Refactored wiggle code and added rsem-bam2readdepth program

[rsem.git] / rsem-calculate-expression

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index e841e4b91e77b311d0ca33dc54b1bde4d468b14e..06604d96a8c415b4eaeaf9e74854d6bf772a8d17 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -286,6 +286,7 @@ if ($genBamF) {
 
 if ($calcCI) {
     $command = $dir."rsem-run-gibbs $refName $sampleName $sampleToken $BURNIN $CHAINLEN $SAMPLEGAP";
+#    $command .= " -p $nThreads";
     if ($quiet) { $command .= " -q"; }
     print "$command\n";
     $status = system($command);
@@ -317,7 +318,7 @@ if ($calcCI) {
 }
 
 if (!$keep_intermediate_files) {
-    $status = system ("rm -rf $tmp_dir");
+    $status = system ("rm -rf $temp_dir");
     if ($status != 0) {
        print "Fail to delete the temporary folder!\n";
        exit(-1);
@@ -660,3 +661,5 @@ Assume the path to the bowtie executables is in the user's PATH environment vari
                            mmliver_paired_end_quals
 
 =cut
+
+#  LocalWords:  usr