dataset GetInput(char *filename, int verbose){ // either char * or char *filename idk
FILE *fin;
int i;
dataset output;
if(verbose == 1)
printf("Opening %s\n",filename);
fin = fopen(filename, "r");
if(fin==0 && verbose == 1) {
printf("Could not open file.\n");
return;
}
// file open routine complete, get linecount
output.length = GetFileLineCount(filename);
// number of data points counted, now to read in the actual data (and create a couple of temporary arrays)
float x[output.length],y[output.length],yerr[output.length];
for (i = 0; i < output.length; ++i){
int invalid = fscanf(fin, "%f,%f,%f", &x[i], &y[i], &yerr[i]);
if(invalid !=3){
printf("Non-numeric data detected in file or more than 3 columns present. Please verify your data!\nProgram exiting.");
return;
}
if (yerr[i] == 0){
if (verbose == 1){
printf("Your data contains errors that are equal to zero. This is invalid.\nProgram exiting.\n");
}
return;
}
}
fclose(fin);
// map temp stuff to actual output stuff to compensate for fscanf being hella gay
for (int i = 0; i < output.length; ++i)
{
output.x[i] = x[i];
output.y[i] = y[i];
output.yerr[i] = yerr[i];
}
if (verbose == 1){
printf("Your dataset has %d constituent points:\n\n",output.length);
for (i = 0; i < output.length; ++i)
{
printf("x = %.2f\ty = %.2f\ty error = %.2f\n",output.x[i],output.y[i],output.yerr[i]);
}
printf("\n");
}
return output;
}
Likelihood::Likelihood( vector< vector<string> > & MEseq, SingleSampleInfo & si, string & ref_file_prefix )
{
string bam_name = si.bam_name;
avr_read_length = si.avr_read_length;
max_ins_size = si.avr_ins_size + 3 * si.var_avr_ins_size;
refStat.resize(NMEI);
nref.resize(NMEI);
log10_total.resize(NMEI);
for(int i=0; i<NMEI; i++) {
refStat[i].resize(3);
nref[i].resize(3, -1);
log10_total[i].resize(3);
}
vector<string> suffix_name;
suffix_name.resize(3);
suffix_name[2] = ".hom-stat.";
suffix_name[1] = ".het-stat.";
suffix_name[0] = ".neg-stat.";
for (int m=0; m<3; m++) {
for(int g=0; g<3; g++) {
string ref_file_name = ref_file_prefix + suffix_name[g] + std::to_string(m);
// line count first
nref[m][g] = GetFileLineCount(ref_file_name);
if (nref[m][g] <= 0) {
string str = "[Likelihood::Likelihood] " + ref_file_name + "is empty";
morphError(str, 35);
}
// read
setFromRefFile( m, g, ref_file_name );
// frequency to log
int sum = 0;
for(int i=0; i<refStat[m][g].frequency.size(); i++) {
sum += refStat[m][g].frequency[i];
refStat[m][g].frequency[i] = log10(refStat[m][g].frequency[i]);
}
log10_total[m][g] = log10(sum);
}
}
// open bam
OpenBamAndBai( bam, bam_header, bam_name );
OpenBamAndBai( alt_bam, alt_bam_header, bam_name );
pMEseq = &MEseq;
}