Bugs in SingleModel.h are fixed.

diff --git a/PairedEndModel.h b/PairedEndModel.h
index acd9f30a2b32ba0a3c30edf3104aa0e85f2a8c0e..e73c03dd779aec9574a20bcb314c3db0eb1d2975 100644 (file)
--- 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 e328779b6675a3579aa221c32f490b99648053e4..bac7135721244a704475e73a6a010a989375d2b7 100644 (file)
--- 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 76c54f1489e15cc87123ef0f3bb3d142c10062db..532f79cd2c126c79199b1072508642394e083445 100644 (file)
--- 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 92d8890c60958f370155b379d018ca80c06fc319..0c2ba34cece15a0e2f48926d126e6cdc390392f8 100644 (file)
--- 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 dfb5052cca2b163c605c20cf08426e0e0092f062..ddeb8ddd4af556a3fea3dc9c194c02722f52ed94 100755 (executable)
--- 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);