/* Initialise KISS generator using /dev/urandom */
void jkiss_init(jkiss *j)
{
j->x = devrand();
while (!(j->y = devrand())); /* y must not be zero! */
j->z = devrand();
/* We don’t really need to set c as well but let's anyway… */
/* NOTE: offset c by 1 to avoid z=c=0 */
j->c = devrand() % 698769068 + 1; /* Should be less than 698769069 */
}
void getParameters(int argc,const char **argv){
int args;
int i,j;
double migR;
int selCheck,nChangeCheck;
if( argc < 3){
usage();
}
sampleSize = atoi(argv[1]);
if(sampleSize > 254){
#ifndef BIG
printf("Error: sampleSize > 254. recompile discoal and set the -DBIG flag\n");
exit(666);
#endif
}
sampleNumber = atoi(argv[2]);
nSites = atoi(argv[3]);
if(nSites>MAXSITES){
printf("Error: number of sites set higher than current compilation limit. Please reduce the number of sites or change the MAXSITES define and recompile\n");
exit(666);
}
args = 4;
npops = 1;
popnSizes[0]=sampleSize;
popnSizes[1]=0;
sampleSizes[0]=sampleSize;
sampleSizes[1]=0;
leftRho = 0.0;
rho = 0.0;
my_gamma = 0.0;
gcMean = 0;
theta = 0.0;
alpha = 0.0;
lambda = 0.0;
tau = 0;
ancestralSizeRatio = 1.0;
f0=0.0;
uA=0.0;
seed1 = (long) (devrand() % 2147483399);
seed2 = (long) (devrand() % 2147483399);
EFFECTIVE_POPN_SIZE = 1000000;
sweepSite = 0.5;
tDiv=666;
gammaCoRatioMode = 0;
priorTheta=priorRho=priorAlpha=priorTau=priorX=priorF0=priorUA=priorC=0;
eventFlag = 1;
effectiveSampleSize = sampleSize;
finiteOutputFlag = 0;
outputStyle = 'h';
mask = 0;
migFlag = 0;
deltaTMod = 40;
recurSweepMode = 0;
treeOutputMode= 0;
partialSweepMode = 0;
softSweepMode = 0;
ancSampleFlag = 0;
ancSampleSize = 0;
hidePartialSNP = 0;
//set up first bogus event
eventNumber = 0;
events[eventNumber].time = 0.0;
events[eventNumber].popID = 0;
events[eventNumber].popnSize = 1.0;
events[eventNumber].type = 'n';
eventNumber++;
currentSize = malloc(sizeof(double) * MAXPOPS);
condRecMode= 0;
while(args < argc){
switch(argv[args][1]){
case 'S' :
runMode = 'S';
fileName = argv[++args];
break;
case 's' :
segSites = atoi(argv[++args]);
break;
case 't' :
theta = atof(argv[++args]);
break;
case 'i' :
deltaTMod = atof(argv[++args]);
break;
case 'r' :
rho = atof (argv[++args]);
break;
case 'g' :
if (argv[args][2] == 'r')
{
gammaCoRatio = atof (argv[++args]);
gcMean = atoi (argv[++args]);
gammaCoRatioMode = 1;
}
else
{
my_gamma = atof (argv[++args]);
gcMean = atoi (argv[++args]);
}
break;
case 'a' :
alpha = atof(argv[++args]);
break;
case 'x' :
sweepSite = atof(argv[++args]);
break;
case 'M' :
if(npops==1){
fprintf(stderr,"Error: attempting to set migration but only one population! Be sure that 'm' flags are specified after 'p' flag\n");
exit(1);
}
migR = atof(argv[++args]);
for(i=0;i<npops;i++){
for(j=0;j<npops;j++){
if(i!=j){
migMatConst[i][j]=migR;
}
else{
migMatConst[i][j]= 0.0;
}
}
}
migFlag = 1;
break;
case 'm' :
if(npops==1){
fprintf(stderr,"Error: attempting to set migration but only one population! Be sure that 'm' flags are specified after 'p' flag\n");
