rsem v1.1.11

diff --git a/LenDist.h b/LenDist.h
index d7b2ba33631dcca513f5acfe1ca6cde41f6daefc..f19babaa1bf79079f22c2fae4e3ce86926f6ea63 100644 (file)
--- a/LenDist.h
+++ b/LenDist.h
@@ -217,12 +217,12 @@ void LenDist::read(FILE *fi) {
        delete[] pdf;
        delete[] cdf;
 
-       fscanf(fi, "%d %d %d", &lb, &ub, &span);
+       assert(fscanf(fi, "%d %d %d", &lb, &ub, &span) == 3);
        pdf = new double[span + 1];
        cdf = new double[span + 1];
        pdf[0] = cdf[0] = 0.0;
        for (int i = 1; i <= span; i++) {
-               fscanf(fi, "%lf", &pdf[i]);
+               assert(fscanf(fi, "%lf", &pdf[i]) == 1);
                cdf[i] = cdf[i - 1] + pdf[i];
        }
 

diff --git a/NoiseProfile.h b/NoiseProfile.h
index 9c3dd2230dec94e1a515473fb741d4eecc16ca8e..c8d21073b3c21e7ded8b50b04f01da458f5b8ab6 100644 (file)
--- a/NoiseProfile.h
+++ b/NoiseProfile.h
@@ -5,6 +5,7 @@
 #include<cstdio>
 #include<cstring>
 #include<string>
+#include<cassert>
 
 #include "utils.h"
 #include "RefSeq.h"
@@ -119,10 +120,10 @@ void NoiseProfile::read(FILE *fi) {
        int tmp_ncodes;
 
        memset(c, 0, sizeof(c));
-       fscanf(fi, "%d", &tmp_ncodes);
+       assert(fscanf(fi, "%d", &tmp_ncodes) == 1);
        assert(tmp_ncodes == NCODES);
        for (int i = 0; i < NCODES; i++)
-               fscanf(fi, "%lf", &p[i]);
+         assert(fscanf(fi, "%lf", &p[i]) == 1);
 }
 
 void NoiseProfile::write(FILE *fo) {

diff --git a/NoiseQProfile.h b/NoiseQProfile.h
index 4c22cbfc1aab6191b7387553a751831697d1ce10..6de12b11faa75180e59bbba52d8fbef3dcf52ece 100644 (file)
--- a/NoiseQProfile.h
+++ b/NoiseQProfile.h
@@ -5,6 +5,7 @@
 #include<cstdio>
 #include<cstring>
 #include<string>
+#include<cassert>
 
 #include "utils.h"
 #include "RefSeq.h"
@@ -131,20 +132,13 @@ void NoiseQProfile::collect(const NoiseQProfile& o) {
 void NoiseQProfile::read(FILE *fi) {
        int tmp_size, tmp_ncodes;
 
-       /* DEBUG */
        memset(c, 0, sizeof(c));
-       //logp = 0.0;
-       /* END */
 
-       fscanf(fi, "%d %d", &tmp_size, &tmp_ncodes);
+       assert(fscanf(fi, "%d %d", &tmp_size, &tmp_ncodes) == 2);
        assert(tmp_size == SIZE && tmp_ncodes == NCODES);
        for (int i = 0; i < SIZE; i++) {
-               for (int j = 0; j < NCODES; j++) {
-                       fscanf(fi, "%lf", &p[i][j]);
-                       /* DEBUG */
-                       //if (c[i][j] > 0) logp += c[i][j] * log(p[i][j]);
-                       /* END */
-               }
+               for (int j = 0; j < NCODES; j++) 
+                 assert(fscanf(fi, "%lf", &p[i][j]) == 1);
        }
 }
 

diff --git a/Orientation.h b/Orientation.h
index 7ff8e87299fc52ce91f94e09bbe77171f087095e..6f31dacbcd2be874ed5a53a73e356bf274193d2f 100644 (file)
--- a/Orientation.h
+++ b/Orientation.h
@@ -3,6 +3,7 @@
 
 #include<cstdio>
 #include<cstring>
+#include<cassert>
 
 #include "simul.h"
 
@@ -23,7 +24,7 @@ public:
        double getProb(int dir) { return prob[dir]; }
 
        void read(FILE* fi) {
-               fscanf(fi, "%lf", &prob[0]);
+               assert(fscanf(fi, "%lf", &prob[0]) == 1);
                prob[1] = 1.0 - prob[0];
        }
 

diff --git a/PairedEndModel.h b/PairedEndModel.h
index 7c8737465c959da2e3089e39d0fcb091ab3e52ff..c9f7a81668f36ece34f2f672c4da1a803fca9be2 100644 (file)
--- a/PairedEndModel.h
+++ b/PairedEndModel.h
@@ -288,7 +288,7 @@ void PairedEndModel::read(const char* inpF) {
        FILE *fi = fopen(inpF, "r");
        if (fi == NULL) { fprintf(stderr, "Cannot open %s! It may not exist.\n", inpF); exit(-1); }
 
