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_t >	vg::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< 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. 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)