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#ifndef chime_h
#define chime_h
#include "seq.h"
struct ChimeHit2
{
string QLabel;
string ALabel;
string BLabel;
string Q3;
string A3;
string B3;
//unsigned LY, LN, LA, LD;
//unsigned RY, RN, RA, RD;
double PctIdQT, PctIdQA, PctIdQB, PctIdQM, PctIdAB;
unsigned ColLo;
unsigned ColXLo;
unsigned ColXHi;
unsigned ColHi;
unsigned QXLo;
unsigned QXHi;
double Div;
double Score;
double H;
unsigned CS_LY, CS_LN, CS_LA, CS_RY, CS_RN, CS_RA;
float AbQ;
float AbA;
float AbB;
ChimeHit2()
{
Clear();
}
void Clear()
{
Q3.clear();
A3.clear();
B3.clear();
QLabel.clear();
ALabel.clear();
BLabel.clear();
//LY = LN = LA = LD = UINT_MAX;
//RY = RN = RA = RD = UINT_MAX;
ColLo = ColHi = QXLo = QXHi = ColXLo = ColXHi = UINT_MAX;
CS_LY = CS_LN = CS_LA = CS_RY = CS_RN = CS_RA = UINT_MAX;
PctIdQT = PctIdQA = PctIdQB = PctIdQM = PctIdAB = -1.0;
Div = -1.0;
H = -1.0;
Score = -1.0;
AbQ = AbA = AbB = -1.0f;
};
bool Accept() const
{
return Score >= opt_minh && Div >= opt_mindiv && CS_LY >= opt_mindiffs && CS_RY >= opt_mindiffs;
}
void LogMe() const
{
Log("@L %c ", yon(Score >= 1.0 && Div >= 1.0));
Log(" %.4f", Score);
Log(" LY %u LN %u LA %u", CS_LY, CS_LN, CS_LA);
Log(" RY %u RN %u RA %u", CS_RY, CS_RN, CS_RA);
Log(" Div %.1f%%", Div);
Log(" Q=%s", QLabel.c_str());
Log(" A=%s", ALabel.c_str());
Log(" B=%s", BLabel.c_str());
Log(" QA %.1f%% QB=%.1f%% AB=%.1f%% QM=%.1f%%", PctIdQA, PctIdQB, PctIdAB, PctIdQM);
Log("\n");
}
bool operator<(const ChimeHit2 &rhs) const
{
if (Score == rhs.Score)
return Div > rhs.Div;
return Score > rhs.Score;
}
};
static inline bool isacgt(char c)
{
return c == 'A' || c == 'C' || c == 'G' || c == 'T';
}
static bool inline isgap(char c)
{
return c == '-' || c == '.';
}
void GetChunkInfo(unsigned L, unsigned &Length, vector<unsigned> &Los);
float GetAbFromLabel(const string &Label);
void WriteChimeHitCS(FILE *f, const ChimeHit2 &Hit);
void WriteChimeHit(FILE *f, const ChimeHit2 &Hit);
void WriteChimeFileHdr(FILE *f);
#endif // chime_h
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