-       fscanf(fi, "%d", &val);
+       assert(fscanf(fi, "%d", &val) == 1);
        assert(val == model_type);
 
        ori->read(fi);
@@ -302,7 +302,7 @@ void PairedEndModel::read(const char* inpF) {
                if (M == 0) M = val;
                if (M == val) {
                        mw = new double[M + 1];
-                       for (int i = 0; i <= M; i++) fscanf(fi, "%lf", &mw[i]);
+                       for (int i = 0; i <= M; i++) assert(fscanf(fi, "%lf", &mw[i]) == 1);
                }
        }
 

diff --git a/PairedEndQModel.h b/PairedEndQModel.h
index dee535dda56ef89113b0ac8d06e470347f1e2249..64e486b66b98d19fafc98bce67ef0a5bd85131ad 100644 (file)
--- a/PairedEndQModel.h
+++ b/PairedEndQModel.h
@@ -298,7 +298,7 @@ void PairedEndQModel::read(const char* inpF) {
        FILE *fi = fopen(inpF, "r");
        if (fi == NULL) { fprintf(stderr, "Cannot open %s! It may not exist.\n", inpF); exit(-1); }
 
-       fscanf(fi, "%d", &val);
+       assert(fscanf(fi, "%d", &val) == 1);
        assert(val == model_type);
 
        ori->read(fi);
@@ -313,7 +313,7 @@ void PairedEndQModel::read(const char* inpF) {
                if (M == 0) M = val;
                if (M == val) {
                        mw = new double[M + 1];
-                       for (int i = 0; i <= M; i++) fscanf(fi, "%lf", &mw[i]);
+                       for (int i = 0; i <= M; i++) assert(fscanf(fi, "%lf", &mw[i]) == 1);
                }
        }
 

diff --git a/Profile.h b/Profile.h
index 899f0d035a32d17ddd1feeb7222ec359e34399c7..ecf059c0ea45cfb2e35c1255a89d314c0a054d62 100644 (file)
--- a/Profile.h
+++ b/Profile.h
@@ -132,7 +132,7 @@ void Profile::collect(const Profile& o) {
 
 void Profile::read(FILE *fi) {
        int tmp_prolen, tmp_ncodes;
-       fscanf(fi, "%d %d", &tmp_prolen, &tmp_ncodes);
+       assert(fscanf(fi, "%d %d", &tmp_prolen, &tmp_ncodes) == 2);
        assert(tmp_ncodes == NCODES);
        if (tmp_prolen != proLen) {
                delete[] p;
@@ -145,7 +145,7 @@ void Profile::read(FILE *fi) {
        for (int i = 0; i < proLen; i++)
                for (int j = 0; j < NCODES; j++)
                        for (int k = 0; k < NCODES; k++)
-                               fscanf(fi, "%lf", &p[i][j][k]);
+                         assert(fscanf(fi, "%lf", &p[i][j][k]) == 1);
 }
 
 void Profile::write(FILE* fo) {

diff --git a/QProfile.h b/QProfile.h
index 0a3b74fef022fb45ca045e342fbb3051ca1193d6..6646342b217cf59a8456a52a11bc6c0df04e5601 100644 (file)
--- a/QProfile.h
+++ b/QProfile.h
@@ -128,12 +128,12 @@ void QProfile::collect(const QProfile& o) {
 
 void QProfile::read(FILE *fi) {
        int tmp_size, tmp_ncodes;
-       fscanf(fi, "%d %d", &tmp_size, &tmp_ncodes);
+       assert(fscanf(fi, "%d %d", &tmp_size, &tmp_ncodes) == 2);
        assert(tmp_size == SIZE && tmp_ncodes == NCODES);
        for (int i = 0; i < SIZE; i++)
                for (int j = 0; j < NCODES; j++)
                        for (int k = 0; k < NCODES; k++)
-                               fscanf(fi, "%lf", &p[i][j][k]);
+                         assert(fscanf(fi, "%lf", &p[i][j][k]) == 1);
 }
 
 void QProfile::write(FILE *fo) {

diff --git a/QualDist.h b/QualDist.h
index fb12e4684dfe603eff5ba4fcd39b573b14a59ba9..5607124c3949f176cb863b775ce4f1cc0f435f1b 100644 (file)
--- a/QualDist.h
+++ b/QualDist.h
@@ -94,12 +94,12 @@ double QualDist::getProb(const std::string& qual) {
 void QualDist::read(FILE *fi) {
        int tmp_size;
 
-       fscanf(fi, "%d", &tmp_size);
+       assert(fscanf(fi, "%d", &tmp_size) == 1);
        assert(tmp_size == SIZE);
 
