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/*
* refmap.h
*
* Created on: Aug 3, 2009
* Author: Ben Langmead
*/
#ifndef REFMAP_H_
#define REFMAP_H_
#include <stdint.h>
#include <cassert>
#include <vector>
#include <iostream>
#include <fstream>
#include "btypes.h"
class ReferenceMap {
typedef std::pair<TIndexOffU, TIndexOffU> UPair;
public:
ReferenceMap(const char *fname, bool parseNames) {
fname_ = fname;
parseNames_ = parseNames;
parse();
}
/**
* Give a reference coordinate in the index, translate it into a
* new reference coordinate via the reference map supplied by the
* user.
*/
void map(UPair& h) const;
/**
* Return true iff we have a name for reference with id 'i'.
*/
bool hasName(size_t i) const {
if(!parseNames_) return false;
return !names_[i].empty();
}
/**
* Get the name for reference with id 'i'.
*/
const std::string& getName(size_t i) const {
assert(parseNames_);
assert(hasName(i));
return names_[i];
}
protected:
/**
* Parse a reference-map file.
*/
void parse();
const char *fname_;
std::vector<UPair> map_;
bool parseNames_;
std::vector<std::string> names_;
};
#endif /* REFMAP_H_ */
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