Antonie
Classes
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
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