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/*
* Copyright (C) 2011 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __SAM_HELPER_H__
#define __SAM_HELPER_H__
#include <stdint.h>
#ifdef DUPLICATE
#undef DUPLICATE
#endif
/// Class for extracting information from a SAM Flag.
class SamHelper
{
public:
/// Helper method that combines the chromosome ID and position into a
/// 64bit number by shifting the chromosome ID to the upper bits.
static inline uint64_t combineChromPos(int32_t chromID, int32_t position)
{
return(((uint64_t)chromID << 32) | (position & 0xFFFFFFFF));
}
private:
SamHelper();
};
#endif
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