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#ifndef _BLASR_FORMAT_SAMPRINTER_HPP_
#define _BLASR_FORMAT_SAMPRINTER_HPP_
#include <cstdint>
#include <sstream>
#include <alignment/datastructures/alignment/Alignment.hpp>
#include <alignment/datastructures/alignment/Alignment.hpp>
#include <alignment/datastructures/alignment/AlignmentCandidate.hpp>
#include <alignment/datastructures/alignment/AlignmentContext.hpp>
#include <alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp>
#include <pbdata/SMRTSequence.hpp>
#define MULTI_SEGMENTS 0x1
#define ALL_SEGMENTS_ALIGNED 0x2
#define SEGMENT_UNMAPPED 0x4
#define NEXT_SEGMENT_UNMAPPED 0x8
#define SEQ_REVERSED 0x10
#define SEQ_NEXT_REVERSED 0x20
#define FIRST_SEGMENT 0x40
#define LAST_SEGMENT 0x80
#define SECONDARY_ALIGNMENT 0x100
#define NO_PASS_QUALITY 0x200
#define PCR_OR_OPTICAL_DUPLICATE 0x400
namespace SAMOutput {
enum Clipping
{
hard,
soft,
subread,
none
};
void BuildFlag(T_AlignmentCandidate &alignment, AlignmentContext &context, uint16_t &flag);
//
// Trimming is used for both hard non-clipping
// so it is called trim instead of clip.
//
void CreateDNAString(DNASequence &seq, DNASequence &clippedSeq, DNALength trimFront = 0,
DNALength trimEnd = 0);
void AddGaps(T_AlignmentCandidate &alignment, int gapIndex, std::vector<int> &opSize,
std::vector<char> &opChar);
// Add sequence match/mismatch CIGAR string Ops for block b.
void AddMatchBlockCigarOps(DNASequence &qSeq, DNASequence &tSeq, blasr::Block &b,
DNALength &qSeqPos, DNALength &tSeqPos, std::vector<int> &opSize,
std::vector<char> &opChar);
// Merge adjacent indels and mismatches.
void MergeAdjacentIndels(std::vector<int> &opSize, std::vector<char> &opChar,
const char mismatchChar);
// If cigarUseSeqMatch is true, cigar string uses '=' and 'X'
// instead of 'M' to represent sequence match and mismatch;
void CreateNoClippingCigarOps(T_AlignmentCandidate &alignment, std::vector<int> &opSize,
std::vector<char> &opChar, bool cigarUseSeqMatch = false,
const bool allowAdjacentIndels = true);
//
//
// The aligned sequence is either the sequence from the first
// aligned base to the last (hard and no clipping), or first high
// quality base to the last high quality base (soft clipping).
//
template <typename T_Sequence>
void SetAlignedSequence(T_AlignmentCandidate &alignment, T_Sequence &read, T_Sequence &alignedSeq,
Clipping clipping = none);
template <typename T_Sequence>
void SetSoftClip(T_AlignmentCandidate &alignment, T_Sequence &read, DNALength hardClipPrefix,
DNALength hardClipSuffix, DNALength &softClipPrefix, DNALength &softClipSuffix);
template <typename T_Sequence>
void SetHardClip(T_AlignmentCandidate &alignment, T_Sequence &read, DNALength &prefixClip,
DNALength &suffixClip);
void CigarOpsToString(std::vector<int> &opSize, std::vector<char> &opChar,
std::string &cigarString);
//
// Straight forward: create the cigar string allowing some clipping
// The read is provided to give length and hq information.
//
template <typename T_Sequence>
void CreateCIGARString(T_AlignmentCandidate &alignment, T_Sequence &read, std::string &cigarString,
Clipping clipping, DNALength &prefixSoftClip, DNALength &suffixSoftClip,
DNALength &prefixHardClip, DNALength &suffixHardClip,
bool cigarUseSeqMatch = false, const bool allowAdjacentIndels = true);
template <typename T_Sequence>
void PrintAlignment(T_AlignmentCandidate &alignment, T_Sequence &read, std::ostream &samFile,
AlignmentContext &context, SupplementalQVList &qvList, Clipping clipping = none,
bool cigarUseSeqMatch = false, const bool allowAdjacentIndels = true);
}
#include "SAMPrinterImpl.hpp"
#endif // _BLASR_FORMAT_SAMPRINTER_HPP_
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