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lhmm1.cpp
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lhmm1.cpp
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/* The MIT License
Copyright (c) 2013 Adrian Tan <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
*/
#include "lhmm1.h"
#include "lhmm1.h"
LHMM1::LHMM1()
{
initialize(500);
};
void LHMM1::initialize(int32_t maxLength)
{
this->maxLength = maxLength;
// delta = 0.01;
// epsilon = 0.1;
// tau = 0.1;
// eta = 0.001;
// delta = 0.01;
// epsilon = 0.1;
// tau = 0.1;
// eta = 0.001;
// last
// delta = 0.001;
// epsilon = 0.5;
// tau = 0.1;
// eta = 0.01;
// delta = 0.01;
// epsilon = 0.5;
// tau = 0.1;
// eta = 0.001;
delta = 0.001;
epsilon = 0.5;
tau = 0.1;
eta = 0.001;
logOneSixteenth = log10(1.0/16.0);
//for matched portion
tMM = log10(1-2*delta-tau);
tMI = log10(delta);
tMD = log10(delta);
tII = log10(epsilon);
tDD = log10(epsilon);
tDM = log10(1-epsilon);
tIM = log10(1-epsilon);
txx = log10((1-eta)/(1-eta));
txy = log10((eta*(1-eta))/(eta*(1-eta)));
tyy = log10((1-eta)/(1-eta));
txm = log10((eta*eta)/(eta*eta*(1-eta)*(1-eta)));
tym = log10((eta)/(eta*(1-eta)*(1-eta)));
tsm = log10((eta*eta)/(eta*eta*eta*(1-eta)*(1-eta)));
tmm = log10((1-2*delta-tau)/((1-eta)*(1-eta)));
tim = log10((1-epsilon)/(1-eta));
tdm = log10((1-epsilon)/(1-eta));
tmd = log10(delta/(1-eta));
tdd = log10(epsilon/(1-eta));
tmi = log10(delta/(1-eta));
tii = log10(epsilon/(1-eta));
tmw = log10((tau*(1-eta))/(eta*(1-eta)));
tww = log10((1-eta)/(1-eta));
tmz = log10((tau*eta*(1-eta))/(eta*eta*(1-eta)));
twz = log10((eta*(1-eta))/(eta*(1-eta)));
tzz = log10((1-eta)/(1-eta));
//assume alignments can't possibly be maxLength bases or more
//todo:: allow for resizing if you do encounter fragments which are really long
std::vector<double> temp(maxLength+1, -DBL_MAX);
std::vector<char> tempX(maxLength+1, 'Y');
tempX[0] = 'X';
std::vector<char> tempY(maxLength+1, 'Y');
tempY[0] = 'X';
X.clear();
Y.clear();
M.clear();
I.clear();
D.clear();
W.clear();
Z.clear();
pathX.clear();
pathY.clear();
pathM.clear();
pathD.clear();
pathI.clear();
pathW.clear();
pathZ.clear();
for (uint32_t i=0; i<maxLength+1; ++i)
{
X.push_back(temp);
Y.push_back(temp);
M.push_back(temp);
I.push_back(temp);
D.push_back(temp);
W.push_back(temp);
Z.push_back(temp);
pathX.push_back(tempX);
pathY.push_back(tempY);
pathM.push_back(tempX);
pathD.push_back(tempX);
pathI.push_back(tempX);
pathW.push_back(tempX);
pathZ.push_back(tempX);
}
logEta = log10(eta);
logTau = log10(tau);
X[0][0] = 0;
Y[0][0] = 0;
M[0][0] = 0;
W[0][0] = 0;
Z[0][0] = 0;
pathX[0][0] = 'N';
pathX[1][0] = 'S';
pathY[0][0] = 'N';
pathY[0][1] = 'S';
pathM[0][0] = 'N';
pathM[1][1] = 'S';
for (uint32_t k=1; k<maxLength+1; ++k)
{
X[k][0] = X[k-1][0] + txx;
X[0][k] = -DBL_MAX;
Y[k][0] = -DBL_MAX;
Y[0][k] = Y[0][k-1] + tyy;
W[k][0] = W[k-1][0] + tww;
W[0][k] = -DBL_MAX;
Z[k][0] = -DBL_MAX;
Z[0][k] = Z[0][k-1] + tzz;
}
X[0][0] = -DBL_MAX;
Y[0][0] = -DBL_MAX;
W[0][0] = -DBL_MAX;
Z[0][0] = -DBL_MAX;
};
bool LHMM1::containsIndel()
{
return (indelStatusInPath.size()!=0);
}
/**
convert PLs to probabilities.
