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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 __CIGAR_HELPER_H__
#define __CIGAR_HELPER_H__
#include "SamRecord.h"
/// Class for helping to filter a SAM/BAM record.
class CigarHelper
{
public:
static const int32_t NO_CLIP = -1;
/// Soft clip the cigar from the beginning of the read at the specified
/// reference position. If the clip position is deleted/skipped
/// or is immediately followed by a deletion/skip/pad/insert, that entire
/// CIGAR operation is also removed.
/// Nothing is clipped if the reference position is before the read starts,
/// everything is clipped if the reference position is after the read ends.
/// \param record record to calculate the clip for.
/// \param refPosition0Based 0-based reference position to end the clip at
/// \param newCigar cigar object to set with the updated cigar.
/// \param new0BasedPosition new 0-based reference position of the read.
/// \param read position where the clip ends (last clipped position) or
// NO_CLIP if nothing is clipped.
static int32_t softClipBeginByRefPos(SamRecord& record,
int32_t refPosition0Based,
CigarRoller& newCigar,
int32_t &new0BasedPosition);
/// Soft clip the cigar from the back of the read at the specified
/// reference position. If the clip position is deleted/skipped
/// or is immediately preceded by a deletion/skip/pad, that entire CIGAR
/// operation is also removed. If the clip position is immediately
/// preceded by an insertion, the insertion is left in the CIGAR.
/// Nothing is clipped if the reference position is after the read ends,
/// everything is clipped if the reference position is before the read
/// starts (including insertions).
/// \param record record to calculate the clip for.
/// \param refPosition0Based 0-based reference position to start clip at
/// \param newCigar cigar object to set with the updated cigar.
/// \param read position where the clip starts or
// NO_CLIP if nothing is clipped.
static int32_t softClipEndByRefPos(SamRecord& record,
int32_t refPosition0Based,
CigarRoller& newCigar);
};
#endif
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