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/*
* Copyright (C) 2010-2011 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_TAGS_H__
#define __SAM_TAGS_H__
#include <stdint.h>
#include <stdexcept>
#include "SamRecord.h"
/// Class for parsing/creating/operating on SAM/BAM record tags.
class SamTags
{
public:
///////////////////////
/// @name Constants for parsing tags.
//@{
static const char* BQ_TAG;
static const char BQ_TAG_TYPE;
static const char* MD_TAG;
static const char MD_TAG_TYPE;
static const char* ORIG_POS_TAG;
static const char ORIG_POS_TAG_TYPE;
static const char* ORIG_CIGAR_TAG;
static const char ORIG_CIGAR_TAG_TYPE;
static const char* ORIG_QUAL_TAG;
static const char ORIG_QUAL_TAG_TYPE;
//@}
/// Create the MD tag for the specified input record and the genome.
/// \return returns true if an MD tag was created, false if one could not
/// be created.
static bool createMDTag(String& outputMDtag, SamRecord& inputRec, GenomeSequence& genome);
/// Check to see if the MD tag in the record is accurate.
static bool isMDTagCorrect(SamRecord& inputRec, GenomeSequence& genome);
// Update/Add the MD tag in the inputRec.
static bool updateMDTag(SamRecord& inputRec, GenomeSequence& genome);
private:
SamTags();
};
#endif
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