*/
double LHMM1::pl2prob(uint32_t PL)
{
if (PL>=PLs.size())
{
if (PL > 3236)
PL = 3236;
for (uint32_t i=PLs.size(); i<=PL; ++i)
{
PLs.push_back(pow(10, -((double) i)/10.0));
}
}
return PLs[PL];
}
/**
*Updates matchStart, matchEnd, globalMaxPath and path.
*/
void LHMM1::tracePath()
{
double globalMax = M[xlen][ylen];
char globalMaxPath = 'M';
if (W[xlen][ylen]>globalMax)
{
globalMax = W[xlen][ylen];
globalMaxPath = 'W';
}
if (Z[xlen][ylen]>globalMax)
{
globalMax = Z[xlen][ylen];
globalMaxPath = 'Z';
}
matchStartX = -1;
matchEndX = -1;
matchStartY = -1;
matchEndY = -1;
noBasesAligned = 0;
if (globalMaxPath == 'M')
{
matchEndX = xlen;
matchEndY = ylen;
++noBasesAligned;
}
maxLogOdds = globalMax;
//std::cerr << "\tGlobal max Path : " << globalMaxPath << "\n";
//std::cerr << "\tGlobal max log odds : " << globalMax << "\n";
std::stringstream ss;
ss << globalMaxPath;
//recursively trace path
tracePath(ss, globalMaxPath, xlen, ylen);
path = reverse(ss.str());
bool inI = false;
bool inD = false;
//std::cerr << "*************************************\n";
//std::cerr << "PATH :" << path << "\n";
////////////////////////////////////////////////
//records appearance of Indels in probe and read
////////////////////////////////////////////////
indelStartsInX.clear();
indelEndsInX.clear();
indelStartsInY.clear();
indelEndsInY.clear();
indelStartsInPath.clear();
indelEndsInPath.clear();
indelStatusInPath.clear();
uint32_t x=0, y=0;
for (uint32_t i=0; i<path.size(); ++i)
{
if (!inI && path[i]=='I')
{
inI = true;
indelStartsInPath.push_back(i);
indelStatusInPath.push_back('I');
indelStartsInX.push_back(x);
indelStartsInY.push_back(y);
}
if (inI && path[i]!='I')
{
inI = false;
indelEndsInPath.push_back(i);
indelEndsInX.push_back(x);
indelEndsInY.push_back(y);
}
if (!inD && path[i]=='D')
{
inD = true;
indelStartsInPath.push_back(i);
indelStatusInPath.push_back('D');
indelStartsInX.push_back(x);
indelStartsInY.push_back(y);
}
if (inD && path[i]!='D')
{
inD = false;
indelEndsInPath.push_back(i);
indelEndsInX.push_back(x);
indelEndsInY.push_back(y);
}
if (path[i]=='M')
{
++x;
++y;
}
if (path[i]=='I' || path[i]=='Y' || path[i]=='Z')
{
++y;
}
if (path[i]=='D' || path[i]=='X' || path[i]=='W')
{
++x;
}
}
// std::cerr << "\t# INS in Path : ";
// for (uint32_t i=0; i<insertionStartsInPath.size(); ++i)
// {
// std::cerr << "(" << insertionStartsInPath[i] << "," << insertionEndsInPath[i] << ") ";
// }
// std::cerr << "\n";
//
// std::cerr << "\t# DEL in Path : ";
// for (uint32_t i=0; i<deletionStartsInPath.size(); ++i)
// {
// std::cerr << "(" << deletionStartsInPath[i] << "," << deletionEndsInPath[i] << ") ";
// }
// std::cerr << "\n";
// std::cerr << "*************************************\n";
//left align path
left_align();
// std::cerr << "*************************************\n";
// printAlignment();
// std::cerr << "*************************************\n";
// std::cerr << "\tPath: " << path << "\n";
}
void LHMM1::tracePath(std::stringstream& ss, char state, uint32_t i, uint32_t j)
{
//std::cout << state << "\n";
if (i>0 && j>0)
{
if (state=='X')
{
//std::cerr << pathX[i][j] << " " << i << " " << j << " " << matchStartY << "\n";