exit(1);
}
i = atoi(argv[++args]);
j = atoi(argv[++args]);
migR = atof(argv[++args]);
migMatConst[i][j]=migR;
migFlag = 1;
break;
case 'p' :
npops = atoi(argv[++args]);
if(npops > MAXPOPS){
fprintf(stderr,"Error: too many populations defined. Current maximum number = %d. Change MAXPOPS define in discoal.h and recompile... if you dare\n",MAXPOPS);
exit(1);
}
for(i=0;i<npops;i++){
sampleSizes[i]=atoi(argv[++args]);
currentSize[i] = 1.0;
}
break;
case 'e' :
switch(argv[args][2]){
case 'n':
events[eventNumber].time = atof(argv[++args]) * 2.0;
events[eventNumber].popID = atoi(argv[++args]);
events[eventNumber].popnSize = atof(argv[++args]);
events[eventNumber].type = 'n'; //size change
eventNumber++;
break;
case 'd' :
tDiv = atof(argv[++args]);
events[eventNumber].time = tDiv * 2.0;
events[eventNumber].popID = atoi(argv[++args]);
events[eventNumber].popID2 = atoi(argv[++args]);
events[eventNumber].type = 'p'; //pop split
eventNumber++;
break;
case 'a' :
events[eventNumber].time = atof(argv[++args]) * 2.0;
events[eventNumber].popID = atoi(argv[++args]);
events[eventNumber].popID2 = atoi(argv[++args]);
events[eventNumber].popID3 = atoi(argv[++args]);
events[eventNumber].admixProp = atof(argv[++args]);
events[eventNumber].type = 'a'; //admix split
eventNumber++;
break;
}
break;
case 'w':
switch(argv[args][2]){
case 'd':
sweepMode = 'd';
break;
case 's':
sweepMode = 's';
break;
case 'n':
sweepMode = 'N';
break;
}
tau = atof(argv[++args]) * 2.0;
events[eventNumber].time = tau;
events[eventNumber].type = 's'; //sweep event
eventNumber++;
break;
case 'l':
switch(argv[args][2]){
case 'd':
sweepMode = 'd';
break;
case 's':
sweepMode = 's';
break;
case 'n':
sweepMode = 'N';
break;
}
sweepSite = -1.0;
tau = atof(argv[++args]) * 2.0;
leftRho = atof(argv[++args]) * 2.0;
leftRhoFlag=1;
events[eventNumber].time = tau;
events[eventNumber].type = 's'; //sweep event
eventNumber++;
break;
case 'f':
f0 = atof(argv[++args]);
softSweepMode = 1;
break;
case 'u':
uA = atof(argv[++args]);
break;
case 'P' :
switch(argv[args][2]){
case 't':
priorTheta = 1;
pThetaLow=atof(argv[++args]);
pThetaUp=atof(argv[++args]);
break;
case 'c':
priorC = 1;
partialSweepMode = 1;
pCLow=atof(argv[++args]);
pCUp=atof(argv[++args]);
break;
case 'r':
if (strlen(argv[args]) == 4 && argv[args][3] == 'e'){
priorRho = 2;
pRhoMean=atof(argv[++args]);
pRhoUp=atof(argv[++args]);
}
else{
priorRho = 1;
pRhoLow=atof(argv[++args]);
pRhoUp=atof(argv[++args]);
}
break;
case 'a':
priorAlpha = 1;
pAlphaLow=atof(argv[++args]);
pAlphaUp=atof(argv[++args]);
break;
case 'u':
if (strlen(argv[args]) == 4 && argv[args][3] == 'A'){
priorUA = 1;
pUALow=atof(argv[++args]);
pUAUp=atof(argv[++args]);
}
else{
priorTau = 1;
pTauLow=atof(argv[++args]) * 2.0;
pTauUp=atof(argv[++args]) * 2.0;
}
break;
case 'x':
priorX = 1;
pXLow=atof(argv[++args]);
pXUp=atof(argv[++args]);
break;
case 'f':
priorF0 = 1;
pF0Low=atof(argv[++args]);
pF0Up=atof(argv[++args]);
