/usr/include/pbseq/alignment/format/SAMPrinter.hpp is in libblasr-dev 0~20161219-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 | #ifndef _BLASR_FORMAT_SAMPRINTER_HPP_
#define _BLASR_FORMAT_SAMPRINTER_HPP_
#include <sstream>
#include <stdint.h>
#include "../../pbdata/SMRTSequence.hpp"
#include "../datastructures/alignment/AlignmentCandidate.hpp"
#include "../datastructures/alignment/AlignmentContext.hpp"
#include "../datastructures/alignment/Alignment.hpp"
#include "../datastructures/alignment/Alignment.hpp"
#include "../datastructures/alignmentset/SAMSupplementalQVList.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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