ss << pathX[i][j];
tracePath(ss, pathX[i][j], i-1, j);
}
else if (state=='Y')
{
//std::cerr << pathY[i][j] << " " << i << " " << j << " " << matchStartY << "\n";
ss << pathY[i][j];
tracePath(ss, pathY[i][j], i, j-1);
}
else if (state=='M')
{
// if (matchEndX==-1)
// {
// matchEndX = i;
// matchEndY = j;
//
// //std::cerr << "set matchEndX " << matchEndX << " " << matchEndY << "\n";
// }
//
if (matchStartX==-1 && (pathM[i][j] =='X' || pathM[i][j]=='Y'))
{
matchStartX = i;
matchStartY = j;
//std::cerr << "set match starts " << matchStartX << " " << matchStartY << "\n";
}
//std::cout << pathM[i][j] << " " << i << " " << j << " " << matchEndY << "\n";
ss << pathM[i][j];
tracePath(ss, pathM[i][j], i-1, j-1);
++noBasesAligned;
}
else if (state=='I')
{
//std::cout << pathI[i][j] << " " << i << " " << j << "\n";
ss << pathI[i][j];
tracePath(ss, pathI[i][j], i, j-1);
}
else if (state=='D')
{
//std::cout << pathD[i][j] << " " << i << " " << j << "\n";
ss << pathD[i][j];
tracePath(ss, pathD[i][j], i-1, j);
++noBasesAligned;
}
else if (state=='W')
{
if (matchEndX==-1 && pathW[i][j] =='M')
{
matchEndX = i-1;
matchEndY = j;
}
//std::cout << pathW[i][j] << " " << i << " " << j << "\n";
ss << pathW[i][j];
tracePath(ss, pathW[i][j], i-1, j);
}
else if (state=='Z')
{
if (matchEndX==-1 && pathZ[i][j] =='M')
{
matchEndX = i;
matchEndY = j-1;
}
//std::cout << pathZ[i][j] << " " << i << " " << j << "\n";
ss << pathZ[i][j];
tracePath(ss, pathZ[i][j], i, j-1);
}
else if (state=='S')
{
//std::cout << "\n";
if (matchStartX==-1)
{
matchStartX = i+1;
}
if (matchStartY==-1)
{
matchStartY = j+1;
}
}
}
else if (i==0 && j>0)
{
if (matchStartY==-1)
{
matchStartY = j+1;
}
// std::cout << pathY[i][j] << " " << i << " " << j << "\n";
ss << pathY[i][j];
tracePath(ss, pathY[i][j], i, j-1);
}
else if (i>0 && j==0)
{
if (matchStartY==-1)
{
matchStartY = j+1;
}
// std::cout << pathX[i][j] << " " << i << " " << j << "\n";
ss << pathX[i][j];
tracePath(ss, pathX[i][j], i-1, j);
}
else
{
//std::cout << "\n";
//ss << pathX[i][j];
}
}
/**
*Left align indels in an alignment
*/
void LHMM1::left_align()
{
//.......... GATAAGTGAG GAGGAAAAGC GA---GGAGA TCTTATTTGACAACTGCE
//YYYYYYYYYY MMMMMMMMMM MMMMMMMMMM MMIIIMMMMM MMMMMWWWWWWWWWWWWE
//ACTGCTTCTA GATAAGTGAG GAGGAAAAGC GATAAGGAGA TCTTA............E
//# INS in Probe : (22,22)
//# INS in Read : (32,35)
for (uint32_t i=0; i<indelStatusInPath.size(); ++i)
{
if (indelStatusInPath[i]=='I')
{
while (indelStartsInX[i]>1 && indelStartsInY[i]>1)
{
// printAlignment();
//
// std::cerr << "X[" << indelStartsInX[i]-1 << "] " << x[indelStartsInX[i]-1] << "\n";
// std::cerr << "Y[" << indelStartsInY[i]-1 << "] " << y[indelStartsInY[i]-1] << "\n";
// std::cerr << "Y[" << indelEndsInY[i]-1 << "] " << y[indelEndsInY[i]-1] << "\n";
//
if (//(indelStartsInY[i]!=indelEndsInY[i]-1) && //single indel need not be shifted
x[indelStartsInX[i]-1]==y[indelStartsInY[i]-1] &&
y[indelStartsInY[i]-1]==y[indelEndsInY[i]-1])
{
// std::cerr << "CHECK BEFORE:" << path << "\n";
// std::cerr << "P[" << indelStartsInPath[i]-1 << "] " << path[indelStartsInPath[i]-1] << "\n";
