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planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
author chrisd
date Sun, 21 Feb 2016 06:05:24 -0500
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#ifndef SAM_H
#define SAM_H

#include "Alignment.h"

class Sam {
public:
	Sam(std::string sam_fp);
	void read_se_sam(const std::string &sam_fp, bool best);
	void read_pe_sam(const std::string &sam_fp, bool best);
	static void sort_by_qname(std::vector<Alignment> &v);

	std::vector<Alignment> alignments;
private:
	std::string _sam_fp;

};



#endif //SAM_H