install the rsem_perl_utils.pm to /usr/bin even though this is wrong

[rsem.git] / calcCI.cpp

diff --git a/calcCI.cpp b/calcCI.cpp
index 97eba64e1ea9965c3983409090dd252abb78cbad..7cb58ffa07c24f5c6eb77f871e847aeb430ae7bf 100644 (file)
--- a/calcCI.cpp
+++ b/calcCI.cpp
@@ -80,6 +80,9 @@ pthread_t *threads;
 pthread_attr_t attr;
 int rc;
 
+bool hasSeed;
+seedType seed;
+
 CIParams *ciParamsArray;
 
 void* sample_theta_from_c(void* arg) {
@@ -103,18 +106,22 @@ void* sample_theta_from_c(void* arg) {
        int cnt = 0;
        while (fscanf(fi, "%d", &cvec[0]) == 1) {
                for (int j = 1; j <= M; j++) assert(fscanf(fi, "%d", &cvec[j]) == 1);
+               assert(cvec[0] > 0);
 
                ++cnt;
 
                for (int j = 0; j <= M; j++) {
-                       gammas[j] = new gamma_dist(cvec[j]);
-                       rgs[j] = new gamma_generator(*(params->engine), *gammas[j]);
+                 gammas[j] = NULL; rgs[j] = NULL;
+                 if (cvec[j] > 0) {
+                   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 <= M; j++) {
-                               theta[j] = ((j == 0 || (eel[j] >= EPSILON && mw[j] >= EPSILON)) ? (*rgs[j])() / mw[j] : 0.0);
+                               theta[j] = ((j == 0 || (cvec[j] > 0 && eel[j] >= EPSILON && mw[j] >= EPSILON)) ? (*rgs[j])() / mw[j] : 0.0);
                                sum += theta[j];
                        }
                        assert(sum >= EPSILON);
@@ -135,8 +142,8 @@ void* sample_theta_from_c(void* arg) {
                }
 
                for (int j = 0; j <= M; j++) {
-                       delete gammas[j];
-                       delete rgs[j];
+                 if (gammas[j] != NULL) delete gammas[j];
+                 if (rgs[j] != NULL) delete rgs[j];
                }
 
                if (verbose && cnt % 100 == 0) { printf("Thread %d, %d count vectors are processed!\n", params->no, cnt); }
@@ -165,6 +172,7 @@ void sample_theta_vectors_from_count_vectors() {
        threads = new pthread_t[num_threads];
 
        char inpF[STRLEN];
+       hasSeed ? engineFactory::init(seed) : engineFactory::init();
        for (int i = 0; i < num_threads; i++) {
                paramsArray[i].no = i;
                sprintf(inpF, "%s%d", cvsF, i);
@@ -172,6 +180,7 @@ void sample_theta_vectors_from_count_vectors() {
                paramsArray[i].engine = engineFactory::new_engine();
                paramsArray[i].mw = model.getMW();
        }
+       engineFactory::finish();
 
        /* set thread attribute to be joinable */
        pthread_attr_init(&attr);
@@ -458,7 +467,7 @@ void calculate_credibility_intervals(char* imdName) {
 
 int main(int argc, char* argv[]) {
        if (argc < 8) {
-               printf("Usage: rsem-calculate-credibility-intervals reference_name imdName statName confidence nCV nSpC nMB [-p #Threads] [-q]\n");
+               printf("Usage: rsem-calculate-credibility-intervals reference_name imdName statName confidence nCV nSpC nMB [-p #Threads] [--seed seed] [-q]\n");
                exit(-1);
        }
 
@@ -473,8 +482,15 @@ int main(int argc, char* argv[]) {
 
        nThreads = 1;
        quiet = false;
+       hasSeed = false;
        for (int i = 8; i < argc; i++) {
                if (!strcmp(argv[i], "-p")) nThreads = atoi(argv[i + 1]);
+               if (!strcmp(argv[i], "--seed")) {
+                 hasSeed = true;
+                 int len = strlen(argv[i + 1]);
+                 seed = 0;
+                 for (int k = 0; k < len; k++) seed = seed * 10 + (argv[i + 1][k] - '0');
+               }
                if (!strcmp(argv[i], "-q")) quiet = true;
        }
        verbose = !quiet;