#include "GroupInfo.h"
#include "Buffer.h"
+
using namespace std;
struct Params {
int no;
FILE *fi;
engine_type *engine;
- double *mw;
+ const double *mw;
};
struct CIType {
double confidence;
int nCV, nSpC, nSamples; // nCV: number of count vectors; nSpC: number of theta vectors sampled per count vector; nSamples: nCV * nSpC
int nThreads;
-int cvlen;
+
+float *l_bars;
char cvsF[STRLEN], tmpF[STRLEN], command[STRLEN];
-CIType *iso_tau, *gene_tau;
+CIType *iso_tpm, *gene_tpm, *iso_fpkm, *gene_fpkm;
int M, m;
Refs refs;
Params *paramsArray;
pthread_t *threads;
pthread_attr_t attr;
-void *status;
int rc;
CIParams *ciParamsArray;
}
void* sample_theta_from_c(void* arg) {
-
int *cvec;
double *theta;
+ float *tpm;
gamma_dist **gammas;
gamma_generator **rgs;
Params *params = (Params*)arg;
FILE *fi = params->fi;
- double *mw = params->mw;
+ const double *mw = params->mw;
- cvec = new int[cvlen];
- theta = new double[cvlen];
- gammas = new gamma_dist*[cvlen];
- rgs = new gamma_generator*[cvlen];
-
- float **vecs = new float*[nSpC];
- for (int i = 0; i < nSpC; i++) vecs[i] = new float[cvlen];
+ cvec = new int[M + 1];
+ theta = new double[M + 1];
+ gammas = new gamma_dist*[M + 1];
+ rgs = new gamma_generator*[M + 1];
+ tpm = new float[M + 1];
+ float l_bar; // the mean transcript length over the sample
int cnt = 0;
while (fscanf(fi, "%d", &cvec[0]) == 1) {
- for (int j = 1; j < cvlen; j++) assert(fscanf(fi, "%d", &cvec[j]) == 1);
+ for (int j = 1; j <= M; j++) assert(fscanf(fi, "%d", &cvec[j]) == 1);
++cnt;
- for (int j = 0; j < cvlen; j++) {
+ for (int j = 0; j <= M; j++) {
gammas[j] = new gamma_dist(cvec[j]);
rgs[j] = new gamma_generator(*(params->engine), *gammas[j]);
}
for (int i = 0; i < nSpC; i++) {
double sum = 0.0;
- for (int j = 0; j < cvlen; j++) {
- theta[j] = ((j == 0 || eel[j] >= EPSILON) ? (*rgs[j])() : 0.0);
+ for (int j = 0; j <= M; j++) {
+ theta[j] = ((j == 0 || (eel[j] >= EPSILON && mw[j] >= EPSILON)) ? (*rgs[j])() / mw[j] : 0.0);
sum += theta[j];
}
assert(sum >= EPSILON);
- for (int j = 0; j < cvlen; j++) theta[j] /= sum;
+ for (int j = 0; j <= M; j++) theta[j] /= sum;
sum = 0.0;
- for (int j = 0; j < cvlen; j++) {
- theta[j] = (mw[j] < EPSILON ? 0.0 : theta[j] / mw[j]);
- sum += theta[j];
- }
- assert(sum >= EPSILON);
- for (int j = 0; j < cvlen; j++) theta[j] /= sum;
-
-
- sum = 0.0;
- vecs[i][0] = theta[0];
- for (int j = 1; j < cvlen; j++)
+ tpm[0] = 0.0;
+ for (int j = 1; j <= M; j++)
if (eel[j] >= EPSILON) {
- vecs[i][j] = theta[j] / eel[j];
- sum += vecs[i][j];
+ tpm[j] = theta[j] / eel[j];
+ sum += tpm[j];
}
else assert(theta[j] < EPSILON);
-
assert(sum >= EPSILON);
- for (int j = 1; j < cvlen; j++) vecs[i][j] /= sum;
+ l_bar = 0.0; // store mean effective length of the sample
+ for (int j = 1; j <= M; j++) { tpm[j] /= sum; l_bar += tpm[j] * eel[j]; tpm[j] *= 1e6; }
+ buffer->write(l_bar, tpm + 1); // ommit the first element in tpm
}
- buffer->write(nSpC, vecs);
-
- for (int j = 0; j < cvlen; j++) {
+ for (int j = 0; j <= M; j++) {
delete gammas[j];
delete rgs[j];
}
delete[] theta;
delete[] gammas;
delete[] rgs;
-
- for (int i = 0; i < nSpC; i++) delete[] vecs[i];
- delete[] vecs;
+ delete[] tpm;
return NULL;
}
model.read(modelF);
calcExpectedEffectiveLengths<ModelType>(model);
-
int num_threads = min(nThreads, nCV);
- buffer = new Buffer(nMB, nSamples, cvlen, tmpF);
+ buffer = new Buffer(nMB, nSamples, M, l_bars, tmpF);
paramsArray = new Params[num_threads];
threads = new pthread_t[num_threads];
pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0) in sample_theta_vectors_from_count_vectors!");
}
for (int i = 0; i < num_threads; i++) {
- rc = pthread_join(threads[i], &status);
+ rc = pthread_join(threads[i], NULL);
pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0) in sample_theta_vectors_from_count_vectors!");
}
}
void* calcCI_batch(void* arg) {
- float *itsamples, *gtsamples;
+ float *itsamples, *gtsamples, *ifsamples, *gfsamples;
ifstream fin;
CIParams *ciParams = (CIParams*)arg;
itsamples = new float[nSamples];
gtsamples = new float[nSamples];
+ ifsamples = new float[nSamples];
+ gfsamples = new float[nSamples];
fin.open(tmpF, ios::binary);
- streampos pos = streampos(gi.spAt(ciParams->start_gene_id)) * nSamples * FLOATSIZE;
+ // minus 1 here for that theta0 is not written!
