roll back to original version plus fixed a small bug in calcCI.cpp

[rsem.git] / calcCI.cpp

diff --git a/calcCI.cpp b/calcCI.cpp
index 3ae71157c58a023bb4cd7fe316e26c7b9e572663..89414f9b02f00ba641b8f987845aea8e977ef1b1 100644 (file)
--- a/calcCI.cpp
+++ b/calcCI.cpp
@@ -27,8 +27,6 @@ using namespace std;
 struct Params {
        int no;
        FILE *fi;
-       bufsize_type size;
-       int sp;
        engine_type *engine;
        double *mw;
 };
@@ -117,14 +115,14 @@ void* sample_theta_from_c(void* arg) {
        Params *params = (Params*)arg;
        FILE *fi = params->fi;
        double *mw = params->mw;
-       Buffer buffer(params->size, params->sp, nSamples, cvlen, tmpF);
 
        cvec = new int[cvlen];
        theta = new double[cvlen];
        gammas = new gamma_dist*[cvlen];
        rgs = new gamma_generator*[cvlen];
 
-       float *vec = new float[cvlen];
+       float **vecs = new float*[nSpC];
+       for (int i = 0; i < nSpC; i++) vecs[i] = new float[cvlen];
 
        int cnt = 0;
        while (fscanf(fi, "%d", &cvec[0]) == 1) {
@@ -156,19 +154,20 @@ void* sample_theta_from_c(void* arg) {
 
 
                        sum = 0.0;
-                       vec[0] = theta[0];
+                       vecs[i][0] = theta[0];
                        for (int j = 1; j < cvlen; j++)
                                if (eel[j] >= EPSILON) {
-                                       vec[j] = theta[j] / eel[j];
-                                       sum += vec[j];
+                                       vecs[i][j] = theta[j] / eel[j];
+                                       sum += vecs[i][j];
                                }
                                else assert(theta[j] < EPSILON);
-                       assert(sum >= EPSILON);
-                       for (int j = 1; j < cvlen; j++) vec[j] /= sum;
 
-                       buffer.write(vec);
+                       assert(sum >= EPSILON);
+                       for (int j = 1; j < cvlen; j++) vecs[i][j] /= sum;
                }
 
+               buffer->write(nSpC, vecs);
+
                for (int j = 0; j < cvlen; j++) {
                        delete gammas[j];
                        delete rgs[j];
@@ -182,7 +181,8 @@ void* sample_theta_from_c(void* arg) {
        delete[] gammas;
        delete[] rgs;
 
-       delete[] vec;
+       for (int i = 0; i < nSpC; i++) delete[] vecs[i];
+       delete[] vecs;
 
        return NULL;
 }
@@ -193,20 +193,10 @@ void sample_theta_vectors_from_count_vectors() {
        model.read(modelF);
        calcExpectedEffectiveLengths<ModelType>(model);
 
-       char splitF[STRLEN];
-       bufsize_type buf_maxcv = bufsize_type(nMB) * 1024 * 1024 / FLOATSIZE / cvlen;
-       bufsize_type quotient, left;
-       int sum = 0;
 
-       sprintf(splitF, "%s.split", imdName);
-       FILE *fi = fopen(splitF, "r");
-       int num_threads;
-       assert(fscanf(fi, "%d", &num_threads) == 1);
-       assert(num_threads <= nThreads);
+       int num_threads = min(nThreads, nCV);
 
-       quotient = buf_maxcv / num_threads;
-       assert(quotient > 0);
-       left = buf_maxcv % num_threads;
+       buffer = new Buffer(nMB, nSamples, cvlen, tmpF);
 
        paramsArray = new Params[num_threads];
        threads = new pthread_t[num_threads];
@@ -216,25 +206,10 @@ void sample_theta_vectors_from_count_vectors() {
                paramsArray[i].no = i;
                sprintf(inpF, "%s%d", cvsF, i);
                paramsArray[i].fi = fopen(inpF, "r");
-
-               int num_samples;
-               assert(fscanf(fi, "%d", &num_samples) == 1);
-               num_samples *= nSpC;
-               if (bufsize_type(num_samples) <= quotient) paramsArray[i].size = num_samples;
-               else {
-                       paramsArray[i].size = quotient;
-                       if (left > 0) { ++paramsArray[i].size; --left; }
-               }
-               paramsArray[i].size *=  cvlen * FLOATSIZE;
-               paramsArray[i].sp = sum;
-               sum += num_samples;
-
                paramsArray[i].engine = engineFactory::new_engine();
                paramsArray[i].mw = model.getMW();
        }
 
-       fclose(fi);
-
        /* set thread attribute to be joinable */
        pthread_attr_init(&attr);
        pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
@@ -258,6 +233,8 @@ void sample_theta_vectors_from_count_vectors() {
        }
        delete[] paramsArray;
 
+       delete buffer; // Must delete here, force the content left in the buffer be written into the disk
+
        if (verbose) { printf("Sampling is finished!\n"); }
 }
 
@@ -344,25 +321,25 @@ void* calcCI_batch(void* arg) {
 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];
 
-       // nThreads must be intact here.
        assert(M > 0);
-       int quotient = M / nThreads;
-       if (quotient < 1) { nThreads = M; quotient = 1; }
+       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[nThreads];
-       for (int i = 0; i < nThreads; i++) {
+       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 > nThreads - i - 1) && (i == nThreads - 1 || num_isoforms < quotient)) {
+               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;
                }
@@ -370,18 +347,18 @@ void calculate_credibility_intervals(char* imdName) {
                ciParamsArray[i].end_gene_id = cur_gene_id;
        }
 
-       threads = new pthread_t[nThreads];
+       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 < nThreads; i++) {
+       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 < nThreads; i++) {
+       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!");
        }