void MessageOut::writeString(const string &string, Sint16 length){
Uint16 stringLength = string.length();
if (length < 0)
{
// Write the length at the start if not fixed.
write2(stringLength);
length = stringLength;
}
else if (length < stringLength)
{
stringLength = length; // Make sure the length of the string is no longer than specified
}
expandData((this->pos) + length);
memcpy((this->myData) + (this->pos), string.c_str(), stringLength); // Write the actual string.
if (length > stringLength) // Pad remaining space with zeros.
{
memset((this->myData) + (this->pos) + stringLength, '\0', length - stringLength);
}
this->pos += length;
}
void MessageOut::write4(Uint32 value){
expandData((this->pos) + 4);
Uint32 tmp = SDL_SwapBE32(value);
memcpy((this->myData)+(this->pos), &tmp, 4);
this->pos += 4;
}
void MessageOut::write1(char value){
expandData((this->pos) + 1);
myData[this->pos] = value;
this->pos += 1;
}
void MessageOut::write2(Uint16 value){
expandData((this->pos) + 2);
Uint16 tmp = SDL_SwapBE16(value);
memcpy((this->myData)+(this->pos), &tmp, 2);
this->pos += 2;
}
void scanFile(Args *args, FILE *fp){
char *line, *name, *token, *chr;
size_t n;
int status, len, l, start, end;
int pos[2], p, i, tp, tn;
Data *data;
double ll, ul, cf;
line = NULL;
while((status = getline(&line,&n,fp)) != -1){
if(line[0] != '#')
break;
}
if(!args->p)
printf("# Int\tChr\tStart\tEnd\tLen\t[%%\t%%\t%%]\t[cM/Mb\tcM/Mb\tcM/Mb]\n");
data = newData(1,args->o);
while(status != -1){
data->n = 0;
name = estrdup(strtok(line,"\t")); /* read name of region */
chr = estrdup(strtok(NULL,"\t")); /* read chromosome */
start = intVal(strtok(NULL,"\t")); /* start position */
end = intVal(strtok(NULL,"\t")); /* end position */
len = end - start + 1; /* length of region in bp */
tp = 0; /* total positives */
tn = 0; /* total negatives */
while((token = strtok(NULL,"\t")) != NULL){ /* iterating across experiments */
if(data->n + 1 == data->maxN)
expandData(data);
l = strlen(token);
p = 0;
for(i=0;i<l;i++){ /* determine positions of commata */
if(token[i] == '|'){
token[i] = '\0';
pos[p++] = i+1;
}
}
data->numMol[data->n] = atoi(token); /* number of molecules */
token += pos[0];
data->numPos[data->n] = atoi(token);
token -= pos[0];
token += pos[1];
data->numNeg[data->n] = atoi(token);
token -= pos[1];
tp += data->numPos[data->n];
tn += data->numNeg[data->n];
data->n++;
}
if(args->d){
printData(name,len,data);
exit(0);
}
if(args->p && tp){
printLikFun(data, args);
return;
}
cf = crossoverFreq(data);
data->mlXover = cf;
data->ci = args->c;
ul = upperCL(data,cf);
ll = lowerCL(data,cf);
/* convert to centi-Morgans */
ll *= 100;
cf *= 100;
ul *= 100;
if(cf < 100){
printf("%s\t%s\t%d\t%d\t%*d\t%.3f\t%.3f\t%.3f",name,chr,start,end,4,len,ll,cf,ul);
/* convert to cM per Mb */
ll = ll / len * 1000000;
cf = cf / len * 1000000;
ul = ul / len * 1000000;
printf("\t%.3f\t%.3f\t%.3f\n",ll,cf,ul);
}else
printf("%s\t%d\t%d\t%*d\tNA\tNA\tNA\tNA\tNA\tNA\n",name,start,end,4,len);
status = getline(&line,&n,fp);
free(name);
}
free(line);
freeData(data);
}
