespaces | Functions
augment.cpp File Reference
#include "vg.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/alignment_emitter.hpp>
#include "augment.hpp"
#include "alignment.hpp"
#include "packer.hpp"
#include "annotation.hpp"

Namespaces

 vg
 

Functions

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)
 
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)
 
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.
More...
 
double vg::get_avg_baseq (const Edit &edit, const string &base_quals, size_t position_in_read)
 
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)
 
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. More...
 
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) More...
 
unordered_map< id_t, set< pos_t > > vg::filter_breakpoints_by_coverage (const Packer &packed_breakpoints, size_t min_bp_coverage)
 
path_handle_t vg::add_path_to_graph (MutablePathHandleGraph *graph, const Path &path)
 
map< pos_t, id_tvg::ensure_breakpoints (MutableHandleGraph *graph, const unordered_map< id_t, set< pos_t >> &breakpoints)
 
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)
 
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
More...
 
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)
 
vector< Translationvg::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. More...
 
void vg::add_edges_only (MutableHandleGraph *graph, function< void(function< void(Alignment &)>, bool, bool)> iterate_gam, double min_mapq, size_t min_bp_coverage)