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calc_prob_data.c
951 lines (905 loc) · 35.4 KB
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calc_prob_data.c
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/* MigSelect 2013-2019 Arun Sethuraman, Vitor Sousa, Jody Hey */
/* This code was developed based on IMa2 2009-2010 Jody Hey, Rasmus Nielsen and Sang Chul Choi*/
#undef GLOBVARS
#include "imamp.h"
/* #include "imagsl.h" */
/*********** LOCAL STUFF **********/
static double *sumlogk[MAXLOCI];
static int makefrac (int ci, int li, int node, double mutrate, double kappa,
int e1, int e2, int e3, int e4);
static double getstandfactor (int ci, int li, double kappa);
/******** LOCAL FUNCTIONS ***********/
#if 0
/* CR 110825.1
* pijt() & makefrac_rasmus() are no longer compiled into code,
* they are being kept for historical reasons only, the
* functions were replaced by Jim Long's makefrac()
*/
// Rasmus's original makefrac and pijt
double pijt(int ci, int li, double mutrate, double t, double kappa, int from, int to)
{ /*ACGT*/
double A, PIj;
double *pi;
pi = C[ci]->G[li].pi;
if (to==0 || to==2) PIj=pi[0]+pi[2];
else PIj=pi[1]+pi[3];
/*A=kappa+1.0; */ /*F84*/
A=1.0+PIj*(kappa-1.0); /*HKY85*/
if (from==to)
return pi[to]+pi[to]*exp(-mutrate*t)*(1.0/PIj-1.0)+exp(-mutrate*t*A)*((PIj-pi[to])/PIj);
else if (from+to==2 || from+to==4)
return pi[to]+pi[to]*(1.0/PIj-1.0)*exp(-mutrate*t)-(pi[to]/PIj)*exp(-mutrate*t*A);
else return pi[to]*(1.0-exp(-mutrate*t));
}
int makefrac_rasmus(int ci, int li, int node, double mutrate, double kappa, int e1, int e2, int e3, int e4)
{
int i, j, k, up1, up2, ret=0;
double **fracpoint1, **fracpoint2, sum[4];
struct edge *gtree;
gtree = C[ci]->G[li].gtree;
if (node == e1 || node == e2 || node == e3 || node == e4 || e1 == -1) ret=1;
up1=gtree[node].up[0];
if (up1!=-1)
{
up2=gtree[node].up[1];
i=makefrac(ci,li,up1, mutrate, kappa, e1, e2, e3, e4);
if (i==0) fracpoint1 = gtree[up1].hkyi.frac;
else {fracpoint1 = gtree[up1].hkyi.newfrac; ret=1;}
i=makefrac(ci,li,up2, mutrate, kappa, e1, e2, e3, e4);
if (i==0) fracpoint2 = gtree[up2].hkyi.frac;
else {fracpoint2 = gtree[up2].hkyi.newfrac; ret=1;}
if (ret>0)
{
if (gtree[up1].up[0]==-1 && gtree[up2].up[0]==-1){
for (i=0; i<L[li].numsites; i++)
for (j=0; j<4; j++)
gtree[node].hkyi.newfrac[i][j]=pijt(ci,li,mutrate, gtree[up1].time, kappa, j, L[li].seq[up1][i])*pijt(ci, li,mutrate, gtree[up2].time, kappa, j, L[li].seq[up2][i]);
}
else if (gtree[up1].up[0]==-1)
{
for (i=0; i<L[li].numsites; i++){
for (j=0; j<4; j++)
{
gtree[node].hkyi.newfrac[i][j]=0;
for (k=0; k<4; k++)
gtree[node].hkyi.newfrac[i][j]+=pijt(ci, li,mutrate, gtree[up2].time-gtree[gtree[up2].up[0]].time, kappa, j, k)*fracpoint2[i][k];
gtree[node].hkyi.newfrac[i][j]=gtree[node].hkyi.newfrac[i][j]*pijt(ci,li,mutrate, gtree[up1].time, kappa, j, L[li].seq[up1][i]);
}
}
}
else
if (gtree[up2].up[0]==-1)
{
for (i=0; i<L[li].numsites; i++)
{
for (j=0; j<4; j++)
{
gtree[node].hkyi.newfrac[i][j]=0;
for (k=0; k<4; k++)
gtree[node].hkyi.newfrac[i][j]+=pijt(ci, li,mutrate, gtree[up1].time-gtree[gtree[up1].up[0]].time, kappa, j, k)*fracpoint1[i][k];
gtree[node].hkyi.newfrac[i][j]=gtree[node].hkyi.newfrac[i][j]*pijt(ci,li,mutrate, gtree[up2].time, kappa, j, L[li].seq[up2][i]);
}
}
}
else
{
for (i=0; i<L[li].numsites; i++){
for (j=0; j<4; j++)
{
sum[j]=0;
for (k=0; k<4; k++)
sum[j]+=pijt(ci, li,mutrate, gtree[up1].time-gtree[gtree[up1].up[0]].time, kappa, j, k)*fracpoint1[i][k];
