From 1794b68d34625b39404d5aba9e72646805b710ce Mon Sep 17 00:00:00 2001
From: Bo Li <bli@cs.wisc.edu>
Date: Thu, 10 Feb 2011 23:39:07 -0600
Subject: [PATCH] Bugs in SingleModel.h are fixed.

---
 PairedEndModel.h          | 2 +-
 PairedEndQModel.h         | 2 +-
 SingleModel.h             | 4 +---
 SingleQModel.h            | 2 +-
 rsem-calculate-expression | 2 +-
 5 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/PairedEndModel.h b/PairedEndModel.h
index acd9f30..e73c03d 100644
--- a/PairedEndModel.h
+++ b/PairedEndModel.h
@@ -321,7 +321,7 @@ void PairedEndModel::write(const char* outF) {
 	npro->write(fo);
 
 	if (mw != NULL) {
-	  fprintf(fo, "%d\n", M);
+	  fprintf(fo, "\n%d\n", M);
 	  for (int i = 0; i < M; i++) {
 	    fprintf(fo, "%.15g ", mw[i]);
 	  }
diff --git a/PairedEndQModel.h b/PairedEndQModel.h
index e328779..bac7135 100644
--- a/PairedEndQModel.h
+++ b/PairedEndQModel.h
@@ -335,7 +335,7 @@ void PairedEndQModel::write(const char* outF) {
 	nqpro->write(fo);
 
 	if (mw != NULL) {
-	  fprintf(fo, "%d\n", M);
+	  fprintf(fo, "\n%d\n", M);
 	  for (int i = 0; i < M; i++) {
 	    fprintf(fo, "%.15g ", mw[i]);
 	  }
diff --git a/SingleModel.h b/SingleModel.h
index 76c54f1..532f79c 100644
--- a/SingleModel.h
+++ b/SingleModel.h
@@ -334,8 +334,6 @@ void SingleModel::read(const char* inpF) {
 	pro->read(fi);
 	npro->read(fi);
 
-	fclose(fi);
-
 	if (fscanf(fi, "%d", &M) == 1) {
 	  mw = new double[M + 1];
 	  for (int i = 0; i <= M; i++) fscanf(fi, "%lf", &mw[i]);
@@ -363,7 +361,7 @@ void SingleModel::write(const char* outF) {
 	npro->write(fo);
 
 	if (mw != NULL) {
-	  fprintf(fo, "%d\n", M);
+	  fprintf(fo, "\n%d\n", M);
 	  for (int i = 0; i < M; i++) {
 	    fprintf(fo, "%.15g ", mw[i]);
 	  }
diff --git a/SingleQModel.h b/SingleQModel.h
index 92d8890..0c2ba34 100644
--- a/SingleQModel.h
+++ b/SingleQModel.h
@@ -377,7 +377,7 @@ void SingleQModel::write(const char* outF) {
 	nqpro->write(fo);
 
 	if (mw != NULL) {
-	  fprintf(fo, "%d\n", M);
+	  fprintf(fo, "\n%d\n", M);
 	  for (int i = 0; i < M; i++) {
 	    fprintf(fo, "%.15g ", mw[i]);
 	  }
diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index dfb5052..ddeb8dd 100755
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -93,7 +93,7 @@ pod2usage(-verbose => 2) if ($help == 1);
 if ($is_sam || $is_bam) {
     pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 3);
     pod2usage(-msg => "--sam and --bam cannot be active at the same time!", -exitval => 2, -verbose => 2) if ($is_sam == 1&& $is_bam == 1);
-    pod2usage(-msg => "--bowtie-path, --bowtie-n, --bowtie-e, --bowtie-m, --phred33-quals, --phred64-quals or --solexa-quals cannot be set if input is SAM/BAM format!", -exitval => 2, -verbose => 2) if ($bowtie_path ne "" || $C != 2 || $E != 999999 || $maxHits != 200 || $phred33 || $phred64 || $solexa);
+    pod2usage(-msg => "--bowtie-path, --bowtie-n, --bowtie-e, --bowtie-m, --phred33-quals, --phred64-quals or --solexa-quals cannot be set if input is SAM/BAM format!", -exitval => 2, -verbose => 2) if ($bowtie_path ne "" || $C != 2 || $E != 99999999 || $maxHits != 200 || $phred33 || $phred64 || $solexa);
 }
 else {
     pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (!$paired_end && scalar(@ARGV) != 3 || $paired_end && scalar(@ARGV) != 4);    
-- 
2.39.2