minimizer_mapper_from_chains.cpp File Reference

#include "minimizer_mapper.hpp"
#include "annotation.hpp"
#include "banded_global_aligner.hpp"
#include "crash.hpp"
#include "path_subgraph.hpp"
#include "multipath_alignment.hpp"
#include "split_strand_graph.hpp"
#include "subgraph.hpp"
#include "statistics.hpp"
#include "algorithms/alignment_path_offsets.hpp"
#include "algorithms/count_covered.hpp"
#include "algorithms/intersect_path_offsets.hpp"
#include "algorithms/extract_containing_graph.hpp"
#include "algorithms/extract_connecting_graph.hpp"
#include "algorithms/extract_extending_graph.hpp"
#include "algorithms/chain_items.hpp"
#include "algorithms/pad_band.hpp"
#include <bdsg/overlays/strand_split_overlay.hpp>
#include <gbwtgraph/algorithms.h>
#include <gbwtgraph/cached_gbwtgraph.h>
#include <iostream>
#include <algorithm>
#include <cmath>
#include <cfloat>

Classes
class	vg::ChainAlignmentFailedError

Namespaces
	vg

Macros
#define	debug

Functions
std::vector< std::pair< size_t, size_t > >	vg::find_anchor_intervals (const std::pair< size_t, size_t > &read_interval, const std::vector< size_t > &mismatch_positions, const std::vector< size_t > &seed_positions)

Detailed Description

Defines the code for the long-read code path for the minimizer-and-GBWT-based mapper (long read Giraffe).

Macro Definition Documentation

debug

#define debug