break;
case 'e':
switch(argv[args][3]){
case '1':
priorE1 = 1;
pE1TLow=atof(argv[++args])*2.0;
pE1THigh=atof(argv[++args])*2.0;
pE1SLow=atof(argv[++args]);
pE1SHigh=atof(argv[++args]);
events[eventNumber].type = 'n';
eventNumber++;
break;
case '2':
priorE2 = 1;
pE2TLow=atof(argv[++args])*2.0;
pE2THigh=atof(argv[++args])*2.0;
pE2SLow=atof(argv[++args]);
pE2SHigh=atof(argv[++args]);
events[eventNumber].type = 'n';
eventNumber++;
break;
}
break;
}
break;
case 'U' :
untilMode= 1;
uTime=atof(argv[++args])*2.0;
break;
case 'd' :
seed1=atoi(argv[++args]);
seed2=atoi(argv[++args]);
break;
case 'N' :
EFFECTIVE_POPN_SIZE=atoi(argv[++args]);
break;
case 'T' :
treeOutputMode= 1;
break;
case 'C' :
condRecMode= 1;
condRecMet = 0;
lSpot=atoi(argv[++args]);
rSpot=atoi(argv[++args]);
break;
case 'R' :
recurSweepMode = 1;
sweepMode = 's';
recurSweepRate = atof(argv[++args]);
break;
case 'L' :
recurSweepMode = 1;
sweepMode = 's';
sweepSite = -1.0;
recurSweepRate = atof(argv[++args]);
if (recurSweepRate <= 0)
{
fprintf(stderr,"recurSweepRate must be > 0\n");
exit(0);
}
break;
case 'c' :
partialSweepMode = 1;
sweepMode = 's';
partialSweepFinalFreq = atof(argv[++args]);
if (partialSweepFinalFreq <= 0.0 || partialSweepFinalFreq >= 1.0)
{
fprintf(stderr,"partialSweepFinalFreq must be > 0 and < 1.0\n");
exit(1);
}
break;
case 'h' :
hidePartialSNP = 1;
break;
case 'A' :
events[eventNumber].lineageNumber = atoi(argv[++args]);
events[eventNumber].popID = atoi(argv[++args]);
events[eventNumber].time = atof(argv[++args]) * 2.0;
ancSampleSize += events[eventNumber].lineageNumber;
events[eventNumber].type = 'A'; //ancient sample
ancSampleFlag = 1;
eventNumber++;
assert(events[eventNumber].lineageNumber < sampleSize);
break;
}
args++;
}
sortEventArray(events,eventNumber);
//make sure events are kosher
selCheck = 0;
nChangeCheck=0;
for(i=0;i<eventNumber;i++){
//printf("event %d: type is %c\n", i, events[i].type);
if(events[i].type == 's'){
selCheck = 1;
}
if(events[i].type == 'n'){
nChangeCheck = 1;
}
}
if(selCheck == 1){
if(recurSweepMode == 1){
printf("Error with event specification: a single sweep event has been found but recurrentSweep mode has been specified\n");
exit(666);
}
if(nChangeCheck==1 && sweepMode=='d'){
printf("Error with event specification: you chose 1 or more population size changes with a determinstic sweep. Please us -ws flag instead\n");
exit(666);
}
if(softSweepMode == 1 && partialSweepMode == 1){
if(f0 >= partialSweepFinalFreq){
printf("Error with event specification: you specified a partial soft sweep but final frequency of partial sweep <= f_0\n");
exit(666);
}
}
}
if(leftRhoFlag && sweepSite >= 0.0){
printf("Error with event specification: you chose leftRho mode but the sweep site is within the locus\n");
exit(666);
}
if(softSweepMode == 1 && recurSweepMode == 1){
printf("Error with event specification: currently recurrent soft sweeps are not implemented. this will be a future addition\n");
exit(666);
}
}