gtree[node].hkyi.newfrac[i][j]=0;
for (k=0; k<4; k++)
gtree[node].hkyi.newfrac[i][j]+=pijt(ci,li,mutrate, gtree[up2].time-gtree[gtree[up2].up[0]].time, kappa, j, k)*fracpoint2[i][k];
gtree[node].hkyi.newfrac[i][j]=gtree[node].hkyi.newfrac[i][j]*sum[j];
}
}
}
}
}
return ret;
} /* Rasmus's original makefrac */
#endif // #if 0
// Jim Long's unwrapped makefrac() - much faster than Rasmus's original makefrac() that used recursion
int
makefrac (int ci, int li, int node, double mutrate, double kappa, int e1,
int e2, int e3, int e4)
{
int i, j, up1, up2, ret = 0;
double **fracpoint1, **fracpoint2;
/* variables to precompute values */
int stmp[2];
double expp[2], kpa, A_j[2], L_to[4], PI_j[2], sum[4], temp[4];
double minus_t_mutrate1, minus_t_mutrate2, exp1[2], exp2[2], onem[2];
double A[2], PIj[2], divm[2], mdiv[2], pijt1, pijt2, ptmp[4];
double *pi;
struct edge *gtree;
double max;
gtree = C[ci]->G[li].gtree;
pi = C[ci]->G[li].pi;
kpa = kappa - 1.0;
if (node == e1 || node == e2 || node == e3 || node == e4 || e1 == -1)
ret = 1;
up1 = gtree[node].up[0];
if (up1 != -1)
{
up2 = gtree[node].up[1];
i = makefrac (ci, li, up1, mutrate, kappa, e1, e2, e3, e4);
if (i == 0)
{
fracpoint1 = gtree[up1].hkyi.frac;
}
else
{
fracpoint1 = gtree[up1].hkyi.newfrac;
ret = 1;
}
i = makefrac (ci, li, up2, mutrate, kappa, e1, e2, e3, e4);
if (i == 0)
{
fracpoint2 = gtree[up2].hkyi.frac;
}
else
{
fracpoint2 = gtree[up2].hkyi.newfrac;
ret = 1;
}
if (ret > 0)
{
if (gtree[up1].up[0] == -1 && gtree[up2].up[0] == -1)
{
minus_t_mutrate1 = -mutrate * gtree[up1].time;
minus_t_mutrate2 = -mutrate * gtree[up2].time;
expp[0] = exp (minus_t_mutrate1);
expp[1] = exp (minus_t_mutrate2);
for (i = 0; i < L[li].numsites; i++)
{
stmp[0] = L[li].seq[up1][i];
stmp[1] = L[li].seq[up2][i];
L_to[0] = pi[stmp[0]];
L_to[1] = pi[stmp[1]];
if (stmp[0] == 0 || stmp[0] == 2)
PIj[0] = pi[0] + pi[2];
else
PIj[0] = pi[1] + pi[3];
if (stmp[1] == 0 || stmp[1] == 2)
PIj[1] = pi[0] + pi[2];
else
PIj[1] = pi[1] + pi[3];
A[0] = 1.0 + PIj[0] * kpa;
divm[0] = 1.0 / PIj[0] - 1.0;
mdiv[0] = (PIj[0] - L_to[0]) / PIj[0];
A[1] = 1.0 + PIj[1] * kpa;
divm[1] = 1.0 / PIj[1] - 1.0;
mdiv[1] = (PIj[1] - L_to[1]) / PIj[1];
max = 0.0;
for (j = 0; j < 4; j++)
{
if (stmp[0] == j)
pijt1 = L_to[0] + L_to[0] * expp[0] * divm[0] + exp (minus_t_mutrate1 * A[0]) * mdiv[0];
else if (stmp[0] + j == 2 || stmp[0] + j == 4)
pijt1 = L_to[0] + L_to[0] * expp[0] * divm[0] - (L_to[0] / PIj[0]) * exp (minus_t_mutrate1 * A[0]);
else
pijt1 = L_to[0] * (1.0 - expp[0]);
if (stmp[1] == j)
pijt2 = L_to[1] + L_to[1] * expp[1] * divm[1] + exp (minus_t_mutrate2 * A[1]) * mdiv[1];
else if (stmp[1] + j == 2 || stmp[1] + j == 4)
pijt2 = L_to[1] + L_to[1] * expp[1] * divm[1] - (L_to[1] / PIj[1]) * exp (minus_t_mutrate2 * A[1]);
else
pijt2 = L_to[1] * (1.0 - expp[1]);
gtree[node].hkyi.newfrac[i][j] = pijt1 * pijt2;
if (gtree[node].hkyi.newfrac[i][j] > max)
max = gtree[node].hkyi.newfrac[i][j];
}
for (j = 0; j < 4; j++)
gtree[node].hkyi.newfrac[i][j] =
gtree[node].hkyi.newfrac[i][j] / max;
gtree[node].hkyi.scalefactor[i] = log (max);
}
}
else if (gtree[up1].up[0] == -1)
{
minus_t_mutrate1 = -mutrate * (gtree[up2].time - gtree[gtree[up2].up[0]].time);
minus_t_mutrate2 = -mutrate * gtree[up1].time;
expp[0] = exp (minus_t_mutrate1);
onem[0] = 1.0 - expp[0];
expp[1] = exp (minus_t_mutrate2);
PI_j[0] = pi[0] + pi[2];
PI_j[1] = pi[1] + pi[3];
A_j[0] = 1.0 + PI_j[0] * kpa;
A_j[1] = 1.0 + PI_j[1] * kpa;
divm[0] = 1.0 / PI_j[0] - 1.0;