// std::cerr << "P[" << indelEndsInPath[i]-1 << "] " << path[indelEndsInPath[i]-1] << "\n";
path[indelStartsInPath[i]-1] = 'I';
path[indelEndsInPath[i]-1] = 'M';
--indelStartsInX[i];
--indelEndsInX[i];
--indelStartsInY[i];
--indelEndsInY[i];
--indelStartsInPath[i];
--indelEndsInPath[i];
// std::cerr << "SHIFT 1 to the left\n";
}
else
{
break;
}
}
}
else
{
// ==================
// 2) 6:81319178:AATTT:A:-4
// ==================
// ref probe ATCTATTAAAGATATATGTCAATTTATTAGTGCATATCAAAGAGCAAGT (20/49)
// read sequence GATATATGTCAATTAGTGCATATCAAAGAGCAAGTTGACATGTTTTTTCAATATATTCATTTCTCTAATTTATCTC
// ==================
// X SATCTATTAAAGATATATGTCAATTTATTAGTGCATATCAAAGAGCAAGT.........................................E
// Path SXXXXXXXXXXMMMMMMMMMMMMMDDDDMMMMMMMMMMMMMMMMMMMMMMZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZE
// Y S..........GATATATGTCAAT----TAGTGCATATCAAAGAGCAAGTTGACATGTTTTTTCAATATATTCATTTCTCTAATTTATCTCE
// Match Start : 0
// Match End : 35
// # Aligned Bases : 39
// # Matched Bases : 35
// # Mismatched Bases : 0
// # INS in Probe :
// # INS in Read :
// # INS in Path :
// # DEL in Probe : (23,27)
// # DEL in Read : (13,13)
// # DEL in Path : (24,28)
while (indelStartsInX[i]>1 && indelStartsInY[i]>1)
{
// printAlignment();
// std::cerr << "X[" << indelStartsInX[i]-1 << "] " << x[indelStartsInX[i]-1] << "\n";
// std::cerr << "Y[" << indelStartsInY[i]-1 << "] " << y[indelStartsInY[i]-1] << "\n";
// std::cerr << "Y[" << indelEndsInY[i]-1 << "] " << y[indelEndsInY[i]-1] << "\n";
if (//(indelStartsInX[i]!=indelEndsInX[i]-1) && //single indel need not be shifted
x[indelStartsInX[i]-1]==y[indelStartsInY[i]-1] &&
x[indelStartsInX[i]-1]==x[indelEndsInX[i]-1])
{
// std::cerr << "CHECK BEFORE:" << path << "\n";
// std::cerr << "P[" << indelStartsInPath[i]-1 << "] " << path[indelStartsInPath[i]-1] << "\n";
// std::cerr << "P[" << indelEndsInPath[i]-1 << "] " << path[indelEndsInPath[i]-1] << "\n";
path[indelStartsInPath[i]-1] = 'D';
path[indelEndsInPath[i]-1] = 'M';
--indelStartsInX[i];
--indelEndsInX[i];
--indelStartsInY[i];
--indelEndsInY[i];
--indelStartsInPath[i];
--indelEndsInPath[i];
// std::cerr << "SHIFT 1 to the left\n";
}
else
{
break;
}
}
}
}
}
/**
Align and compute genotype likelihood.
*/
void LHMM1::align(double& llk, const char* _x, const char* _y, const char* _qual, bool debug)
{
x = _x;
y = _y;
qual = _qual;
//adds a starting character at the fron of each string that must be matched
xlen = strlen(x);
ylen = strlen(y);
int32_t mlen = xlen>ylen?xlen:ylen;
if (mlen>this->maxLength)
{
initialize(mlen+10);
}
double max = 0;
char maxPath = 'X';
//std::cerr << "x: " << x << " " << xlen << "\n" ;
//std::cerr << "y: " << y << " " << ylen << "\n" ;
//construct possible solutions
for (uint32_t i=1; i<=xlen; ++i)
{
for (uint32_t j=1; j<=ylen; ++j)
{
//std::cerr << i << " " << j << "\n" ;
//X
double xx = X[i-1][j] + txx;
max = xx;
maxPath = 'X';
X[i][j] = max;
pathX[i][j] = maxPath;
//Y
double xy = X[i][j-1] + txy;
double yy = Y[i][j-1] + tyy;
max = xy;
maxPath = 'X';
if (yy>max)
{
max = yy;
maxPath = 'Y';
}
Y[i][j] = max;
pathY[i][j] = maxPath;
//M
double xm = X[i-1][j-1] + txm;
