coverage_depth.hpp File Reference

#include <iostream>
#include <algorithm>
#include <functional>
#include <cmath>
#include <limits>
#include <unordered_set>
#include <tuple>
#include "handle.hpp"
#include "statistics.hpp"
#include "packer.hpp"

Namespaces
	vg
	vg::algorithms

Typedefs
using	vg::algorithms::BinnedDepthIndex = unordered_map< string, map< size_t, map< size_t, pair< float, float > >> >

Functions
void	vg::algorithms::packed_depths (const Packer &packer, const string &path_name, size_t min_coverage, ostream &out_stream)
pair< double, double >	vg::algorithms::packed_depth_of_bin (const Packer &packer, step_handle_t start_step, step_handle_t end_plus_one_step, size_t min_coverage, bool include_deletions)
vector< tuple< size_t, size_t, double, double > >	vg::algorithms::binned_packed_depth (const Packer &packer, const string &path_name, size_t bin_size, size_t min_coverage, bool include_deletions)
BinnedDepthIndex	vg::algorithms::binned_packed_depth_index (const Packer &packer, const vector< string > &path_names, size_t min_bin_size, size_t max_bin_size, double exp_growth_factor, size_t min_coverage, bool include_deletions, bool std_err)
pair< float, float >	vg::algorithms::get_depth_from_index (const BinnedDepthIndex &depth_index, const string &path_name, size_t start_offset, size_t end_offset)
	Query index created above. More...
pair< double, double >	vg::algorithms::sample_mapping_depth (const HandleGraph &graph, const string &input_filename, size_t max_nodes, size_t random_seed, size_t min_coverage, size_t min_mapq, const string &format)
pair< double, double >	vg::algorithms::sample_mapping_depth (const HandleGraph &graph, const vector< Alignment > &alignments, size_t max_nodes, size_t random_seed, size_t min_coverage, size_t min_mapq)
	As above, but read a vector instead of a stream. More...
void	vg::algorithms::path_depths (const PathHandleGraph &graph, const string &path_name, size_t min_coverage, bool count_cycles, ostream &out_stream)
pair< double, double >	vg::algorithms::path_depth_of_bin (const PathHandleGraph &graph, step_handle_t start_step, step_handle_t end_plus_one_step, size_t min_coverage, bool count_cycles)
	like packed_depth_of_bin (above), but use paths (as in path_depths) for measuring coverage More...
vector< tuple< size_t, size_t, double, double > >	vg::algorithms::binned_path_depth (const PathHandleGraph &graph, const string &path_name, size_t bin_size, size_t min_coverage, bool count_cycles)