-       for (int i = 0; i < SIZE; i++) { fscanf(fi, "%lf", &p_init[i]); }
+       for (int i = 0; i < SIZE; i++) { assert(fscanf(fi, "%lf", &p_init[i]) == 1); }
        for (int i = 0; i < SIZE; i++) {
-               for (int j = 0; j < SIZE; j++) { fscanf(fi, "%lf", &p_tran[i][j]); }
+               for (int j = 0; j < SIZE; j++) { assert(fscanf(fi, "%lf", &p_tran[i][j]) == 1); }
        }
 }
 

diff --git a/RSPD.h b/RSPD.h
index 4b8e25ff37fb860c3c537ea8b0925b9fdc115da8..8c484a5d95bbe1ed81d6d2f5adce1a1ea60c58a4 100644 (file)
--- a/RSPD.h
+++ b/RSPD.h
@@ -1,6 +1,10 @@
 #ifndef RSPD_H_
 #define RSPD_H_
 
+#include<cstdio>
+#include<cstring>
+#include<cassert>
+
 #include "utils.h"
 #include "RefSeq.h"
 #include "Refs.h"
@@ -137,17 +141,17 @@ void RSPD::read(FILE *fi) {
        delete[] cdf;
 
        int val;
-       fscanf(fi, "%d", &val);
+       assert(fscanf(fi, "%d", &val) == 1);
        estRSPD = (val != 0);
 
        if (estRSPD) {
-               fscanf(fi, "%d", &B);
+               assert(fscanf(fi, "%d", &B) == 1);
                pdf = new double[B + 2];
                cdf = new double[B + 2];
                memset(pdf, 0, sizeof(double) * (B + 2));
                memset(cdf, 0, sizeof(double) * (B + 2));
                for (int i = 1; i <= B; i++) {
-                       fscanf(fi, "%lf", &pdf[i]);
+                       assert(fscanf(fi, "%lf", &pdf[i]) == 1);
                        cdf[i] = cdf[i - 1] + pdf[i];
                }
        }

diff --git a/SingleModel.h b/SingleModel.h
index 756e3d5cdecf386339eb90c303e9aa6b908a26e5..bdf920ff271c133c749214244604fa319eac80c4 100644 (file)
--- a/SingleModel.h
+++ b/SingleModel.h
@@ -321,12 +321,12 @@ void SingleModel::read(const char* inpF) {
        FILE *fi = fopen(inpF, "r");
        if (fi == NULL) { fprintf(stderr, "Cannot open %s! It may not exist.\n", inpF); exit(-1); }
 
-       fscanf(fi, "%d", &val);
+       assert(fscanf(fi, "%d", &val) == 1);
        assert(val == model_type);
 
        ori->read(fi);
        gld->read(fi);
-       fscanf(fi, "%d", &val);
+       assert(fscanf(fi, "%d", &val) == 1);
        if (val > 0) {
                if (mld == NULL) mld = new LenDist();
                mld->read(fi);
@@ -339,7 +339,7 @@ void SingleModel::read(const char* inpF) {
                if (M == 0) M = val;
                if (M == val) {
                        mw = new double[M + 1];
-                       for (int i = 0; i <= M; i++) fscanf(fi, "%lf", &mw[i]);
+                       for (int i = 0; i <= M; i++) assert(fscanf(fi, "%lf", &mw[i]) == 1);
                }
        }
 

diff --git a/SingleQModel.h b/SingleQModel.h
index f01920f2bfcf908e26aad049ca8bf8222733ec89..f32b747ad298d2bcc94f109083025a3c4277dac0 100644 (file)
--- a/SingleQModel.h
+++ b/SingleQModel.h
@@ -334,7 +334,7 @@ void SingleQModel::read(const char* inpF) {
        FILE *fi = fopen(inpF, "r");
        if (fi == NULL) { fprintf(stderr, "Cannot open %s! It may not exist.\n", inpF); exit(-1); }
 
-       fscanf(fi, "%d", &val);
+       assert(fscanf(fi, "%d", &val) == 1);
        assert(val == model_type);
 
        ori->read(fi);
@@ -353,7 +353,7 @@ void SingleQModel::read(const char* inpF) {
                if (M == 0) M = val;
                if (M == val) {
                        mw = new double[M + 1];
-                       for (int i = 0; i <= M; i++) fscanf(fi, "%lf", &mw[i]);
+                       for (int i = 0; i <= M; i++) assert(fscanf(fi, "%lf", &mw[i]) == 1);
                }
        }
 

diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index ecea8d763470ece4a6480057305740036ead881f..47d7d9c07549e4dc6cfcab51c0a79414bf60a6a4 100755 (executable)
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -109,7 +109,7 @@ if (!$no_bowtie) {
     print "$command\n";
     $status = system($command);
     if ($status != 0) {
-       print "bowtie-build failed! Please check if you provide correct parameters/options for the pipeline!\n";
+       print "bowtie-build failed! Please check if you have a copy of bowtie-build in the path you specified!\n";
        exit(-1);
     }
     print "\n";