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#ifndef _BLASR_SAM_ALIGNMENT_HPP_
#define _BLASR_SAM_ALIGNMENT_HPP_
#include <sstream>
#include <string>
#include <pbdata/sam/CigarString.h>
#include <pbdata/sam/SAMKeywordValuePair.hpp>
class SAMAlignment
{
public:
enum SAMAlignmentRequiredFields
{
S_QNAME,
S_FLAG,
S_RNAME,
S_POS,
S_MAPQV,
S_CIGAR,
S_RNEXT,
S_PNEXT,
S_TLEN,
S_SEQ,
S_QUAL
};
static const char* SAMAlignmentRequiredFieldNames[];
std::string qName;
unsigned int flag;
std::string rName;
unsigned int pos;
short mapQV;
CigarString cigar;
std::string rNext;
int pNext;
int tLen;
std::string seq;
std::string qual;
// Optional tags defined in blasr:
// "RG" read group Id
// "AS" alignment score
// "XS" read alignment start position without counting previous soft clips (1 based)
// "XE" read alignment end position without counting previous soft clips (1 based)
// "XL" aligned read length
// "XQ" query read length
// "XT" # of continues reads, always 1 for blasr
// "NM" # of subreads
// "FI" read alignment start position (1 based)
//
float score;
int xs, xe;
int xl;
int xq;
std::string rg;
int as;
int xt;
int nm;
int fi;
std::string optTagStr;
//
// Quality values.
//
std::string iq, dq, sq, mq, st, dt;
static const char* optionalQVTags[];
static const char* optionalQVNames[];
//
// Initialize all optional fields. Required fields will be
// assigned a value later.
//
SAMAlignment();
void PrintSAMAlignment(std::ostream& out = std::cout);
// Find position of the nth character in a string.
size_t FindPosOfNthChar(std::string str, int n, char c);
// Trim the end '\n\r' characters from a string.
std::string TrimStringEnd(std::string str);
bool StoreValues(std::string& line, int lineNumber = 0);
// CopyQVs writes the strings from the optional QV tags to a vector. The
// order of QVs in the vector is given by optionalQVNames[]
void CopyQVs(std::vector<std::string>* optionalQVs);
};
class SAMPosAlignment : public SAMAlignment
{
public:
unsigned int qStart, qEnd;
unsigned int tStart, tEnd;
int qStrand, tStrand;
};
#endif
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