divm[1] = 1.0 / PI_j[1] - 1.0;
exp1[0] = exp (minus_t_mutrate1 * A_j[0]);
exp1[1] = exp (minus_t_mutrate1 * A_j[1]);
exp2[0] = exp (minus_t_mutrate2 * A_j[0]);
exp2[1] = exp (minus_t_mutrate2 * A_j[1]);
for (i = 0; i < L[li].numsites; i++)
{
max = 0.0;
gtree[node].hkyi.newfrac[i][0] = 0;
gtree[node].hkyi.newfrac[i][1] = 0;
gtree[node].hkyi.newfrac[i][2] = 0;
gtree[node].hkyi.newfrac[i][3] = 0;
stmp[0] = L[li].seq[up1][i];
if (stmp[0] == 0 || stmp[0] == 2) /* use PI_j[0] & A_j[0] */
{
for (j = 0; j < 4; j++)
{
if (stmp[0] == j)
ptmp[j] = pi[stmp[0]] + pi[stmp[0]] * expp[1] * divm[0] + exp2[0] * ((PI_j[0] - pi[stmp[0]]) / PI_j[0]);
else if (stmp[0] + j == 2 || stmp[0] + j == 4)
ptmp[j] = pi[stmp[0]] + pi[stmp[0]] * expp[1] * divm[0] - (pi[stmp[0]] / PI_j[0]) * exp2[0];
else
ptmp[j] = pi[stmp[0]] * (1.0 - expp[1]);
}
}
else /* use PI_j[1] & A_j[1] */
{
for (j = 0; j < 4; j++)
{
if (stmp[0] == j)
ptmp[j] = pi[stmp[0]] + pi[stmp[0]] * expp[1] * divm[1] + exp2[1] * ((PI_j[1] - pi[stmp[0]]) / PI_j[1]);
else if (stmp[0] + j == 2 || stmp[0] + j == 4)
ptmp[j] = pi[stmp[0]] + pi[stmp[0]] * expp[1] * divm[1] - (pi[stmp[0]] / PI_j[1]) * exp2[1];
else
ptmp[j] = pi[stmp[0]] * (1.0 - expp[1]);
}
}
temp[0] = (pi[0] + pi[0] * expp[0] * divm[0] + exp1[0] * ((PI_j[0] - pi[0]) / PI_j[0])) * fracpoint2[i][0];
assert (fracpoint2 != 0x00000000);
temp[1] = (pi[1] * onem[0]) * fracpoint2[i][1];
temp[2] = (pi[2] + pi[2] * expp[0] * divm[0] - exp1[0] * (pi[2] / PI_j[0])) * fracpoint2[i][2];
temp[3] = (pi[3] * onem[0]) * fracpoint2[i][3];
gtree[node].hkyi.newfrac[i][0] += temp[0] + temp[1] + temp[2] + temp[3];
gtree[node].hkyi.newfrac[i][0] *= ptmp[0];
temp[0] = (pi[0] * onem[0]) * fracpoint2[i][0];
temp[1] = (pi[1] + pi[1] * expp[0] * divm[1] + exp1[1] * ((PI_j[1] - pi[1]) / PI_j[1])) * fracpoint2[i][1];
temp[2] = (pi[2] * onem[0]) * fracpoint2[i][2];
temp[3] = (pi[3] + pi[3] * expp[0] * divm[1] - exp1[1] * (pi[3] / PI_j[1])) * fracpoint2[i][3];
gtree[node].hkyi.newfrac[i][1] += temp[0] + temp[1] + temp[2] + temp[3];
gtree[node].hkyi.newfrac[i][1] *= ptmp[1];
temp[0] = (pi[0] + pi[0] * expp[0] * divm[0] - exp1[0] * (pi[0] / PI_j[0])) * fracpoint2[i][0];
temp[1] = (pi[1] * onem[0]) * fracpoint2[i][1];
temp[2] = (pi[2] + pi[2] * expp[0] * divm[0] + exp1[0] * ((PI_j[0] - pi[2]) / PI_j[0])) * fracpoint2[i][2];
temp[3] = (pi[3] * onem[0]) * fracpoint2[i][3];
gtree[node].hkyi.newfrac[i][2] += temp[0] + temp[1] + temp[2] + temp[3];
gtree[node].hkyi.newfrac[i][2] *= ptmp[2];
temp[0] = (pi[0] * onem[0]) * fracpoint2[i][0];
temp[1] = (pi[1] + pi[1] * expp[0] * divm[1] - exp1[1] * (pi[1] / PI_j[1])) * fracpoint2[i][1];
temp[2] = (pi[2] * onem[0]) * fracpoint2[i][2];
temp[3] = (pi[3] + pi[3] * expp[0] * divm[1] + exp1[1] * ((PI_j[1] - pi[3]) / PI_j[1])) * fracpoint2[i][3];
gtree[node].hkyi.newfrac[i][3] += temp[0] + temp[1] + temp[2] + temp[3];
gtree[node].hkyi.newfrac[i][3] *= ptmp[3];
for (j = 0; j < 4; j++)
if (gtree[node].hkyi.newfrac[i][j] > max)
max = gtree[node].hkyi.newfrac[i][j];
for (j = 0; j < 4; j++)
gtree[node].hkyi.newfrac[i][j] =
gtree[node].hkyi.newfrac[i][j] / max;
gtree[node].hkyi.scalefactor[i] =
gtree[up2].hkyi.scalefactor[i] + log (max);
}
}
else if (gtree[up2].up[0] == -1)
{
minus_t_mutrate1 = -mutrate * (gtree[up1].time - gtree[gtree[up1].up[0]].time);
minus_t_mutrate2 = -mutrate * gtree[up2].time;
expp[0] = exp (minus_t_mutrate1);
onem[0] = 1.0 - expp[0];
expp[1] = exp (minus_t_mutrate2);
PI_j[0] = pi[0] + pi[2];
PI_j[1] = pi[1] + pi[3];