+ streampos pos = streampos(gi.spAt(ciParams->start_gene_id) - 1) * 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);
+ memset(gfsamples, 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];
+ ifsamples[k] = 1e3 / l_bars[k] * itsamples[k];
+ gfsamples[k] += ifsamples[k];
}
- calcCI(nSamples, itsamples, iso_tau[j].lb, iso_tau[j].ub);
+ calcCI(nSamples, itsamples, iso_tpm[j].lb, iso_tpm[j].ub);
+ calcCI(nSamples, ifsamples, iso_fpkm[j].lb, iso_fpkm[j].ub);
+ }
+
+ if (e - b > 1) {
+ calcCI(nSamples, gtsamples, gene_tpm[i].lb, gene_tpm[i].ub);
+ calcCI(nSamples, gfsamples, gene_fpkm[i].lb, gene_fpkm[i].ub);
+ }
+ else {
+ gene_tpm[i].lb = iso_tpm[b].lb; gene_tpm[i].ub = iso_tpm[b].ub;
+ gene_fpkm[i].lb = iso_fpkm[b].lb; gene_fpkm[i].ub = iso_fpkm[b].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); }
char outF[STRLEN];
int num_threads = nThreads;
- iso_tau = new CIType[M + 1];
- gene_tau = new CIType[m];
+ iso_tpm = new CIType[M + 1];
+ gene_tpm = new CIType[m];
+ iso_fpkm = new CIType[M + 1];
+ gene_fpkm = new CIType[m];
assert(M > 0);
int quotient = M / num_threads;
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);
+ rc = pthread_join(threads[i], NULL);
pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0) in calculate_credibility_intervals!");
}
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'));
+ fprintf(fo, "%.6g%c", iso_tpm[i].lb, (i < M ? '\t' : '\n'));
+ for (int i = 1; i <= M; i++)
+ fprintf(fo, "%.6g%c", iso_tpm[i].ub, (i < M ? '\t' : '\n'));
+ for (int i = 1; i <= M; i++)
+ fprintf(fo, "%.6g%c", iso_fpkm[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'));
+ fprintf(fo, "%.6g%c", iso_fpkm[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'));
+ fprintf(fo, "%.6g%c", gene_tpm[i].lb, (i < m - 1 ? '\t' : '\n'));
+ for (int i = 0; i < m; i++)
+ fprintf(fo, "%.6g%c", gene_tpm[i].ub, (i < m - 1 ? '\t' : '\n'));
+ for (int i = 0; i < m; i++)
+ fprintf(fo, "%.6g%c", gene_fpkm[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'));
+ fprintf(fo, "%.6g%c", gene_fpkm[i].ub, (i < m - 1 ? '\t' : '\n'));
fclose(fo);
- delete[] iso_tau;
- delete[] gene_tau;
+ delete[] iso_tpm;
+ delete[] gene_tpm;
+ delete[] iso_fpkm;
+ delete[] gene_fpkm;
if (verbose) { printf("All credibility intervals are calculated!\n"); }
}
m = gi.getm();
nSamples = nCV * nSpC;
- cvlen = M + 1;
- assert(nSamples > 0 && cvlen > 1); // for Buffter.h: (bufsize_type)nSamples
+ assert(nSamples > 0 && M > 0); // for Buffter.h: (bufsize_type)nSamples
+ l_bars = new float[nSamples];
sprintf(tmpF, "%s.tmp", imdName);
sprintf(cvsF, "%s.countvectors", imdName);
// Phase II
calculate_credibility_intervals(imdName);
+ delete l_bars;
/*
sprintf(command, "rm -f %s", tmpF);
int status = system(command);
projects / rsem.git / blobdiff