/**
SAMIO.H
**/

#ifndef SAMIO_H
#define SAMIO_H

#include <string>
#include <vector>
#include "structdef.h"

using namespace std;

/**
 * Parese CIGAR strings
 * notice that the range should be interpreted as [startpos, endpos], not [startpos,endpos).
 * Handle I and D Cigar characters
 */
void parsecigar(string cigar, long pos, vector<long>& startpos, vector<long>&endpos);

/*
Main entry for analyzing sam file
read sam file, and generate read mapping file for isoinfer
*/

int readSamFile(string inSamFile, 
		vector<string> args
		);






#endif