A_j[0] = 1.0 + PI_j[0] * kpa;
A_j[1] = 1.0 + PI_j[1] * kpa;
divm[0] = 1.0 / PI_j[0] - 1.0;
divm[1] = 1.0 / PI_j[1] - 1.0;
exp1[0] = exp (minus_t_mutrate1 * A_j[0]);
exp1[1] = exp (minus_t_mutrate1 * A_j[1]);
exp2[0] = exp (minus_t_mutrate2 * A_j[0]);
exp2[1] = exp (minus_t_mutrate2 * A_j[1]);
for (i = 0; i < L[li].numsites; i++)
{
max = 0.0;
gtree[node].hkyi.newfrac[i][0] = 0;
gtree[node].hkyi.newfrac[i][1] = 0;
gtree[node].hkyi.newfrac[i][2] = 0;
gtree[node].hkyi.newfrac[i][3] = 0;
stmp[0] = L[li].seq[up2][i];
if (stmp[0] == 0 || stmp[0] == 2) /* use PI_j[0] & A_j[0] */
{
for (j = 0; j < 4; j++)
{
if (stmp[0] == j)
ptmp[j] = pi[stmp[0]] + pi[stmp[0]] * expp[1] * divm[0] + exp2[0] * ((PI_j[0] - pi[stmp[0]]) / PI_j[0]);
else if (stmp[0] + j == 2 || stmp[0] + j == 4)
ptmp[j] = pi[stmp[0]] + pi[stmp[0]] * expp[1] * divm[0] - (pi[stmp[0]] / PI_j[0]) * exp2[0];
else
ptmp[j] = pi[stmp[0]] * (1.0 - expp[1]);
}
}
else /* use PI_j[1] & A_j[1] */
{
for (j = 0; j < 4; j++)
{
if (stmp[0] == j)
ptmp[j] = pi[stmp[0]] + pi[stmp[0]] * expp[1] * divm[1] + exp2[1] * ((PI_j[1] - pi[stmp[0]]) / PI_j[1]);
else if (stmp[0] + j == 2 || stmp[0] + j == 4)
ptmp[j] = pi[stmp[0]] + pi[stmp[0]] * expp[1] * divm[1] - (pi[stmp[0]] / PI_j[1]) * exp2[1];
else
ptmp[j] = pi[stmp[0]] * (1.0 - expp[1]);
}
}
temp[0] = (pi[0] + pi[0] * expp[0] * divm[0] + exp1[0] * ((PI_j[0] - pi[0]) / PI_j[0])) * fracpoint1[i][0];
temp[1] = (pi[1] * onem[0]) * fracpoint1[i][1];
temp[2] = (pi[2] + pi[2] * expp[0] * divm[0] - exp1[0] * (pi[2] / PI_j[0])) * fracpoint1[i][2];
temp[3] = (pi[3] * onem[0]) * fracpoint1[i][3];
gtree[node].hkyi.newfrac[i][0] += temp[0] + temp[1] + temp[2] + temp[3];
gtree[node].hkyi.newfrac[i][0] *= ptmp[0];
temp[0] = (pi[0] * onem[0]) * fracpoint1[i][0];
temp[1] = (pi[1] + pi[1] * expp[0] * divm[1] + exp1[1] * ((PI_j[1] - pi[1]) / PI_j[1])) * fracpoint1[i][1];
temp[2] = (pi[2] * onem[0]) * fracpoint1[i][2];
temp[3] = (pi[3] + pi[3] * expp[0] * divm[1] - exp1[1] * (pi[3] / PI_j[1])) * fracpoint1[i][3];
gtree[node].hkyi.newfrac[i][1] += temp[0] + temp[1] + temp[2] + temp[3];
gtree[node].hkyi.newfrac[i][1] *= ptmp[1];
temp[0] = (pi[0] + pi[0] * expp[0] * divm[0] - exp1[0] * (pi[0] / PI_j[0])) * fracpoint1[i][0];
temp[1] = (pi[1] * onem[0]) * fracpoint1[i][1];
temp[2] = (pi[2] + pi[2] * expp[0] * divm[0] + exp1[0] * ((PI_j[0] - pi[2]) / PI_j[0])) * fracpoint1[i][2];
temp[3] = (pi[3] * onem[0]) * fracpoint1[i][3];
gtree[node].hkyi.newfrac[i][2] += temp[0] + temp[1] + temp[2] + temp[3];
gtree[node].hkyi.newfrac[i][2] *= ptmp[2];
temp[0] = (pi[0] * onem[0]) * fracpoint1[i][0];
temp[1] = (pi[1] + pi[1] * expp[0] * divm[1] - exp1[1] * (pi[1] / PI_j[1])) * fracpoint1[i][1];
temp[2] = (pi[2] * onem[0]) * fracpoint1[i][2];
temp[3] = (pi[3] + pi[3] * expp[0] * divm[1] + exp1[1] * ((PI_j[1] - pi[3]) / PI_j[1])) * fracpoint1[i][3];
gtree[node].hkyi.newfrac[i][3] += temp[0] + temp[1] + temp[2] + temp[3];
gtree[node].hkyi.newfrac[i][3] *= ptmp[3];
for (j = 0; j < 4; j++)
if (gtree[node].hkyi.newfrac[i][j] > max)
max = gtree[node].hkyi.newfrac[i][j];
for (j = 0; j < 4; j++)
gtree[node].hkyi.newfrac[i][j] = gtree[node].hkyi.newfrac[i][j] / max;
gtree[node].hkyi.scalefactor[i] = gtree[up1].hkyi.scalefactor[i] + log (max);
}
}
else
{
minus_t_mutrate1 = -mutrate * (gtree[up1].time - gtree[gtree[up1].up[0]].time);
minus_t_mutrate2 = -mutrate * (gtree[up2].time - gtree[gtree[up2].up[0]].time);
expp[0] = exp (minus_t_mutrate1);
onem[0] = 1.0 - expp[0];
