void* calcCI_batch(void* arg) {
float *itsamples, *gtsamples;
ifstream fin;
CIParams *ciParams = (CIParams*)arg;
itsamples = new float[nSamples];
gtsamples = new float[nSamples];
fin.open(tmpF, ios::binary);
streampos pos = streampos(gi.spAt(ciParams->start_gene_id)) * nSamples * FLOATSIZE;
fin.seekg(pos, ios::beg);
int cnt = 0;
for (int i = ciParams->start_gene_id; i < ciParams->end_gene_id; i++) {
int b = gi.spAt(i), e = gi.spAt(i + 1);
memset(gtsamples, 0, FLOATSIZE * nSamples);
for (int j = b; j < e; j++) {
for (int k = 0; k < nSamples; k++) {
fin.read((char*)(&itsamples[k]), FLOATSIZE);
gtsamples[k] += itsamples[k];
}
calcCI(nSamples, itsamples, iso_tau[j].lb, iso_tau[j].ub);
}
calcCI(nSamples, gtsamples, gene_tau[i].lb, gene_tau[i].ub);
++cnt;
if (verbose && cnt % 1000 == 0) { printf("In thread %d, %d genes are processed for CI calculation!\n", ciParams->no, cnt); }
}
fin.close();
delete[] itsamples;
delete[] gtsamples;
return NULL;
}
void writeResults(ModelType& model, double* counts) {
double denom;
char outF[STRLEN];
FILE *fo;
sprintf(modelF, "%s.model", statName);
model.write(modelF);
//calculate tau values
double *tau = new double[M + 1];
memset(tau, 0, sizeof(double) * (M + 1));
denom = 0.0;
for (int i = 1; i <= M; i++)
if (eel[i] >= EPSILON) {
tau[i] = theta[i] / eel[i];
denom += tau[i];
}
general_assert(denom > 0, "No alignable reads?!");
for (int i = 1; i <= M; i++) {
tau[i] /= denom;
}
//isoform level results
sprintf(outF, "%s.iso_res", imdName);
fo = fopen(outF, "w");
for (int i = 1; i <= M; i++) {
const Transcript& transcript = transcripts.getTranscriptAt(i);
fprintf(fo, "%s%c", transcript.getTranscriptID().c_str(), (i < M ? '\t' : '\n'));
}
for (int i = 1; i <= M; i++)
fprintf(fo, "%.2f%c", counts[i], (i < M ? '\t' : '\n'));
for (int i = 1; i <= M; i++)
fprintf(fo, "%.15g%c", tau[i], (i < M ? '\t' : '\n'));
for (int i = 1; i <= M; i++) {
const Transcript& transcript = transcripts.getTranscriptAt(i);
fprintf(fo, "%s%c", transcript.getGeneID().c_str(), (i < M ? '\t' : '\n'));
}
fclose(fo);
//gene level results
sprintf(outF, "%s.gene_res", imdName);
fo = fopen(outF, "w");
for (int i = 0; i < m; i++) {
const string& gene_id = transcripts.getTranscriptAt(gi.spAt(i)).getGeneID();
fprintf(fo, "%s%c", gene_id.c_str(), (i < m - 1 ? '\t' : '\n'));
}
for (int i = 0; i < m; i++) {
double sumC = 0.0; // sum of counts
int b = gi.spAt(i), e = gi.spAt(i + 1);
for (int j = b; j < e; j++) sumC += counts[j];
fprintf(fo, "%.2f%c", sumC, (i < m - 1 ? '\t' : '\n'));
}
for (int i = 0; i < m; i++) {
double sumT = 0.0; // sum of tau values
int b = gi.spAt(i), e = gi.spAt(i + 1);
for (int j = b; j < e; j++) sumT += tau[j];
fprintf(fo, "%.15g%c", sumT, (i < m - 1 ? '\t' : '\n'));
}
for (int i = 0; i < m; i++) {
int b = gi.spAt(i), e = gi.spAt(i + 1);
for (int j = b; j < e; j++) {
fprintf(fo, "%s%c", transcripts.getTranscriptAt(j).getTranscriptID().c_str(), (j < e - 1 ? ',' : (i < m - 1 ? '\t' :'\n')));
}
}
fclose(fo);
delete[] tau;
if (verbose) { printf("Expression Results are written!\n"); }
}
void calculate_credibility_intervals(char* imdName) {
FILE *fo;
char outF[STRLEN];
int num_threads = nThreads;
iso_tau = new CIType[M + 1];
gene_tau = new CIType[m];
assert(M > 0);
int quotient = M / num_threads;
if (quotient < 1) { num_threads = M; quotient = 1; }
int cur_gene_id = 0;
int num_isoforms = 0;
// A just so so strategy for paralleling
ciParamsArray = new CIParams[num_threads];
for (int i = 0; i < num_threads; i++) {
ciParamsArray[i].no = i;
ciParamsArray[i].start_gene_id = cur_gene_id;
num_isoforms = 0;
while ((m - cur_gene_id > num_threads - i - 1) && (i == num_threads - 1 || num_isoforms < quotient)) {
num_isoforms += gi.spAt(cur_gene_id + 1) - gi.spAt(cur_gene_id);
++cur_gene_id;
}
ciParamsArray[i].end_gene_id = cur_gene_id;
}
threads = new pthread_t[num_threads];
/* set thread attribute to be joinable */
pthread_attr_init(&attr);
pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
// paralleling
for (int i = 0; i < num_threads; i++) {
rc = pthread_create(&threads[i], &attr, &calcCI_batch, (void*)(&ciParamsArray[i]));
pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0) in calculate_credibility_intervals!");
}
for (int i = 0; i < num_threads; i++) {
rc = pthread_join(threads[i], &status);
pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0) in calculate_credibility_intervals!");
}
// releasing resources
/* destroy attribute */
pthread_attr_destroy(&attr);
delete[] threads;
delete[] ciParamsArray;
//isoform level results
sprintf(outF, "%s.iso_res", imdName);
fo = fopen(outF, "a");
for (int i = 1; i <= M; i++)
fprintf(fo, "%.6g%c", iso_tau[i].lb, (i < M ? '\t' : '\n'));
for (int i = 1; i <= M; i++)
fprintf(fo, "%.6g%c", iso_tau[i].ub, (i < M ? '\t' : '\n'));
fclose(fo);
//gene level results
sprintf(outF, "%s.gene_res", imdName);
fo = fopen(outF, "a");
for (int i = 0; i < m; i++)
fprintf(fo, "%.6g%c", gene_tau[i].lb, (i < m - 1 ? '\t' : '\n'));
for (int i = 0; i < m; i++)
fprintf(fo, "%.6g%c", gene_tau[i].ub, (i < m - 1 ? '\t' : '\n'));
fclose(fo);
delete[] iso_tau;
delete[] gene_tau;
if (verbose) { printf("All credibility intervals are calculated!\n"); }
}