From: Bo Li <bli@cs.wisc.edu>
Date: Thu, 25 Aug 2011 12:49:30 +0000 (-0500)
Subject: rsem v1.1.11
X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=7b8405a9fe481d041d7e50d1d8abb4b589bdc0d3

rsem v1.1.11
---

diff --git a/LenDist.h b/LenDist.h
index d7b2ba3..f19baba 100644
--- 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 9c3dd22..c8d2107 100644
--- 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 4c22cbf..6de12b1 100644
--- 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 7ff8e87..6f31dac 100644
--- 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 7c87374..c9f7a81 100644
--- 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 dee535d..64e486b 100644
--- 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 899f0d0..ecf059c 100644
--- 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 0a3b74f..6646342 100644
--- 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 fb12e46..5607124 100644
--- 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 4b8e25f..8c484a5 100644
--- 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 756e3d5..bdf920f 100644
--- 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 f01920f..f32b747 100644
--- 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 ecea8d7..47d7d9c 100755
--- 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";