expp[1] = exp (minus_t_mutrate2);
onem[1] = 1.0 - expp[1];
PI_j[0] = pi[0] + pi[2];
PI_j[1] = pi[1] + pi[3];
A_j[0] = 1.0 + PI_j[0] * kpa;
A_j[1] = 1.0 + PI_j[1] * kpa;
divm[0] = 1.0 / PI_j[0] - 1.0;
divm[1] = 1.0 / PI_j[1] - 1.0;
exp1[0] = exp (minus_t_mutrate1 * A_j[0]);
exp1[1] = exp (minus_t_mutrate1 * A_j[1]);
exp2[0] = exp (minus_t_mutrate2 * A_j[0]);
exp2[1] = exp (minus_t_mutrate2 * A_j[1]);
for (i = 0; i < L[li].numsites; i++)
{
max = 0.0;
sum[0] = 0;
sum[1] = 0;
sum[2] = 0;
sum[3] = 0;
gtree[node].hkyi.newfrac[i][0] = 0;
gtree[node].hkyi.newfrac[i][1] = 0;
gtree[node].hkyi.newfrac[i][2] = 0;
gtree[node].hkyi.newfrac[i][3] = 0;
temp[0] = (pi[0] + pi[0] * expp[0] * divm[0] + exp1[0] * ((PI_j[0] - pi[0]) / PI_j[0])) * fracpoint1[i][0];
temp[1] = (pi[1] * onem[0]) * fracpoint1[i][1];
temp[2] = (pi[2] + pi[2] * expp[0] * divm[0] - exp1[0] *
(pi[2] / PI_j[0])) * fracpoint1[i][2];
temp[3] = (pi[3] * onem[0]) * fracpoint1[i][3];
sum[0] += temp[0] + temp[1] + temp[2] + temp[3];
temp[0] = (pi[0] + pi[0] * expp[1] * divm[0] + exp2[0] * ((PI_j[0] - pi[0]) / PI_j[0])) * fracpoint2[i][0];
temp[1] = (pi[1] * onem[1]) * fracpoint2[i][1];
temp[2] = (pi[2] + pi[2] * expp[1] * divm[0] - exp2[0] * (pi[2] / PI_j[0])) * fracpoint2[i][2];
temp[3] = (pi[3] * onem[1]) * fracpoint2[i][3];
gtree[node].hkyi.newfrac[i][0] += temp[0] + temp[1] + temp[2] + temp[3];
gtree[node].hkyi.newfrac[i][0] *= sum[0];
temp[0] = (pi[0] * onem[0]) * fracpoint1[i][0];
temp[1] = (pi[1] + pi[1] * expp[0] * divm[1] + exp1[1] * ((PI_j[1] - pi[1]) / PI_j[1])) * fracpoint1[i][1];
temp[2] = (pi[2] * onem[0]) * fracpoint1[i][2];
temp[3] = (pi[3] + pi[3] * expp[0] * divm[1] - exp1[1] * (pi[3] / PI_j[1])) * fracpoint1[i][3];
sum[1] += temp[0] + temp[1] + temp[2] + temp[3];
temp[0] = (pi[0] * onem[1]) * fracpoint2[i][0];
temp[1] = (pi[1] + pi[1] * expp[1] * divm[1] + exp2[1] * ((PI_j[1] - pi[1]) / PI_j[1])) * fracpoint2[i][1];
temp[2] = (pi[2] * onem[1]) * fracpoint2[i][2];
temp[3] = (pi[3] + pi[3] * expp[1] * divm[1] - exp2[1] * (pi[3] / PI_j[1])) * fracpoint2[i][3];
gtree[node].hkyi.newfrac[i][1] += temp[0] + temp[1] + temp[2] + temp[3];
gtree[node].hkyi.newfrac[i][1] *= sum[1];
temp[0] = (pi[0] + pi[0] * expp[0] * divm[0] - exp1[0] * (pi[0] / PI_j[0])) * fracpoint1[i][0];
temp[1] = (pi[1] * onem[0]) * fracpoint1[i][1];
temp[2] = (pi[2] + pi[2] * expp[0] * divm[0] + exp1[0] * ((PI_j[0] - pi[2]) / PI_j[0])) * fracpoint1[i][2];
temp[3] = (pi[3] * onem[0]) * fracpoint1[i][3];
sum[2] += temp[0] + temp[1] + temp[2] + temp[3];
temp[0] = (pi[0] + pi[0] * expp[1] * divm[0] - exp2[0] * (pi[0] / PI_j[0])) * fracpoint2[i][0];
temp[1] = (pi[1] * onem[1]) * fracpoint2[i][1];
temp[2] = (pi[2] + pi[2] * expp[1] * divm[0] + exp2[0] * ((PI_j[0] - pi[2]) / PI_j[0])) * fracpoint2[i][2];
temp[3] = (pi[3] * onem[1]) * fracpoint2[i][3];
gtree[node].hkyi.newfrac[i][2] += temp[0] + temp[1] + temp[2] + temp[3];
gtree[node].hkyi.newfrac[i][2] *= sum[2];
temp[0] = (pi[0] * onem[0]) * fracpoint1[i][0];
temp[1] = (pi[1] + pi[1] * expp[0] * divm[1] - exp1[1] * (pi[1] / PI_j[1])) * fracpoint1[i][1];
temp[2] = (pi[2] * onem[0]) * fracpoint1[i][2];
temp[3] = (pi[3] + pi[3] * expp[0] * divm[1] + exp1[1] *
((PI_j[1] - pi[3]) / PI_j[1])) * fracpoint1[i][3];
sum[3] += temp[0] + temp[1] + temp[2] + temp[3];
temp[0] = (pi[0] * onem[1]) * fracpoint2[i][0];
temp[1] = (pi[1] + pi[1] * expp[1] * divm[1] - exp2[1] * (pi[1] / PI_j[1])) * fracpoint2[i][1];
temp[2] = (pi[2] * onem[1]) * fracpoint2[i][2];
