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/*
* annot.h
*
* Created on: Aug 3, 2009
* Author: Ben Langmead
*/
#ifndef ANNOT_H_
#define ANNOT_H_
#include <stdint.h>
#include <map>
#include <iostream>
#include <fstream>
#include "btypes.h"
/**
* Encapsulates a sorted list of reference positions that are annotated
* somehow (e.g. as a SNP).
*/
class AnnotationMap {
public:
typedef std::pair<TIndexOffU, TIndexOffU> UPair;
typedef std::pair<char, char> CharPair;
typedef std::map<UPair, CharPair> AnnotMap;
typedef std::map<UPair, CharPair>::const_iterator Iter;
AnnotationMap(const char *fname) {
fname_ = fname;
parse();
}
/**
* Give a reference coordinate in the index, translate it into a
* new reference coordinate via the reference map supplied by the
* user.
*/
Iter lower_bound(const UPair& h) const {
return map_.lower_bound(h);
}
Iter begin() const {
return map_.begin();
}
Iter end() const {
return map_.end();
}
protected:
/**
* Parse an annotation-map file.
*/
void parse();
/// filename of file containing the annotation map
const char *fname_;
/// maps reference positions to character annotations
AnnotMap map_;
};
#endif /* ANNOT_H_ */
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