double ym = Y[i-1][j-1] + tym;
double mm = M[i-1][j-1] + ((i==1&&j==1) ? tsm : tmm);
double im = I[i-1][j-1] + tim;
double dm = D[i-1][j-1] + tdm;
max = xm;
maxPath = 'X';
if (ym>max) //special case
{
max = ym;
maxPath = 'Y';
}
if (mm>max)
{
max = mm;
maxPath = (i==1&&j==1) ? 'S' : 'M';
}
if (im>max)
{
max = im;
maxPath = 'I';
}
if (dm>max)
{
max = dm;
maxPath = 'D';
}
M[i][j] = max + logEmissionOdds(x[i-1], y[j-1], pl2prob((uint32_t) qual[j-1]-33));
pathM[i][j] = maxPath;
//D
double md = M[i-1][j] + tmd;
double dd = D[i-1][j] + tdd;
max = md;
maxPath = 'M';
if (dd>max)
{
max = dd;
maxPath = 'D';
}
D[i][j] = max;
pathD[i][j] = maxPath;
//I
double mi = M[i][j-1] + tmi;
double ii = I[i][j-1] + tii;
max = mi;
maxPath = 'M';
if (ii>max)
{
max = ii;
maxPath = 'I';
}
I[i][j] = max;
pathI[i][j] = maxPath;
//W
double mw = M[i-1][j] + tmw;
double ww = W[i-1][j] + tww;
max = mw;
maxPath = 'M';
if (ww>max)
{
max = ww;
maxPath = 'W';
}
W[i][j] = max;
pathW[i][j] = maxPath;
//Z
double mz = M[i][j-1] + tmz;
double wz = W[i][j-1] + twz;
double zz = Z[i][j-1] + tzz;
max = mz;
maxPath = 'M';
if (wz>max)
{
max = wz;
maxPath = 'W';
}
if (zz>max)
{
max = zz;
maxPath = 'Z';
}
Z[i][j] = max;
pathZ[i][j] = maxPath;
}
M[xlen][ylen] += logTau-logEta;
}
if (debug)
{
std::cerr << "\n=X=\n";
printVector(X, xlen+1, ylen+1);
std::cerr << "\n=Y=\n";
printVector(Y, xlen+1, ylen+1);
std::cerr << "\n=M=\n";
printVector(M, xlen+1, ylen+1);
std::cerr << "\n=D=\n";
printVector(D, xlen+1, ylen+1);
std::cerr << "\n=I=\n";
printVector(I, xlen+1, ylen+1);
std::cerr << "\n=W=\n";
printVector(W, xlen+1, ylen+1);
std::cerr << "\n=Z=\n";
printVector(Z, xlen+1, ylen+1);
std::cerr << "\n=Path X=\n";
printVector(pathX, xlen+1, ylen+1);
std::cerr << "\n=Path Y=\n";
printVector(pathY, xlen+1, ylen+1);
std::cerr << "\n=Path M=\n";
printVector(pathM, xlen+1, ylen+1);
std::cerr << "\n=Path D=\n";
printVector(pathD, xlen+1, ylen+1);
std::cerr << "\n=Path I=\n";
printVector(pathI, xlen+1, ylen+1);
std::cerr << "\n=Path W=\n";
printVector(pathW, xlen+1, ylen+1);
std::cerr << "\n=Path Z=\n";
printVector(pathZ, xlen+1, ylen+1);
}
tracePath();
};
/**
*Compute log likelihood of matched portion of alignment
*/
void LHMM1::computeLogLikelihood(double& llk, std::string& _path, const char* qual)
{
// std::cerr <<" basequals " << qual << "\n";
// std::cerr <<" read " << y << "\n";
// std::cerr <<" path " << path << "\n";
matchedBases = 0;
mismatchedBases = 0;
llk = 0;
double q = 0;
char lastState = 'S';
uint32_t xIndex=0, yIndex=0;
for (uint32_t i=0; i<_path.size(); ++i)
{
char state = _path.at(i);
//std::cerr << state << " " << xIndex << " " << yIndex << "\n";
if (state=='M')
{
q = pl2prob((uint32_t) qual[yIndex]-33);
llk = lt.log10prod(llk, logEmission(x[xIndex], y[yIndex], q));
//compute for perfect fit
if (x[xIndex]== y[yIndex])
{
++matchedBases;
}
else
{
++mismatchedBases;
}
if (lastState=='M')
{
llk = lt.log10prod(llk, tMM);
}
else if (lastState=='D')
{
llk = lt.log10prod(llk, tDM);
}
else if (lastState=='I')
{
llk = lt.log10prod(llk, tIM);
}