temp[3] = (pi[3] + pi[3] * expp[1] * divm[1] + exp2[1] * ((PI_j[1] - pi[3]) / PI_j[1])) * fracpoint2[i][3];
gtree[node].hkyi.newfrac[i][3] += temp[0] + temp[1] + temp[2] + temp[3];
gtree[node].hkyi.newfrac[i][3] *= sum[3];
for (j = 0; j < 4; j++)
if (gtree[node].hkyi.newfrac[i][j] > max)
max = gtree[node].hkyi.newfrac[i][j];
for (j = 0; j < 4; j++)
gtree[node].hkyi.newfrac[i][j] = gtree[node].hkyi.newfrac[i][j] / max;
gtree[node].hkyi.scalefactor[i] = gtree[up1].hkyi.scalefactor[i] + gtree[up2].hkyi.scalefactor[i] + log (max);
}
}
}
}
return ret;
} // Jim Long's unwrapped makefrac()
double
getstandfactor (int ci, int li, double kappa)
{
int i, j;
double p = 0;
for (i = 0; i < 4; i++)
{
for (j = 0; j < 4; j++)
{
if (i != j)
{
if (i + j == 2 || i + j == 4)
p += C[ci]->G[li].pi[i] * C[ci]->G[li].pi[j] * kappa;
/*HKY*/
else
p += C[ci]->G[li].pi[i] * C[ci]->G[li].pi[j];
}
}
}
return p;
}
/************ GLOBAL FUNCTIONS ******************/
/* older version with recursion
void labelgtree( int ci, int li, int edge)
{
int dow1, sis;
struct edge *gtree = C[ci]->G[li].gtree;
dow1 = gtree[edge].down;
if (dow1 != -1)
{
if ((sis = gtree[dow1].up[0]) == edge)
sis = gtree[dow1].up[1];
if (gtree[dow1].mut != gtree[edge].mut)
{
if (gtree[edge].mut == 2)
{
if (gtree[sis].mut != -1)
gtree[dow1].mut = gtree[sis].mut;
else
gtree[dow1].mut = 2;
}
else if ((gtree[sis].mut != -1 && gtree[sis].mut != 2) && (gtree[sis].mut != gtree[edge].mut))
gtree[dow1].mut = 2;
else
gtree[dow1].mut = gtree[edge].mut;
labelgtree(ci, li, dow1);
}
else if (gtree[dow1].mut == 2)
{
if (gtree[sis].mut != -1 && gtree[sis].mut != 2)
{
gtree[dow1].mut = gtree[sis].mut;
labelgtree(ci, li, dow1);
}
}
}
} older version labelgtree */
/* version without recursion, suggested by Jim Long as it allows inlining of the function */
__forceinlineVS void
labelgtree (int ci, int li, int edge)
{
int dow1, sis, flag;
struct edge *gtree = C[ci]->G[li].gtree;
flag = 1;
while (flag)
{
flag = 0;
dow1 = gtree[edge].down;
if (dow1 == -1)
break;
if ((sis = gtree[dow1].up[0]) == edge)
sis = gtree[dow1].up[1];
if (gtree[dow1].mut != gtree[edge].mut)
{
if (gtree[edge].mut == 2)
{
if (gtree[sis].mut != -1)
gtree[dow1].mut = gtree[sis].mut;
else
gtree[dow1].mut = 2;
}
else if ((gtree[sis].mut != -1 && gtree[sis].mut != 2)
&& (gtree[sis].mut != gtree[edge].mut))
{
gtree[dow1].mut = 2;
}
else
{
gtree[dow1].mut = gtree[edge].mut;
}
flag = 1;
}
else if (gtree[dow1].mut == 2)
{
if (gtree[sis].mut != -1 && gtree[sis].mut != 2)
{
gtree[dow1].mut = gtree[sis].mut;
flag = 1;
}
}
edge = dow1;
}
} /* labelgtree non-recursive */
double
likelihoodHKY (int ci, int li, double mutrate, double kappa, int e1, int e2,
int e3, int e4)
{
int i, j;
double fracp, p = 0;
struct edge *gtree = C[ci]->G[li].gtree;
if (calcoptions[DONTCALCLIKELIHOODMUTATION])
return 0;
/*JH 5/15/09 fixed bad HKY model bug replaced numsites with totsites */
mutrate = mutrate / (L[li].totsites * getstandfactor (ci, li, kappa));
for (i = L[li].numgenes; i < 2 * L[li].numgenes - 1; i++)
gtree[i].hkyi.newfrac[0][0] = -1;
makefrac (ci, li, C[ci]->G[li].root, mutrate, kappa, e1, e2, e3, e4);
for (i = 0; i < L[li].numsites; i++)
{
fracp = 0;
for (j = 0; j < 4; j++)
{
fracp += C[ci]->G[li].pi[j] * gtree[C[ci]->G[li].root].hkyi.newfrac[i][j];
}
p += L[li].mult[i] * (log (fracp) + gtree[C[ci]->G[li].root].hkyi.scalefactor[i]);
}
return p;
}
void
calc_sumlogk (int ci, int li, double *psumlogk)
