refgenome.hh File Reference

#include <string>
#include <vector>
#include <unordered_map>
#include <forward_list>
#include <map>
#include "antonie.hh"
#include "fastq.hh"

Go to the source code of this file.

Classes
struct	FASTQMapping
	Position of a FastQRead that is mapped here, and how (reverse complemented or with an indel, and where) More...
struct	GenomeLocusMapping
	List of all FASTQMapping s that map to a locus, plus coverage statistic. More...
struct	Unmatched
	A region with little coverage. More...
class	ReferenceGenome
	Represents a reference genome to be aligned against. More...
struct	ReferenceGenome::MatchDescriptor
	Describes how a FastQRead (not mentioned) matches to the reference (straight or in reverse), and what the matching score is. More...
struct	ReferenceGenome::LociStats
	statistics for a locus More...
struct	ReferenceGenome::LociStats::Difference
	A difference in this locus. More...
struct	ReferenceGenome::HashPos