//std::cerr << "M) "<< lastState << " " << llk << " " << x[xIndex] << " " << y[yIndex] << " " << pl2prob((uint32_t) qual[yIndex]-33) << " "<< qual[yIndex-1]-33 << "\n";
++xIndex;
++yIndex;
}
else if (state=='D')
{
if (lastState=='M')
{
llk = lt.log10prod(llk, tMD);
}
else if (lastState=='D')
{
llk = lt.log10prod(llk, tDD);
}
//std::cerr << "D) " << lastState << " " << llk << " " << x[xIndex] << " " << y[yIndex] << "\n";
++xIndex;
}
else if (state=='I')
{
if (lastState=='M')
{
llk = lt.log10prod(llk, tMI);
}
else if (lastState=='I')
{
llk = lt.log10prod(llk, tII);
}
//std::cerr << "I) " << lastState << " " << llk << " " << x[xIndex] << " " << y[yIndex] << "\n";
++yIndex;
}
else if (state=='X')
{
++xIndex;
}
else if (state=='Y')
{
++yIndex;
}
else if (state=='W')
{
++xIndex;
}
else if (state=='Z')
{
++yIndex;
}
lastState = state;
}
};
/**
* Compute log likelihood of matched portion of alignment
*/
void LHMM1::computeLogLikelihood(double& llk, double& perfectllk, std::string& _path, const char* qual)
{
// std::cerr <<" basequals " << qual << "\n";
// std::cerr <<" read " << y << "\n";
// std::cerr <<" path " << path << "\n";
matchedBases = 0;
mismatchedBases = 0;
llk = 0;
perfectllk = 0;
double q = 0;
char lastState = 'S';
uint32_t xIndex=0, yIndex=0;
for (uint32_t i=0; i<_path.size(); ++i)
{
char state = _path.at(i);
//std::cerr << state << " " << xIndex << " " << yIndex << "\n";
if (state=='M')
{
q = pl2prob((uint32_t) qual[yIndex]-33);
llk = lt.log10prod(llk, logEmission(x[xIndex], y[yIndex], q));
//compute for perfect fit
perfectllk = lt.log10prod(perfectllk, logEmission(x[xIndex], x[xIndex], q));
if (x[xIndex]== y[yIndex])
{
++matchedBases;
}
else
{
++mismatchedBases;
}
if (lastState=='M')
{
llk = lt.log10prod(llk, tMM);
}
else if (lastState=='D')
{
llk = lt.log10prod(llk, tDM);
}
else if (lastState=='I')
{
llk = lt.log10prod(llk, tIM);
}
perfectllk = lt.log10prod(llk, tMM);
//std::cerr << "M) "<< lastState << " " << llk << " " << x[xIndex] << " " << y[yIndex] << " " << pl2prob((uint32_t) qual[yIndex]-33) << " "<< qual[yIndex-1]-33 << "\n";
++xIndex;
++yIndex;
}
else if (state=='D')
{
if (lastState=='M')
{
llk = lt.log10prod(llk, tMD);
}
else if (lastState=='D')
{
llk = lt.log10prod(llk, tDD);
}
// std::cerr << "D) " << lastState << " " << llk << " " << x[xIndex] << " " << y[yIndex] << "\n";
++xIndex;
}
else if (state=='I')
{
if (lastState=='M')
{
llk = lt.log10prod(llk, tMI);
}
else if (lastState=='I')
{
llk = lt.log10prod(llk, tII);
}
// std::cerr << "I) " << lastState << " " << llk << " " << x[xIndex] << " " << y[yIndex] << "\n";
++yIndex;
}
else if (state=='X')
{
++xIndex;
}
else if (state=='Y')
{
++yIndex;
}
else if (state=='W')
{
++xIndex;
}
else if (state=='Z')
{
++yIndex;
}
lastState = state;
}
};
/**
*Compute log likelihood of matched portion of alignment
*/
void LHMM1::computeLogLikelihood(double& llk, const char* qual)
{
tracePath();
llk = 0;
char lastState = 'S';
uint32_t xIndex=0, yIndex=0;
for (uint32_t i=0; i<path.size(); ++i)
{
//std::cerr << xIndex << " " << yIndex << "\n";
char state = path.at(i);
if (state=='M')
{
llk = lt.log10prod(llk, logEmission(x[xIndex], y[yIndex], pl2prob((uint32_t) qual[yIndex-1]-33)));
if (lastState=='M')