/* basically a copy of the likelihood function, and probably overkill for what it does */
{
int ret, node, site, up1, up2, upup;
#if 0
/*
* CR 110929.3 from JH 9/27/2011
* no longer compiled into code, kept for historical reasons only
*/
/* double t; stopped using. it was left over from the original
* likelihood function that Rasmus wrote, but it is needed
* to get the sumlogk constant
*/
#endif // #if 0
int summ = 0, *mutcount, i, j;
double fact, sum;
struct edge *gtree = C[ci]->G[li].gtree;
int ng = L[li].numgenes;
mutcount = calloc ((size_t) ng, (sizeof (int *)));
for (site = 0; site < L[li].numsites; site++)
{
for (j = 0; j < ng; j++)
gtree[j].mut = L[li].seq[j][site];
for (j = ng; j < L[li].numlines; j++)
gtree[j].mut = -1;
for (j = 0; j < ng; j++)
labelgtree (ci, li, j);
ret = -1;
#if 0
/*
* CR 110929.3 from JH 9/27/2011
* no longer compiled into code, kept for historical reasons only
*/
t = 0;
#endif // #if 0
for (node = ng; node < L[li].numlines; node++)
{
i = node - ng;
up1 = gtree[node].up[0];
up2 = gtree[node].up[1];
if ((gtree[up1].mut == 0 && gtree[up2].mut == 1)
|| (gtree[up1].mut == 1 && gtree[up2].mut == 0))
{
if (node != ret && ret != -1)
{
XFREE (mutcount);
return;
}
else
{
#if 0
/*
* CR 110929.3 from JH 9/27/2011
* no longer compiled into code, kept for historical reasons only
*/
/* stopped using. this block of code was left
* over from the original likelihood function that Rasmus wrote,
* but it is not needed to get the sumlogk constant
if (gtree[node].down == -1)
{
if ((upup = gtree[up1].up[0]) == -1)
t = gtree[up1].time;
else
t = gtree[up1].time - gtree[upup].time;
if ((upup = gtree[up2].up[0]) == -1)
t = t + gtree[up2].time;
else
t = t + gtree[up2].time - gtree[upup].time;
}
else
{
if (gtree[gtree[node].down].mut == gtree[up1].mut)
{
if ((upup = gtree[up2].up[0]) == -1)
t = gtree[up2].time;
else
t = gtree[up2].time - gtree[upup].time;
}
else
{
if ((upup = gtree[up1].up[0]) == -1)
t = gtree[up1].time;
else
t = gtree[up1].time - gtree[upup].time;
}
} */
#endif // #if 0
ret = node;
mutcount[i]++;
summ++;
}
}
}
if (ret == -1)
{
IM_err(IMERR_INFINITESITESFAIL,"Data incompatible with current genealogy, likelihood calculation failed, chain %d, locus %d, site %d, step %d",ci,li,site, step);
}
}
for (sum = 0.0, i = 0; i < L[li].numlines - ng; i++)
{
fact = 1.0;
for (j = 1; j <= mutcount[i]; j++)
fact *= (double) j;
sum += log (fact);
}
*psumlogk = sum;
XFREE (mutcount);
} //calc_sumlogk
void
free_sumlogk (void)
{
int li;
for (li = 0; li < nloci; li++)
if (sumlogk[li])
XFREE (sumlogk[li]);
}
double
likelihoodIS (int ci, int li, double mutrate)
/* written by Rasmus to return the following value
- (total length of gtree in time) * theta + SUM(log(t_i * theta)*k_i, over all branches)
where k_i is the number of mutations on branch i.
This is equal to the logarithm of the product of a bunch of poisson variables, one for each branch, except that
one term is dropped out. [ -SUM(log(k_i !) ] is not included. However this will be the same for two infinite
sites gtrees that fit the same data set.
*/
/* under new parameterization
- (total length of gtree in time) * mutrate + SUM(log(t_i * mutrate)*k_i, over all branches) - SUM(log(k_i !)
where k_i is the number of mutations on branch i.
as before, do not need to include the term : -SUM(log(k_i !)
Can also do it as
- (total length of gtree in time) * mutrate + log(mutrate) * SUM(k_i) + Sum(log(t_i)*k_i, over all branches) - SUM(log(k_i !)
check out the method of getting gtree length - seems ok.
*/
{
int ret, j, node, site, up1, up2, upup;
double ptime, p;
static int done_sumlogk[MAXLOCI] = { 0 };
int ng = L[li].numgenes;
struct edge *gtree;
if (calcoptions[DONTCALCLIKELIHOODMUTATION])
{
return 0;
}
if (done_sumlogk[li] == 0)
{
sumlogk[li] = calloc (1, sizeof (double));
calc_sumlogk (ci, li, sumlogk[li]);
done_sumlogk[li] = 1;
}
p = -C[ci]->G[li].length * mutrate;
gtree = C[ci]->G[li].gtree;
for (site = 0; site < L[li].numsites; site++)
{
for (j = 0; j < ng; j++)
gtree[j].mut = L[li].seq[j][site];
for (j = ng; j < L[li].numlines; j++)
gtree[j].mut = -1;
for (j = 0; j < ng; j++)
labelgtree (ci, li, j);
ret = -1;
for (node = ng; node < L[li].numlines; node++)
{
up1 = gtree[node].up[0];
up2 = gtree[node].up[1];
if ((gtree[up1].mut == 0 && gtree[up2].mut == 1)
|| (gtree[up1].mut == 1 && gtree[up2].mut == 0))
{
if (node != ret && ret != -1)
{
return REJECTINFINITESITESCONSTANT;
}
else
{
/* i is the root node add together both branch times */
if (gtree[node].down == -1)
{
if ((upup = gtree[up1].up[0]) == -1)
ptime = gtree[up1].time;
else
ptime = gtree[up1].time - gtree[upup].time;
if ((upup = gtree[up2].up[0]) == -1)
ptime = ptime + gtree[up2].time;
else
ptime = ptime + gtree[up2].time - gtree[upup].time;
}
else /* i is not the root node */
{
if (gtree[gtree[node].down].mut == gtree[up1].mut)
{
if ((upup = gtree[up2].up[0]) == -1)
ptime = gtree[up2].time;
else
ptime = gtree[up2].time - gtree[upup].time;
}
else
{
if ((upup = gtree[up1].up[0]) == -1)
ptime = gtree[up1].time;
else
ptime = gtree[up1].time - gtree[upup].time;
}
}
ret = node;
}
}
}
if (ret == -1)
{
IM_err(IMERR_INFINITESITESFAIL,"Data incompatible with current genealogy, likelihood calculation failed, chain %d, locus %d, site %d, step %d",ci,li,site, step);
}
else
{
assert (ptime * mutrate != 0);
p = p + log (ptime * mutrate);
}
}
p -= *sumlogk[li];
return p;
} /* likelihood */
/* likelihoodSW() calculates and sums the dlikeA values on each branch */
/* if a locus is joint then ai goes from 0 to nlinked - 1 otherwise ai goes from 0 to nlinked */
double
likelihoodSW (int ci, int li, int ai, double u, double tr)
{
int i, up, d;
double t, like;
struct edge *gtree;
double bessiv;
int iszero;
gtree = C[ci]->G[li].gtree;
like = 0.0;
iszero = 0;
for (i = 0; i < L[li].numlines; i++)
{
if (gtree[i].down != -1)
{
assert (gtree[i].A[ai] >= L[li].minA[ai]
&& gtree[i].A[ai] <= L[li].maxA[ai]);
d = gtree[i].A[ai] - gtree[gtree[i].down].A[ai];
if (gtree[i].up[0] == -1)
{
t = gtree[i].time * tr;
}
else
{
up = gtree[i].up[0];
t = tr * (gtree[i].time - gtree[up].time);
}
/* SANGCHUL: Wed Apr 15 17:40:24 EDT 2009
* When d is positive,
* u is very small, bessi(d,t*u) would return 0, which makes
* log infinity. If t * u is too small then, we have zero probability
* of likelihood and we should reject any proposal. */
bessiv = bessi (d, t * u);
if (!(bessiv > 0.0))
{
iszero = 1;
gtree[i].dlikeA[ai] = IM_BESSI_MIN;
}
else
{
gtree[i].dlikeA[ai] = -(t * u) + log (bessiv);
}
like += gtree[i].dlikeA[ai];
}
else
{
gtree[i].dlikeA[ai] = 0.0;
}
}
/* SANGCHUL: We return the smallest value for the likelihood */
if (iszero == 1)
{
like = -DBL_MAX;
}
/* SANGCHUL: Wed Apr 15 17:42:29 EDT 2009
* Can this statement be called before the for-loop above? */
if (calcoptions[DONTCALCLIKELIHOODMUTATION])
{
return 0.0;
}
else
{
return like;
}
} /* likelihoodSW */
/* use this for debugging, to make sure likelihoodSW has set the dlikeA values properly */
void
checklikelihoodSW (int ci, int li, int ai, double u)
{
int i, up, d;
double t, dlikeA;
struct edge *gtree;
double bessiv;
gtree = C[ci]->G[li].gtree;
for (i = 0; i < L[li].numlines; i++)
{
if (gtree[i].down != -1)
{
d = gtree[i].A[ai] - gtree[gtree[i].down].A[ai];
if (gtree[i].up[0] == -1)
{
t = gtree[i].time;
}
else
{
up = gtree[i].up[0];
t = gtree[i].time - gtree[up].time;
}
bessiv = bessi (d, t * u);
if (!(bessiv > 0.0))
{
IM_err (IMERR_SWCHECK,
"Negative or zero value (%lf) of Bessel function", bessiv);
}
dlikeA = -(t * u) + log (bessi (d, t * u));
if (gtree[i].dlikeA[ai] != dlikeA)
{
IM_err (IMERR_SWCHECK, "Chain %d, Locus %d", ci, li);
}
}
}
return;
} /* checklikelihoodSW */